Ironwood Pharmaceuticals (IRWD) 10-K 13 Feb 20 2019 FY Annual report Financial data

Document and Entity Information

Document and Entity Information - USD ($)	12 Months Ended
	Dec. 31, 2019	Feb. 10, 2020	Jun. 30, 2019
Cover [Abstract]
Entity Central Index Key	0001446847
Document Type	10-K
Document Annual Report	true
Document Period End Date	Dec. 31, 2019
Document Transition Report	false
Entity File Number	001-34620
Entity Registrant Name	IRONWOOD PHARMACEUTICALS, INC.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	04-3404176
Entity Address, Address Line One	100 Summer Street
Entity Address, Address Line Two	Suite 2300
Entity Address, City or Town	Boston
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	02110
City Area Code	617
Local Phone Number	621-7722
Title of 12(b) Security	Class A Common Stock, $0.001 par value
Entity Listing, Par Value Per Share	$ 0.001
Trading Symbol	IRWD
Security Exchange Name	NASDAQ
Entity Well-known Seasoned Issuer	Yes
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Shell Company	false
Entity Public Float			$ 1,697,372,212
Entity Common Stock, Shares Outstanding		158,206,912
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	FY
Amendment Flag	false

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 177,023	$ 173,172
Accounts receivable, net	11,279	20,991
Related party accounts receivable, net	105,967	59,959
Inventory, net	648
Prepaid expenses and other current assets	10,685	10,216
Restricted cash	1,250	1,250
Current assets of discontinued operations		847
Total current assets	306,852	266,435
Restricted cash, net of current portion	971	6,426
Accounts receivable, net of current portion	32,597
Property and equipment, net	12,429	7,652
Operating lease right-of-use assets	17,743
Convertible note hedges	31,366	41,020
Goodwill	785	785
Other assets	5	89
Non-current assets of discontinued operations		9,643
Total assets	402,748	332,050
Current liabilities:
Accounts payable	3,978	14,891
Related party accounts payable, net	1,509
Accrued research and development costs	2,956	2,963
Accrued expenses and other current liabilities	30,465	38,001
Capital lease obligations		73
Current portion of deferred rent		252
Current portion of 2026 Notes		47,554
Current portion of contingent consideration		51
Current portion of operating lease liabilities	1,146
Deferred revenue	875
Current liabilities of discontinued operations		15,739
Total current liabilities	40,929	119,524
Capital lease obligations, net of current portion		158
Deferred rent, net of current portion		6,308
Note hedge warrants	24,260	33,763
Convertible senior notes	407,994	265,601
2026 Notes, net of current portion		100,537
Operating lease obligations, net of current portion	22,082
Other liabilities	734	2,530
Commitments and contingencies
Stockholders' deficit:
Preferred stock, $0.001 par value, 75,000,000 shares authorized, no shares issued and outstanding
Class A Common Stock, $0.001 par value, 500,000,000 shares authorized and 154,417,812 issued and outstanding at December 31, 2019 and 500,000,000 shares authorized and 154,414,691 shares issued and outstanding at December 31, 2018	158	154
Additional paid-in capital	1,478,823	1,394,603
Accumulated deficit	(1,572,232)	(1,591,128)
Total stockholders' deficit	(93,251)	(196,371)
Total liabilities and stockholders' deficit	$ 402,748	$ 332,050

Condensed Consolidated Balanc_2

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 31, 2019	Dec. 31, 2018
Preferred stock
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, shares authorized	75,000,000	75,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, shares authorized	500,000,000	500,000,000
Common stock, shares issued	157,535,962	154,414,691
Common stock, shares outstanding	157,535,962	154,414,691

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Revenues:
Total revenues	$ 428,413	$ 346,639	$ 298,276
Cost and expenses:
Cost of revenues, excluding amortization of acquired intangible assets	23,875	32,751	19,097
Write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancellable purchase commitments	(3,530)	247	309
Research and development	115,044	101,060	88,145
Selling, general and administrative	172,450	219,676	231,184
Amortization of acquired intangible assets		8,111	6,214
Gain on fair value remeasurement of contingent consideration		(31,045)	(31,310)
Gain on lease modification	(3,169)
Restructuring expenses	3,620	14,715
Impairment of intangible assets		151,794
Total cost and expenses	308,290	497,309	313,639
Income (loss) from operations	120,123	(150,670)	(15,363)
Other (expense) income:
Interest expense	(36,602)	(37,724)	(36,370)
Interest and investment income	2,862	2,991	2,111
Gain (loss) on derivatives	3,023	(8,743)	(3,284)
Loss on extinguishment of debt	(30,977)		(2,009)
Other income	514
Other expense, net	(61,180)	(43,476)	(39,552)
Net income (loss) from continuing operations	58,943	(194,146)	(54,915)
Net loss from discontinued operations	(37,438)	(88,222)	(62,022)
Net income (loss)	$ 21,505	$ (282,368)	$ (116,937)
Net income (loss) per share from continuing operations-basic and diluted (in dollars per share)	$ 0.38	$ (1.27)	$ (0.37)
Net loss per share from discontinued operations - basic and diluted	(0.24)	(0.58)	(0.42)
Net income (loss) per share-basic and diluted	$ 0.14	$ (1.85)	$ (0.78)
Weighted average common shares outstanding used in computing net income (loss) per share- basic and diluted:	156,023	152,634	148,993
Collaborative arrangements revenue
Revenues:
Total revenues	$ 379,652	$ 272,839	$ 265,533
Product revenue, net
Revenues:
Total revenues		3,445	3,061
Sale of active pharmaceutical ingredient
Revenues:
Total revenues	$ 48,761	$ 70,355	$ 29,682

Condensed Consolidated Statem_2

Condensed Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Condensed Consolidated Statements of Comprehensive Income (Loss)
Net income (loss)	$ 21,505	$ (282,368)	$ (116,937)
Other comprehensive income (loss):
Unrealized gains (losses) on available-for-sale securities		79	(72)
Total other comprehensive income (loss)		79	(72)
Comprehensive income (loss)	$ 21,505	$ (282,289)	$ (117,009)

Condensed Consolidated Statem_3

Condensed Consolidated Statements of Stockholders' Deficit - USD ($) $ in Thousands	Class A common stockCommon Stock	Class B common stockCommon Stock	Additional paid-in capital	Accumulated deficit	Accumulated other comprehensive income (loss)	Total
Balance at Dec. 31, 2016	$ 133	$ 15	$ 1,258,398	$ (1,191,823)	$ (7)	$ 66,716
Balance (in shares) at Dec. 31, 2016	132,631,387	14,484,077
Increase (Decrease) in Stockholders' Equity
Issuance of common stock upon exercise of stock options and employee stock purchase plan	$ 3		26,318			26,321
Issuance of common stock upon exercise of stock options and employee stock purchase plan (in shares)	2,156,152	1,042,047
Issuance of common stock awards			14			14
Issuance of common stock awards (in shares)	135,625
Conversion of Class B common stock to Class A common stock	$ 1	$ (1)
Conversion of Class B common stock to Class A common stock (in shares)	1,542,362	(1,542,362)
Share-based compensation expense related to share-based awards to non-employees			301			301
Share-based compensation expense related to share-based awards to employees and employee stock purchase plan			33,505			33,505
Unrealized gains (losses) on available-for-sale securities					(72)	(72)
Net income (loss)				(116,937)		(116,937)
Balance at Dec. 31, 2017	$ 137	$ 14	1,318,536	(1,308,760)	(79)	9,848
Balance (in shares) at Dec. 31, 2017	136,465,526	13,983,762
Increase (Decrease) in Stockholders' Equity
Issuance of common stock upon exercise of stock options and employee stock purchase plan	$ 3		32,058			32,061
Issuance of common stock upon exercise of stock options and employee stock purchase plan (in shares)	3,070,139	764,361
Issuance of common stock awards (in shares)	130,903
Conversion of Class B common stock to Class A common stock	$ 14	$ (14)
Conversion of Class B common stock to Class A common stock (in shares)	14,748,123	(14,748,123)
Share-based compensation expense related to share-based awards to employees and employee stock purchase plan			44,009			44,009
Unrealized gains (losses) on available-for-sale securities					$ 79	79
Net income (loss)				(282,368)		(282,368)
Balance at Dec. 31, 2018	$ 154		1,394,603	(1,591,128)		(196,371)
Balance (in shares) at Dec. 31, 2018	154,414,691
Increase (Decrease) in Stockholders' Equity
Issuance of common stock upon exercise of stock options and employee stock purchase plan, net of cancellations	$ 4		13,597			13,601
Issuance of common stock upon exercise of stock options and employee stock purchase plan, net of cancellations (in shares)	3,121,271
Share-based compensation expense related to share-based awards to employees and employee stock purchase plan			32,331			32,331
Equity component of convertible senior notes			92,502			92,502
Equity component of issuance costs for convertible senior notes			(2,092)			(2,092)
Purchase of capped calls			(25,159)			(25,159)
Equity component of the partial repurchase of the 2022 Convertible Notes			(26,959)			(26,959)
Dividend of sGC business				(2,609)		(2,609)
Net income (loss)				21,505		21,505
Balance at Dec. 31, 2019	$ 158		$ 1,478,823	$ (1,572,232)		$ (93,251)
Balance (in shares) at Dec. 31, 2019	157,535,962

Condensed Consolidated Statem_4

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Cash flows from operating activities:
Net Income (Loss)	$ 21,505	$ (282,368)	$ (116,937)
Adjustments to reconcile net income (loss) to net cash used in operating activities:
Depreciation and amortization	5,580	3,859	6,442
Amortization of acquired intangible assets		8,111	6,214
Impairment of intangible assets		151,794
Loss (gain) on disposal of property and equipment	146	(1,867)	694
Share-based compensation expense	31,278	40,526	30,905
Gain on lease modification	(3,169)
Change in fair value of note hedge warrants	16,232	(58,425)	(21,049)
Change in fair value of convertible note hedges	(19,255)	67,168	24,333
Write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancellable purchase commitments	(3,530)	219	1,313
Write-down of excess non-cancellable ZURAMPIC and DUZALLO sample purchase commitments		390	309
Gain on facility subleases			(1,579)
Accretion of discount/premium on investment securities		(165)	(75)
Non-cash interest expense	19,590	17,601	16,080
Non-cash change in fair value of contingent consideration		(31,045)	(31,310)
Loss on extinguishment of debt	30,977		2,009
Changes in assets and liabilities:
Accounts receivable and related party accounts receivable, net	(68,893)	1,207	(17,303)
Prepaid expenses and other current assets	(1,046)	(3,727)	2,271
Inventory, net		(806)	346
Other assets	159	702	195
Accounts payable, related party accounts payable and accrued expenses	(32,700)	2,678	(7,725)
Accrued research and development costs	(483)	542	(2,120)
Deferred revenue	875
Operating lease right-of-use assets	14,141
Operating lease liabilities	(12,046)
Deferred rent		916	(1,053)
Net cash used in continuing operating activities	(639)	(82,690)	(108,040)
Net cash provided by discontinued operating activities	11,364	11,808	7,287
Net cash provided by (used in) operating activities	10,725	(70,882)	(100,753)
Cash flows from investing activities:
Purchases of available-for-sale securities		(3,241)	(191,354)
Sales and maturities of available-for-sale securities		99,165	346,890
Purchases of property and equipment	(7,189)	(351)	(2,803)
Proceeds from sale of property and equipment	268	1,563	135
Net cash (used in) provided by continuing investing activities	(6,921)	97,136	152,868
Net cash used in discontinued investing activities	(4,223)	(8,270)	(1,408)
Net cash (used in) provided by investing activities	(11,144)	88,866	151,460
Cash flows from financing activities:
Proceeds from issuance of convertible senior notes	400,000
Purchase of capped calls	(25,159)
Proceeds from partial termination of convertible note hedges and note hedge warrants	3,174
Costs associated with issuance of convertible senior notes	(9,048)
Proceeds from exercise of stock options and employee stock purchase plan	13,595	32,061	26,370
Payments on capital lease obligations		(1,824)	(3,234)
Payments for partial repurchase of 2022 Convertible Notes	(227,338)
Payments on 2026 Notes	(156,409)
Principal payments on PhaRMA notes			(134,258)
Costs associated with issuance of 2026 Notes			(235)
Proceeds from issuance of 2026 Notes, net of discount to lender			146,250
Payments on contingent purchase price consideration		(165)	(15,058)
Net cash (used in) provided by continuing financing activities	(1,185)	30,072	19,835
Net cash (used in) provided financing activities	(1,185)	30,072	19,835
Net increase (decrease) in cash, cash equivalents and restricted cash	(1,604)	48,056	70,542
Cash, cash equivalents and restricted cash, beginning of period	180,848	132,792	62,250
Cash, cash equivalents and restricted cash, end of period	179,244	180,848	132,792
Supplemental cash flow disclosure:
Cash paid for interest	17,584	18,235	20,388
Non-cash investing and financing activities
Purchases under capital leases		664	1,151
Extinguishment of capital leases		2,687	149
Recognition of asset retirement obligation	486
Fixed asset purchases in accounts payable and accrued expenses	$ 1,282	$ 439	$ 1,136

Condensed Consolidated Statem_5

Condensed Consolidated Statements of Cash Flows (Parenthetical) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Reconciliation of cash, cash equivalents, and restricted cash to the condensed consolidated balance sheets
Cash and cash equivalents	$ 177,023	$ 173,172	$ 125,736
Restricted cash	2,221	7,676	7,056
Total cash, cash equivalents, and restricted cash	$ 179,244	$ 180,848	$ 132,792	$ 62,250

Nature of Business

Nature of Business	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Nature of Business	1. Nature of Business Ironwood Pharmaceuticals, Inc. (“Ironwood” or the “Company”) is a gastrointestinal (“GI”) healthcare company dedicated to advancing the treatment of GI diseases and redefining the standard of care for millions of GI patients. The Company is focused on the development and commercialization of innovative GI product opportunities in areas of large unmet need, leveraging its demonstrated expertise and capabilities in GI diseases. On April 1, 2019, the Company completed its tax-free spin-off of its soluble guanylate cyclase (“sGC”) business into a separate publicly traded company, Cyclerion Therapeutics, Inc. (“Cyclerion”). ​ LINZESS ® ® ​ The Company has strategic partnerships with leading pharmaceutical companies to support the development and commercialization of linaclotide throughout the world. The Company and its partner, Allergan plc (together with its affiliates) (“Allergan”), began commercializing LINZESS in the U.S. in December 2012. Under the Company’s collaboration with Allergan for North America, total net sales of LINZESS in the U.S., as recorded by Allergan, are reduced by commercial costs incurred by each party, and the resulting amount is shared equally between the Company and Allergan. Allergan also has an exclusive license from the Company to develop and commercialize linaclotide in all countries other than China (including Hong Kong and Macau), Japan and the countries and territories of North America (the “Allergan License Territory”). On a country-by-country and product-by-product basis in the Allergan License Territory, Allergan pays the Company a royalty as a percentage of net sales of products containing linaclotide as an active ingredient. In addition, Allergan has exclusive rights to commercialize linaclotide in Canada as CONSTELLA and in Mexico as LINZESS. ​ Astellas Pharma Inc. (“Astellas”), the Company’s partner in Japan, has an exclusive license to develop and commercialize linaclotide in Japan. In March 2017, Astellas began commercializing LINZESS for the treatment of adults with IBS-C in Japan, and in September 2018, Astellas began commercializing LINZESS for the treatment of adults with chronic constipation in Japan. On August 1, 2019, the Company amended and restated its license agreement with Astellas. Beginning in 2020, the Company will no longer be responsible for the supply of linaclotide active pharmaceutical ingredient (“API”) to Astellas (Note 6). ​ In October 2012, the Company and AstraZeneca AB (together with its affiliates) (“AstraZeneca”) entered into a collaboration agreement to co-develop and co-commercialize linaclotide in China (including Hong Kong and Macau) (the “AstraZeneca License Territory”). In January 2019, the Chinese National Medical Products Administration approved the marketing application for LINZESS for adults with IBS-C in China. As of September 16, 2019, AstraZeneca has the exclusive right to develop, manufacture, and commercialize products containing linaclotide in the AstraZeneca License Territory (Note 6). AstraZeneca launched LINZESS in China in November 2019. ​ The Company and Allergan are exploring ways to enhance the clinical profile of LINZESS by studying linaclotide in additional indications, populations and formulations to assess its potential to treat various conditions. In June 2019, the Company announced positive topline data from its Phase IIIb trial demonstrating the efficacy and safety of LINZESS 290 mcg on the overall abdominal symptoms of bloating, pain and discomfort, in adult patients with IBS-C. ​ The Company and Allergan are advancing MD-7246, a delayed release formulation of linaclotide, as an oral, intestinal, non-opioid, pain-relieving agent for patients with abdominal pain associated with certain GI diseases. In May 2019, the Company and Allergan announced the initiation of a Phase II clinical trial evaluating the safety and efficacy of MD-7246 in adult patients with IBS with diarrhea (“IBS-D”). ​ The Company is advancing IW-3718, a gastric retentive formulation of a bile acid sequestrant, for the potential treatment of refractory gastroesophageal reflux disease (“refractory GERD”). In June 2018, the Company initiated two Phase III clinical trials evaluating the safety and efficacy of IW-3718 in patients with refractory GERD . ​ Additionally, the Company periodically enters into co-promotion agreements to bolster its salesforce productivity. For example, in April 2019, the Company entered into an agreement with Allergan to continue to perform sales detailing activities for VIBERZI ® TM ​ These and other agreements are more fully described in Note 6, Collaboration, License, Co-Promotion and Other Commercial Agreements, ​ On April 1, 2019, Ironwood completed the separation of its sGC business, and certain other assets and liabilities, into Cyclerion (the “Separation”). The Separation was effected by means of a distribution of all of the outstanding shares of common stock, with no par value, of Cyclerion through a dividend of all outstanding shares of Cyclerion’s common stock, to Ironwood’s stockholders of record as of the close of business on March 19, 2019 (Note 3). ​ On June 11, 2019, the Company entered into a non-cancelable operating lease (the “Summer Street Lease”) for approximately 39,000 square feet of office space on the 23 rd ​ In August 2019, the Company issued $200.0 million in aggregate principal amount of 0.75% Convertible Senior Notes due 2024 (the “2024 Convertible Notes”) and $200.0 million in aggregate principal amount of 1.50% Convertible Senior Notes due 2026 (the “2026 Convertible Notes”). The Company received net proceeds of approximately $391.0 million from the sale of the 2024 Convertible Notes and the 2026 Convertible Notes, after deducting fees and expenses of approximately $9.0 million. The proceeds from the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes were used in August 2019 to pay the cost of associated capped call transactions (the “Capped Calls”) and to repurchase $215.0 million aggregate principal amount of the existing 2.25% Convertible Senior Notes due 2022 (the “2022 Convertible Notes”) and in September 2019 to redeem all of the outstanding principal balance of the 8.375% Notes due 2026 (the “2026 Notes”) (Note 12). The Company retired the 2026 Notes, which had an outstanding aggregate principal balance of approximately $116.5 million, for a redemption price of approximately $123.0 million. During the year ended December 31, 2019, the Company recognized a loss on extinguishment of debt of approximately $31.0 million related to the redemption of the 2026 Notes and the partial repurchase of the 2022 Convertible Notes. These transactions are more fully described in Note 12, Notes Payable ​ The Company was incorporated in Delaware on January 5, 1998 as Microbia, Inc. On April 7, 2008, the Company changed its name to Ironwood Pharmaceuticals, Inc. To date, the Company has dedicated a majority of its activities to the research, development and commercialization of linaclotide, as well as to the research and development of its other product candidates. Prior to the year ended December 31, 2019, the Company incurred net losses in each year since its inception in 1998. For the year ended December 31, 2019, the Company recorded net income of approximately $21.5 million. As of December 31, 2019, the Company had an accumulated deficit of approximately $1.6 billion.

Summary of Significant Accounti

Summary of Significant Accounting Policies	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Summary of Significant Accounting Policies	2. Summary of Significant Accounting Policies Principles of Consolidation The accompanying consolidated financial statements include the accounts of Ironwood and its wholly-owned subsidiaries, as of December 31, 2019, Ironwood Pharmaceuticals Securities Corporation and Ironwood Pharmaceuticals GmbH. Cyclerion was a wholly-owned subsidiary until it became an independent publicly-traded company on April 1, 2019. All intercompany transactions and balances are eliminated in consolidation. ​ Segment Information Operating segments are components of an enterprise for which separate financial information is available and is evaluated regularly by the Company’s chief operating decision-maker in deciding how to allocate resources and in assessing performance. The Company currently operates in one reportable business segment—human therapeutics. Reclassifications and Revisions to Prior Period Financial Statements Certain prior period financial statement items have been reclassified to conform to current period presentation. The Company has presented its business as discontinued operations in its consolidated financial statements for all periods presented. The historical financial statements and footnotes have been recast accordingly. Discontinued Operations ​ During the three months ended June 30, 2019, the Company determined that its sGC business met the criteria for classification as a discontinued operation in accordance with Accounting Standards Codification (“ASC”) Subtopic 205-20, Discontinued Operations Cyclerion Separation ​ Use of Estimates The preparation of consolidated financial statements in accordance with U.S. generally accepted accounting principles requires the Company’s management to make estimates and judgments that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the consolidated financial statements, and the amounts of revenues and expenses during the reported periods. On an ongoing basis, the Company’s management evaluates its estimates, judgments and methodologies. Significant estimates and assumptions in the consolidated financial statements include those related to revenue recognition; accounts receivable; inventory valuation and related reserves; useful lives of long-lived assets, impairment of long-lived assets, including its acquired intangible assets and goodwill; valuation procedures for right-of-use assets and operating lease liabilities; valuation procedures for the issuance and repurchase of convertible notes; valuation of assets and liabilities held for disposition and losses related to discontinued operations; fair value of derivatives; balance sheet classification of notes payable and convertible notes; income taxes, including the valuation allowance for deferred tax assets; research and development expenses; contingencies and share-based compensation. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results may differ materially from these estimates under different assumptions or conditions. Changes in estimates are reflected in reported results in the period in which they become known. Cash and Cash Equivalents The Company considers all highly liquid investment instruments with a remaining maturity when purchased of three months or less to be cash equivalents. Investments qualifying as cash equivalents primarily consist of money market funds, U.S. government-sponsored securities, and repurchase agreements. The carrying amount of cash equivalents approximates fair value. The amount of cash equivalents included in cash and cash equivalents was approximately $177.0 million and approximately $173.1 million at December 31, 2019 and 2018, respectively. Restricted Cash The Company is contingently liable under unused letters of credit with a bank, related to the Company’s facility lease and vehicle lease agreements, in the amount of approximately $2.2 million and approximately $7.7 million as of December 31, 2019 and 2018, respectively. The Company records as restricted cash the collateral used to secure these letters of credit. During the year ended December 31, 2019, approximately $6.4 million of the Company’s restricted cash related to the termination of its former headquarters lease in Cambridge, Massachusetts was released. The amount of restricted cash in current assets and non-current assets was approximately $1.2 million and $1.0 million at December 31, 2019, respectively. Inventory Inventory is stated at the lower of cost or net realizable value with cost determined under the first-in, first-out basis in accordance with ASC 330, Inventory Inventory (Topic 330): Simplifying the Measurement of Inventory The Company evaluates inventory levels quarterly and any inventory that has a cost basis in excess of its expected net realizable value, inventory that becomes obsolete, inventory in excess of expected sales requirements, inventory that fails to meet commercial sale specifications or is otherwise impaired is written down with a corresponding charge to the statement of operations in the period that the impairment is first identified. The Company also assesses, on a quarterly basis, whether it has any excess non-cancelable purchase commitments resulting from its minimum supply agreements with its suppliers. The Company relies on data from several sources to estimate the net realizable value of inventory and non-cancelable purchase commitments, including partner forecasts of projected inventory purchases that are received quarterly, the Company’s internal forecasts and related process, historical sales by geographic region, and the status of and progress toward commercialization of linaclotide in partnered territories. The Company capitalizes inventories manufactured in preparation for initiating sales of a product candidate when the related product candidate is considered to have a high likelihood of regulatory approval and the related costs are expected to be recoverable through sales of the inventories. In determining whether or not to capitalize such inventories, the Company evaluates, among other factors, information regarding the product candidate’s safety and efficacy, the status of regulatory submissions and communications with regulatory authorities and the outlook for commercial sales, including the existence of current or anticipated competitive drugs and the availability of reimbursement. In addition, the Company evaluates risks associated with manufacturing the product candidate, including the ability of the Company’s third-party suppliers to complete the validation batches, and the remaining shelf life of the inventories. Costs associated with developmental products prior to satisfying the inventory capitalization criteria are charged to research and development expense as incurred. ​ Concentrations of Suppliers The Company relies on third-party manufacturers and its collaboration partners to manufacture linaclotide API, linaclotide finished drug product, and finished goods. Currently, the Company uses three third-party facilities actively producing linaclotide API and finished drug product. The Company also has an agreement with another independent third party to serve as a redundant linaclotide API manufacturing capacity to support its partnered territories. Beginning in 2020, each of the Company’s partners for linaclotide will be responsible for API, finished drug product and finished goods manufacturing (including bottling and packaging) for its respective territories and distributing the finished goods to wholesalers. If any of the Company’s suppliers were to limit or terminate production or otherwise fail to meet the quality or delivery requirements needed to satisfy the supply commitments, the process of locating and qualifying alternate sources could require up to several months, during which time the Company’s production could be delayed. Such delays could have a material adverse effect on the Company’s business, financial position and results of operations. Accounts Receivable and Related Valuation Account The Company makes judgments as to its ability to collect outstanding receivables and provides an allowance for receivables when collection becomes doubtful. Provisions are made based upon a specific review of all significant outstanding invoices and the overall quality and age of those invoices not specifically reviewed. The Company’s receivables relate primarily to amounts reimbursed under its collaboration, license and co-promotion agreements, as well as historical amounts due from product sales to wholesalers. The Company believes that credit risks associated with these partners and wholesalers are not significant. To date, the Company has not had any significant write-offs of bad debt, and the Company did not have an allowance for doubtful accounts as of December 31, 2019 or 2018. Concentrations of Credit Risk Financial instruments that subject the Company to credit risk primarily consist of cash and cash equivalents, restricted cash, and accounts receivable. The Company maintains its cash and cash equivalent balances with high-quality financial institutions and, consequently, the Company believes that such funds are subject to minimal credit risk. The Company has adopted an investment policy which limits the amounts the Company may invest in certain types of investments, and requires all investments held by the Company to be at least AA- rated, thereby reducing credit risk exposure. Accounts receivable, including related party accounts receivable, primarily consist of amounts due under the linaclotide collaboration agreement with Allergan for North America and linaclotide license agreement with Astellas for Japan (Note 6). The Company does not obtain collateral for its accounts receivable. Accounts receivable or payable to or from Allergan and Cyclerion are presented as related party accounts receivable and related party accounts payable, respectively, on the consolidated balance sheets. The percentages of revenue recognized from significant customers of the Company in the years ended December 31, 2019, 2018 and 2017 as well as the account receivable balances, net of any payables due, at December 31, 2019 and 2018 are included in the following table: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accounts ​ Revenue ​ ​ December 31, ​ Year Ended December 31, ​ 2019 2018 2019 2018 2017 Collaborative Partner: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Allergan (North America and Europe) 90 % 72 % 78 % 77 % 88 % Astellas (Japan) 8 % 26 % 13 % 20 % 10 % ​ For the years ended December 31, 2019, 2018 and 2017, no additional customers accounted for more than 10% of the Company’s revenue. ​ Property and Equipment ​ Property and equipment, including leasehold improvements, are recorded at cost, and are depreciated when placed into service using the straight-line method based on their estimated useful lives as follows: ​ ​ ​ ​ ​ ​ Estimated Useful Life Asset Description (In Years) Manufacturing equipment 10 ​ Laboratory equipment 5 ​ Computer and office equipment 3 ​ Furniture and fixtures 7 ​ Software 3 ​ ​ Included in property and equipment are certain costs of software obtained for internal use. Costs incurred during the preliminary project stage are expensed as incurred, while costs incurred during the application development stage are capitalized and amortized over the estimated useful life of the software. The Company also capitalizes costs related to specific upgrades and enhancements when it is probable the expenditures will result in additional functionality. Maintenance and training costs related to software obtained for internal use are expensed as incurred. Leasehold improvements are amortized over the shorter of the estimated useful life of the asset or the lease term. Under ASC Topic 840, Leases Costs for capital assets not yet placed into service have been capitalized as construction in process, and will be depreciated in accordance with the above guidelines once placed into service. Maintenance and repair costs are expensed as incurred. ​ Finite Lived Intangible Assets The Company records the fair value of purchased intangible assets with finite useful lives as of the transaction date of a business combination. Purchased intangible assets with finite useful lives are amortized to their estimated residual values over their estimated useful lives. The value of the Company’s finite-lived intangible assets was based on the future expected net cash flows related to ZURAMPIC and DUZALLO (the “Lesinurad Products”), which included significant assumptions around future net sales and the respective investment to support these products. During the year ended December 31, 2018, the Company recorded an impairment charge of approximately $151.8 million to fully write-off its ZURAMPIC and DUZALLO intangible assets. ​ Goodwill ​ Goodwill represents the difference between the purchase price and the fair value of the identifiable tangible and intangible net assets when accounting for business combinations. Goodwill is not amortized, but is reviewed for impairment. The Company tests its goodwill for impairment annually as of October 1 st ​ Impairment of Long-Lived Assets The Company regularly reviews the carrying amount of its long-lived assets to determine whether indicators of impairment may exist, which warrant adjustments to carrying values or estimated useful lives. If indications of impairment exist, projected future undiscounted cash flows associated with the asset are compared to the carrying amount to determine whether the asset’s value is recoverable. If the carrying value of the asset exceeds such projected undiscounted cash flows, the asset will be written down to its estimated fair value. There were no significant impairments of long-lived assets for the years ended December 31, 2019, 2018, or 2017. ​ Income Taxes The Company provides for income taxes under the liability method. Deferred tax assets and liabilities are determined based on differences between financial reporting and tax bases of assets and liabilities and are measured using the enacted tax rates in effect when the differences are expected to reverse. Deferred tax assets are reduced by a valuation allowance to reflect the uncertainty associated with their ultimate realization. The Company accounts for uncertain tax positions recognized in the consolidated financial statements in accordance with the provisions of ASC Topic 740, Income Taxes ​ Financing Costs Financing costs include costs directly attributable to the Company’s offerings of its equity securities and its debt financings. Costs attributable to equity offerings are charged as a reduction to stockholders’ equity against the proceeds of the offering once the offering is completed. Costs attributable to debt financings are deferred and amortized to interest expense over the term of the debt using the effective interest method. Portions of the financing costs incurred in connection with the 2022 Convertible Notes, 2024 Convertible Notes and 2026 Convertible Notes were deemed to relate to the equity components and were recorded as a reduction to additional paid in capital. In accordance with ASC 835, Interest Notes Payable ​ Leases Effective January 1, 2019 , the Company adopted ASC Topic 842, Leases (“ASC 842”), using the optional transition method. The adoption of ASC 842 represents a change in accounting principle that aims to increase transparency and comparability among organizations by requiring the recognition of right-of-use assets and lease liabilities on the balance sheet for both operating and finance leases. In addition, the standard requires enhanced disclosures that meet the objective of enabling financial statement users to assess the amount, timing, and uncertainty of cash flows arising from leases. The reported results for the year ended December 31, 2019 reflect the application of ASC 842 guidance, while the reported results for prior periods were prepared in conjunction with ASC 840. Because there were no material changes to the values of capital leases as a result of adoption of ASC 842, the Company concluded that no cumulative-effect adjustment to the accumulated deficit as of January 1, 2019 was necessary. ​ The recognition of right-of-use assets and lease liabilities related to the Company’s operating leases under ASC 842 has had a material impact on the Company’s consolidated financial statements. ​ As part of the ASC 842 adoption, the Company elected certain practical expedients outlined in the guidance. These practical expedients include: ​ ● Accounting policy election to use the short-term lease exception by asset class; and ● Election of the practical expedient package during transition, which includes: o An entity need not reassess whether any expired or existing contracts are or contain leases. o An entity need not reassess the classification for any expired or existing leases. As a result, all leases that were classified as operating leases in accordance with ASC 840 are classified as operating leases under ASC 842, and all leases that were classified as capital leases in accordance with ASC 840 are classified as finance leases under ASC 842. o An entity need not reassess initial direct costs for any existing leases. ​ Subsequent to the Company’s adoption of ASC 842, the Company elected the post-transition practical expedient, by class of underlying asset, to account for lease components and non-lease components together as a single component for the asset class of operating lease right-of-use real estate assets. ​ The Company’s lease portfolio for year ended December 31, 2019 includes: leases for its prior and current headquarters locations, a data center colocation lease, vehicle leases for its salesforce representatives, and leases for computer and office equipment. The Company determines if an arrangement is a lease at the inception of the contract. The asset component of the Company’s operating leases is recorded as operating lease right-of-use assets, and the liability component is recorded as current portion of operating lease liabilities and operating lease liabilities, net of current portion in the Company’s consolidated balance sheets. As of December 31, 2019, the Company did not record any finance leases. ​ Right-of-use assets and operating lease liabilities are recognized based on the present value of lease payments over the lease term at the lease inception date. Existing leases in the Company’s lease portfolio as of the adoption date were valued as of January 1, 2019. The Company uses an incremental borrowing rate based on the information available at lease inception in determining the present value of lease payments, if an implicit rate of return is not provided with the lease contract. Operating lease right-of-use assets are adjusted for incentives expected to be received. ​ Right-of-use assets and operating lease liabilities are remeasured upon certain modifications to leases using the present value of remaining lease payments and estimated incremental borrowing rate upon lease modification. ​ Lease cost is recognized on a straight-line basis over the lease term, and includes amounts related to short-term leases. The Company recognizes variable lease payments as operating expenses in the period in which the obligation for those payments is incurred. Variable lease payments primarily include common area maintenance, utilities, real estate taxes, insurance, and other operating costs that are passed on from the lessor in proportion to the space leased by the Company. ​ Derivative Assets and Liabilities In June 2015, in connection with the issuance of the 2022 Convertible Notes, the Company entered into convertible note hedge transactions (the “Convertible Note Hedges”). Concurrently with entering into the Convertible Note Hedges, the Company also entered into certain warrant transactions in which it sold note hedge warrants (the “Note Hedge Warrants”) to the Convertible Note Hedge counterparties to acquire shares of the Company’s Class A Common Stock, subject to customary anti-dilution adjustments (Note 12). In connection with the partial repurchase of the 2022 Convertible Notes in August 2019, the Company terminated its Convertible Note Hedges and Note Hedge Warrants proportionately. These instruments are derivative financial instruments under ASC Topic 815, Derivatives and Hedging These derivatives are recorded as assets or liabilities at fair value each reporting date and the fair value is determined using the Black-Scholes option-pricing model. The changes in fair value are recorded as a component of other (expense) income in the consolidated statements of operations. Significant inputs used to determine the fair value include the price per share of the Company’s Class A Common Stock on the date of valuation, expected term of the derivative instruments, strike prices of the derivative instruments, risk-free interest rate, and expected volatility of the Company’s Class A Common Stock. Changes to these inputs could materially affect the valuation of the Convertible Note Hedges and Note Hedge Warrants in future periods. In August 2019, in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into the Capped Calls. The Capped Calls cover the same number of shares of Class A Common Stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes (subject to anti-dilution and certain other adjustments). These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met. ​ Revenue Recognition Effective January 1, 2018 , the Company adopted ASU No. 2014 -09, Revenue from Contracts with Customers (Topic 606) and related amendments (“ASU 2014 -09”) using the modified retrospective transition method. The adoption of ASU 2014-09 represented a change in accounting principle that aimed to more closely align revenue recognition with the delivery of the Company's products or services and provided financial statement readers with enhanced disclosures. ASU 2014-09 also included Subtopic 340-40, Other Assets and Deferred Costs—Contracts with Customers , which required the deferral of incremental costs of obtaining a contract with a customer. In accordance with ASC Topic 606, Revenue from Contracts with Customers (“ASC 606”), the Company recognizes revenue when the customer obtains control of a promised good or service, in an amount that reflects the consideration which the Company expects to receive in exchange for the good or service. Upon adoption of ASC 606, the Company concluded that no cumulative-effect adjustment to the accumulated deficit as of January 1, 2018 was necessary. There were no remaining or ongoing deliverables or unrecognized consideration as of December 31, 2017 that required an adjustment to the accumulated deficit. The adoption of ASC 606 had no impact on the Company’s consolidated statement of operations, balance sheets, or statement of cash flows. The reported results for the years ended December 31, 2019 and 2018 reflect the application of ASC 606 guidance, while the reported results for the year ended December 31, 2017 were prepared in accordance with ASC 605, Revenue Recognition (“ASC 605”). As part of the ASC 606 adoption, the Company has utilized certain practical expedients outlined in the guidance. These practical expedients include: ● Expensing as incurred incremental costs of obtaining a contract, such as sales commissions, if the amortization period of the asset would be less than one year; ● Recognizing revenue in the amount that the Company has the right to invoice, when consideration from the customer corresponds directly with the value to the customer of the Company’s performance completed to date; and ● For contracts that were modified before the beginning of the earliest reporting period presented in accordance with the pending content that links to this paragraph, an entity need not retrospectively restate the contract for those contract modifications in accordance with paragraphs ASC 606-10-25-12 through 25-13. Instead, an entity shall reflect the aggregate effect of all modifications that occur before the beginning of the earliest period presented in accordance with the pending content that links to this paragraph when: (a) Identifying the satisfied and unsatisfied performance obligations, (b) Determining the transaction price, and (c) Allocating the transaction price to the satisfied and unsatisfied performance obligations. Prior to the adoption of ASC 606, the Company recognized revenue when there was persuasive evidence that an arrangement existed, services had been rendered or delivery had occurred, the price was fixed or determinable, and collection was reasonably assured. The Company’s revenues are generated primarily through collaborative arrangements and license agreements related to the research and development and commercialization of linaclotide, as well as co-promotion arrangements in the U.S. The terms of the collaborative research and development, license, co-promotion and other agreements contain multiple performance obligations which may include (i) licenses, (ii) research and development activities, including participation on joint steering committees, (iii) the manufacture of finished drug product, API, or development materials for a partner, which are reimbursed at a contractually determined rate, and (iv) education or co-promotion activities by the Company’s clinical sales specialists. Non-refundable payments to the Company under these agreements may include (i) up-front license fees, (ii) payments for research and development activities, (iii) payments for the manufacture of finished drug product, API, or development materials, (iv) payments based upon the achievement of certain milestones, (v) payments for sales detailing, promotional support services and medical education initiatives, and (vi) royalties on product sales. The Company receives its share of the net profits or bears its share of the net losses from the sale of linaclotide in the U.S. through its collaboration agreement with Allergan for North America. Prior to the execution of the amended and restated collaboration agreement with AstraZeneca (the “Amended AstraZeneca Agreement”) on September 16, 2019, the Company received its share of the net profits and bore its share of the net losses from the sale of linaclotide in the China (including Hong Kong and Macau), through its collaboration with AstraZeneca. The Company has adopted a policy to recognize revenue net of tax withholdings, as applicable. Revenue recognition under ASC 606 Upon executing a revenue generating arrangement, the Company assesses whether it is probable the Company will collect consideration in exchange for the good or service it transfers to the customer. To determine revenue recognition for arrangements that the Company determines are within the scope of ASC 606, it performs the following five steps: (i) identify the contract(s) with a customer; (ii) identify the performance obligations in the contract; (iii) determine the transaction price; (iv) allocate the transaction price to the performance obligations in the contract; and (v) recognize revenue when (or as) the Company satisfies the performance obligations. The Company must develop assumptions that require significant judgment to determine the standalone selling price for each performance obligation identified in the contract. The assumptions that are used to determine the standalone selling price may include forecasted revenues, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success. Collaboration, License, Co-Promotion and Other Commercial Agreements Upon licensing intellectual property to a customer, the Company determines if the license is distinct from the other performance obligations identified in the arrangement. The Company recognizes revenues from the transaction price, including non-refundable, up-front fees allocated to the license when the license is transferred to the customer if the license has distinct benefit to the customer. For licenses that are combined with other promises, the Company assesses the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time. For performance obligations that are satisfied over time, the Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. The Company’s license and collaboration agreements include milestone payments, such as development and other milestones. The Company evaluates whether the milestones are considered probable of being reached and estimates the amount to be included in the transaction price using the most likely amount method at the inception of the agreement. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within the control of the Company, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. The transaction price is then allocated to each performance obligation on a relative standalone selling price basis, for which the Company recognizes revenue as or when the performance obligations under the contract are satisfied. The Company re-evaluates the probability of achievement of such milestones and any related constraint at each reporting period, and any adjustments are recorded on a cumulative catch-up basis. Agreements that include the supply of API or drug product for either clinical development or commercial supply at the customer’s discretion are generally considered as options. The Company assesses if these options provide a material right to its partner, and if so, they are accounted for as separate performance obligations. If the Company is entitled to additional payments when the customer exercises these options, any additional payments are recorded as revenue when the customer obtains control of the goods, which is typically upon shipment for sales of API and finished drug product. For agreements that include sales-based royalties, including milestone payments based on the level of sales, and the license is deemed to be the predominant item to which the royalties relate, the Company recognizes revenue when the related sales occur in accordance with the sales-based royalty exception under ASC 606-10-55-65. Net Profit or Net Loss Sharing In accordance with ASC 808 Topic, Collaborative Arrangements (“ASC 808”), the Company considered the nature and contractual terms of the arrangement and the nature of the Company’s business operations to determine the classification of payments under the Company’s collaboration agreements. While ASC 808 provides guidance on classification, the standard is silent on matters of separation, initial measurement, and recognition. Therefore, the Company, consistent with its accounting policies prior to the adoption of ASC 606, applies the separation, initial measurement, and recognition principles of ASC 606 to its collaboration agreements. The Company adopted ASU No. 2018-18, Collaborative Arrangements (Topic 808): Clarifying the Interaction between Topic 808 and Topic 606, The Company’s collaborative arrangements revenues generated from sales of LINZESS in the U.S. are considered akin to sales-based royalties. In accordance with the sales-based royalty exception, the Company recognizes its share of the pre-tax commercial net profit or net loss generated from the sales of LINZESS in the U.S. in the period the product sales are earned, as reported by Allergan, and related cost of goods sold and selling, general and administrative expenses are incurred by the Company and its collaboration partner. These amounts are partially determined based on amounts provided by Allergan and involve the use of estimates and judgments, such as product sales allowances and accruals related to prompt payment discounts, chargebacks, governmental and contractual rebates, wholesaler fees, product returns, and co-payment assistance costs, which could be adjusted based on actual results in the future. The Company is highl

Cyclerion Separation

Cyclerion Separation	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Cyclerion Separation	​ 3. Cyclerion Separation ​ On April 1, 2019, Ironwood completed the separation of its sGC business, and certain other assets and liabilities, into Cyclerion. The Separation was effected by means of a distribution of all of the outstanding shares of common stock, with no par value, of Cyclerion through a dividend of Cyclerion’s common stock, to Ironwood’s stockholders of record as of the close of business on March 19, 2019. Prior to the Separation on April 1, 2019, as described in Note 1, Nature of Business ​ Agreements with Cyclerion ​ The separation agreement with Cyclerion, dated as of March 30, 2019, sets forth, among other things, the Company’s agreements with Cyclerion regarding the principal actions to be taken in connection with the Separation, including the dividend, which was effective as of April 1, 2019. The separation agreement identifies assets transferred, liabilities assumed by and contracts assigned to each of Cyclerion and Ironwood as part of the Separation, and provides for when and how these transfers, assumptions and assignments occur. The purpose of the separation agreement was to provide Cyclerion and Ironwood with assets to operate their respective businesses and retain or assume liabilities related to those assets. ​ The transfer of assets and liabilities to Cyclerion was effected through a contribution in accordance with the separation agreement as summarized below (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ As of April 1, 2019 ​ Assets: ​ ​ ​ ​ Prepaid expenses and other current assets ​ $ 1,169 ​ Property and equipment, net ​ ​ 10,241 ​ Other assets ​ ​ 21 ​ ​ ​ $ 11,431 ​ Liabilities: ​ ​ ​ ​ Accrued research and development costs ​ $ 5,673 ​ Accrued expenses and other current liabilities ​ ​ 3,149 ​ ​ ​ $ 8,822 ​ Net Assets Transferred to Cyclerion ​ $ 2,609 ​ ​ In addition, the Company received approximately $1.3 million during the three months ended September 30, 2019 associated with tenant improvement reimbursement provisions related to the Cyclerion lease in accordance with the separation agreement. ​ The tax matters agreement, dated as of March 30, 2019, governs each party’s rights, responsibilities and obligations with respect to taxes, including taxes, if any, incurred as a result of any failure of the Separation to qualify as tax-free. In general, if the parties incur tax liabilities in the event that the Separation is not tax-free, each party is expected to be responsible for any taxes imposed on Ironwood or Cyclerion that arise from the failure of the Separation to qualify as a transaction that is generally tax-free for U.S. federal income tax purposes, under Sections 355 and 368(a)(1)(D) and certain other relevant provisions of the Internal Revenue Code of 1986, as amended, to the extent that the failure to so qualify is attributable to an acquisition of stock or assets of, or certain actions, omissions or failures to act of, such party. If both Ironwood and Cyclerion are responsible for such failure, liability will be shared according to relative fault. U.S. tax otherwise resulting from the failure of the Separation to qualify as a transaction that is tax-free generally will be the responsibility of Ironwood. Each party otherwise agreed to indemnify the other party from and against any liability for taxes allocated to such party under the tax matters agreement and any taxes resulting from breach of any such party’s covenants under the tax matters agreement, the separation agreement, or any ancillary agreement entered into in connection with the Separation. Cyclerion agreed to certain covenants that contain restrictions intended to preserve the tax-free status of the distribution and certain related transactions. ​ The employee matters agreement, dated as of March 30, 2019, allocates assets, liabilities and responsibilities relating to the employment, compensation, and employee benefits of Ironwood and Cyclerion employees, and other related matters in connection with the Separation, including the treatment of outstanding Ironwood incentive equity awards. Pursuant to the employee matters agreement, the outstanding Ironwood equity awards held by Cyclerion and Ironwood employees were adjusted in connection with the Separation, with the intent to maintain, immediately following the Separation, the economic value of the awards. No incremental stock-based compensation expense related to the Separation-related adjustments was recognized during the year ended December 31, 2019 (Note 15). ​ Additionally, the Company entered into two transition services agreements and a development agreement with Cyclerion. ​ Pursuant to the transition service agreements, the Company is obligated to provide and is entitled to receive certain transition services related to corporate functions, such as finance, procurement, facilities and development. Services provided by the Company to Cyclerion will continue for an initial term of one to two years from the date of the Separation (as applicable), unless earlier terminated or extended according to the terms of the transition services agreement. Services provided by Cyclerion to the Company will continue for an initial term of one year from the date of the Separation, unless earlier terminated or extended according to the terms of such transition services agreement. Services received and performed are paid at a mutually agreed upon rate. Amounts received for services provided to Cyclerion are recorded as other income and amounts paid for services provided by Cyclerion are recorded as selling, general and administrative expense and research and development expense, as applicable. During the year ended December 31, 2019, the Company recorded approximately $0.3 million as other income for services provided to Cyclerion. During the year ended December 31, 2019, the Company recorded an insignificant amount in both selling, general and administrative expense and research and development expense for services provided by Cyclerion, respectively. ​ Pursuant to the development agreement, Cyclerion is obligated to provide the Company with certain research and development services with respect to certain of Ironwood’s products and product candidates, including MD-7246 and IW-3718. Such research and development activities are governed by a joint steering committee comprised of representatives from both Cyclerion and Ironwood. Services received are paid at a mutually agreed upon rate. The Company recorded approximately $4.5 million in research and development expenses under the development agreement during the year ended December 31, 2019. ​ Discontinued Operations ​ Upon Separation, the Company determined its sGC business qualified for discontinued operations accounting treatment in accordance with ASC 205-20. The following is a summary of expenses of Cyclerion for years ended December 31, 2019, 2018 and 2017 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Costs and expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Research and development ​ ​ 21,792 ​ 65,443 ​ 60,083 ​ Selling, general and administrative ​ ​ 15,646 ​ 21,615 ​ 1,939 ​ Restructuring expenses ​ ​ — ​ ​ 1,164 ​ ​ — ​ Net loss from discontinued operations ​ $ 37,438 ​ $ 88,222 ​ $ 62,022 ​ ​ There were no assets and liabilities related to discontinued operations as of December 31, 2019, as all balances were transferred to Cyclerion upon Separation. The following is a summary of assets and liabilities of discontinued operations as of December 31, 2018 (in thousands): ​ ​ ​ ​ ​ Assets: ​ ​ ​ Prepaid expenses and other current assets ​ $ 847 Property and equipment, net ​ ​ 9,618 Other assets ​ ​ 25 ​ ​ $ 10,490 Liabilities: ​ ​ ​ Accounts payable ​ $ 3,232 Accrued research and development costs ​ ​ 5,256 Accrued expenses and other current liabilities ​ ​ 7,251 ​ ​ $ 15,739 ​

Net Income (Loss) Per Share

Net Income (Loss) Per Share	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Net Income (Loss) Per Share	4. Net Income (Loss) Per Share The following table sets forth the computation of basic and diluted net income (loss) per common share (in thousands, except per share amounts), which is computed by dividing net (income) loss by the weighted average number of common shares outstanding during the period: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Numerator: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Net income (loss) ​ $ 21,505 ​ $ (282,368) ​ $ (116,937) ​ Denominator: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average number of common shares outstanding used in net income (loss) per share — basic and diluted ​ 156,023 ​ 152,634 ​ 148,993 ​ Net income (loss) per share — basic and diluted ​ $ 0.14 ​ $ (1.85) ​ $ (0.78) ​ ​ In June 2015, in connection with the issuance of approximately $335.7 million in aggregate principal amount of the 2022 Convertible Notes (Note 12), the Company entered into the Convertible Note Hedges. The Convertible Note Hedges are generally expected to reduce the potential dilution to the Company’s Class A common stockholders upon a conversion of the 2022 Convertible Notes and/or offset any cash payments the Company is required to make in excess of the principal amount of converted 2022 Convertible Notes in the event that the market price per share of the Company’s Class A Common Stock, as measured under the terms of the Convertible Note Hedges, is greater than the conversion price of the 2022 Convertible Notes. The Convertible Note Hedges are not considered for purposes of calculating the number of diluted weighted average shares outstanding, as their effect would be antidilutive. Concurrently with entering into the Convertible Note Hedges, the Company also sold Note Hedge Warrants with the Convertible Note Hedge counterparties to acquire shares of the Company’s Class A Common Stock, subject to customary anti-dilution adjustments (Note 12). The Note Hedge Warrants could have a dilutive effect on the Company’s Class A Common Stock to the extent that the market price per share of the Class A Common Stock exceeds the applicable strike price of such warrants. The Note Hedge Warrants are not considered for purposes of calculating the number of diluted weighted averages shares outstanding, as their effect would be antidilutive. In August 2019, in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into the Capped Calls. The Capped Calls are generally expected to reduce the potential dilution to the Company’s Class A common stockholders upon a conversion of the 2024 Convertible Notes or the 2026 Convertible Notes and/or offset any cash payments that the Company is required to make in excess of the principal amount of converted 2024 Convertible Notes or 2026 Convertible Notes in the event that the market price per share of the Company’s Class A Common Stock, as measured under the terms of the Capped Calls, is greater than the conversion price of the 2024 Convertible Notes or the 2026 Convertible Notes. The Capped Calls are not considered for purposes of calculating the number of diluted weighted average shares outstanding, as their effect would be anti-dilutive. ​ The following potentially dilutive securities have been excluded from the computation of diluted weighted average shares outstanding, as applicable, as their effect would be anti-dilutive (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Options to purchase Class A Common Stock 17,194 20,457 21,086 ​ Shares subject to repurchase 182 65 62 ​ Restricted stock units ​ 3,207 ​ 3,058 ​ 2,277 ​ Note Hedge Warrants ​ 8,318 ​ 20,250 ​ 20,250 ​ 2022 Convertible Notes ​ 8,318 ​ 20,250 ​ 20,250 ​ 2024 Convertible Notes ​ 14,934 ​ — ​ — ​ 2026 Convertible Notes ​ 14,934 ​ — ​ — ​ ​ 67,087 64,080 63,925 ​ ​

Goodwill and Intangible Assets

Goodwill and Intangible Assets	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Goodwill and Intangible Assets	5. Goodwill and Intangible Assets ​ The Company closed a transaction with AstraZeneca (the “Lesinurad Transaction”) on June 2, 2016 (the “Acquisition Date”) pursuant to which the Company received an exclusive license to develop, manufacture and commercialize the Lesinurad Products in the U.S. On August 2, 2018, the Company delivered to AstraZeneca a notice of termination of the lesinurad license agreement, which termination was made with respect to all products under the lesinurad license agreement. ​ The value of the developed technology – ZURAMPIC and developed technology – DUZALLO intangible assets as of the Acquisition Date was approximately $22.0 million and approximately $145.1 million, respectively. As of July 31, 2018, the accumulated amortization for developed technology – ZURAMPIC and developed technology – DUZALLO intangible assets was approximately $3.6 million and approximately $11.7 million, respectively. ​ During the year ended December 31, 2018, the Company completed its initiative to evaluate the optimal mix of investments for the lesinurad franchise for uncontrolled gout using a comprehensive marketing mix in select test markets (with paired controls). Data from the test markets did not meet expectations. As a result, during the year ended December 31, 2018, the Company reduced its projected revenue and net cash flow assumptions associated with the value of its developed technology – ZURAMPIC and developed technology – DUZALLO intangible assets. Accordingly, the Company evaluated its developed technology – ZURAMPIC and developed technology – DUZALLO intangible assets for impairment and recorded an approximately $151.8 million impairment charge during the year ended December 31, 2018. The impairment assessment performed utilized the revised projected revenue and net cash flows assumed through the termination of the lesinurad license agreement, resulting in an impairment of the full carrying value of the intangible assets. The impairment charge was recorded as impairment of intangible assets in the Company’s consolidated statement of operations. ​ The Company tests its goodwill for impairment annually as of October 1 st ​

Collaboration, License, Co-Prom

Collaboration, License, Co-Promotion and Other Commercial Agreements	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Collaboration, License, Co-Promotion and Other Commercial Agreements	6. Collaboration, License, Co-Promotion and Other Commercial Agreements For the year ended December 31, 2019, the Company had linaclotide collaboration agreements with Allergan for North America and AstraZeneca for China (including Hong Kong and Macau), as well as linaclotide license agreements with Astellas for Japan and with Allergan for the Allergan License Territory. The Company also had agreements with Allergan to co-promote VIBERZI in the U.S. and with Alnylam to perform disease awareness activities for AHP and sales detailing activities for GIVLAARI. The following table provides amounts included in the Company’s consolidated statements of operations as collaborative arrangements revenue and sale of API primarily attributable to transactions from these arrangements (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, Collaborative Arrangements Revenue 2019 2018 2017 Linaclotide Collaboration Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Allergan (North America) ​ $ 327,591 $ 266,177 $ 260,210 ​ Allergan (Europe and other) ​ ​ 1,718 ​ ​ 1,146 ​ ​ 617 ​ AstraZeneca (China, including Hong Kong and Macau) ​ ​ 32,628 ​ — ​ 208 ​ Astellas (Japan) ​ ​ 10,147 ​ — ​ — ​ Co-Promotion and Other Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Exact Sciences (COLOGUARD) (1) ​ ​ — ​ ​ — ​ ​ 2,544 ​ Allergan (VIBERZI) ​ ​ 3,723 ​ ​ 4,290 ​ ​ 1,535 ​ Alnylam (GIVLAARI) ​ ​ 2,000 ​ ​ — ​ ​ — ​ Other ​ ​ 1,845 ​ ​ 1,226 ​ ​ 419 ​ Total collaborative arrangements revenue ​ $ 379,652 ​ $ 272,839 ​ $ 265,533 ​ Sale of API ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Linaclotide License Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Astellas (Japan) ​ $ 45,788 ​ $ 69,599 ​ $ 29,682 ​ AstraZeneca (China, including Hong Kong and Macau) ​ ​ 2,973 ​ ​ — ​ ​ — ​ Other (2) ​ ​ — ​ ​ 756 ​ ​ — ​ Total sale of API ​ $ 48,761 ​ $ 70,355 ​ $ 29,682 ​ (1) In August 2016, the Company terminated the Co-Promotion Agreement for COLOGUARD with Exact Sciences Corp. Under the terms of the agreement, the Company continued to receive royalty payments through July 2017. (2) During the year ended December 31, 2018, the Company recorded approximately $0.8 million in revenue related to the sale of API to Allergan, separate from its existing revenue agreements. Accounts receivable, net included approximately $43.9 million and approximately $21.0 million related to collaborative arrangements revenue and sale of API, collectively, as of December 31, 2019 and 2018, respectively. Related party accounts receivable, net included approximately $110.1 million and approximately $63.0 million related to collaborative arrangements revenue, net of approximately $4.1 million and approximately $3.1 million related to related party accounts payable as of December 31, 2019 and 2018, respectively. As of December 31, 2019, deferred revenue was approximately $0.9 million related to the disease education and promotional agreement with Alnylam. As of December 31, 2019 and 2018, there were no impairment indicators for the accounts receivable recorded. Linaclotide Agreements Collaboration Agreement for North America with Allergan In September 2007, the Company entered into a collaboration agreement with Allergan to develop and commercialize linaclotide for the treatment of IBS-C, CIC, and other GI conditions in North America. Under the terms of this collaboration agreement, the Company received a non-refundable, upfront licensing fee and shares equally with Allergan all development costs as well as net profits or losses from the development and sale of linaclotide in the U.S. The Company receives royalties in the mid-teens' percent based on net sales in Canada and Mexico. Allergan is solely responsible for the further development, regulatory approval and commercialization of linaclotide in those countries and funding any costs. The collaboration agreement for North America also includes contingent milestone payments, as well as a contingent equity investment, based on the achievement of specific development and commercial milestones. At December 31, 2019, $205.0 million in license fees and all six development milestone payments had been received by the Company, as well as a $25.0 million equity investment in the Company’s capital stock. The Company can also achieve up to $100.0 million in a sales-related milestone if certain conditions are met, which will be recognized as collaborative arrangements revenue when it is probable that a significant reversal of revenue would not occur, and the associated constraints have been lifted. During the years ended December 31, 2019, 2018 and 2017, the Company incurred approximately $37.6 million, approximately $39.2 million, and approximately $28.5 million in total research and development expenses under the linaclotide collaboration for North America. As a result of the research and development cost-sharing provisions of the linaclotide collaboration for North America, the Company offset approximately $7.2 million and approximately Agreement with Allergan for VIBERZI ® ® Commercial Agreement with Allergan The Company evaluated its collaboration arrangement for North America with Allergan under ASC 606 and concluded that all development-period performance obligations had been satisfied as of September 2012. However, the Company has determined that there are three remaining commercial-period performance obligations, which include the sales detailing of LINZESS, participation in the joint commercialization committee, and approved additional trials. The consideration remaining includes cost reimbursements in the U.S., as well as commercial sales-based milestones and net profit and loss sharing payments based on net sales in the U.S. Additionally, the Company receives royalties in the mid-teens’ percent based on net sales in Canada and Mexico. Royalties, commercial sales-based milestones, and net profit and loss sharing payments will be recorded as collaborative arrangements revenue or expense in the period earned, in accordance with the sales-based royalty exception, as these payments relate predominately to the license granted to Allergan. The Company records royalty revenue in the period earned based on royalty reports from its partner, if available, or based on the projected sales and historical trends. The cost reimbursements received from Allergan during the commercialization period will be recognized as earned in accordance with the right-to-invoice practical expedient, as the Company’s right to consideration corresponds directly with the value of the services transferred during the commercialization period. Under the Company’s collaboration agreement with Allergan for North America, LINZESS net sales are calculated and recorded by Allergan and include gross sales net of discounts, rebates, allowances, sales taxes, freight and insurance charges, and other applicable deductions, as noted above. These amounts include the use of estimates and judgments, which could be adjusted based on actual results in the future. The Company records its share of the net profits or net losses from the sales of LINZESS in the U.S. on a net basis less commercial expenses, and presents the settlement payments to and from Allergan as collaboration expense or collaborative arrangements revenue, as applicable. This treatment is in accordance with the Company’s revenue recognition policy, given that the Company is not the primary obligor and does not have the inventory risks in the collaboration agreement with Allergan for North America. The Company relies on Allergan to provide accurate and complete information related to net sales of LINZESS in accordance with U.S. generally accepted accounting principles in order to calculate its settlement payments to and from Allergan and record collaboration expense or collaborative arrangements revenue, as applicable. From time to time, in accordance with the terms of the collaboration with Allergan for North America, the Company engages an independent certified public accounting firm to review the accuracy of the financial reporting from Allergan to the Company. In connection with such a review during the three months ended September 30, 2018, Allergan reported to the Company an approximately $59.3 million negative adjustment to LINZESS net sales. The adjustment related to the cumulative difference between certain previously estimated LINZESS gross-to-net sales reserves and allowances made by Allergan during the years ended December 31, 2015, 2016 and 2017, and subsequent actual payments made. This adjustment was primarily associated with estimated governmental and contractual rebates, as reported by Allergan. Upon receiving this information from Allergan, the Company recorded a change in accounting estimate to reduce collaborative arrangements revenue by approximately $29.7 million during the three months ended September 30, 2018 related to the Company’s share of this adjustment. In addition, during the three months ended December 31, 2018, Allergan reported to the Company a true-up of approximately $0.2 million related to the previously reported adjustment for the cumulative difference between certain previously estimated LINZESS gross-to-net sales reserves and allowances. ​ The Company recognized collaborative arrangements revenue from the Allergan collaboration agreement for North America during the years ended December 31, 2019, 2018 and 2017 as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Collaborative arrangements revenue related to sales of LINZESS in the U.S. ​ $ 325,429 ​ $ 264,243 $ 256,238 ​ Royalty revenue ​ 2,162 ​ 1,934 ​ 2,295 ​ Other (1) ​ ​ — ​ ​ — ​ ​ 1,677 ​ Total collaborative arrangements revenue ​ $ 327,591 ​ $ 266,177 ​ $ 260,210 ​ (1) Includes net profit share adjustments of approximately $1.7 million recorded during the year ended December 31, 2017 related to a change in estimated selling expenses previously recorded. The collaborative arrangements revenue recognized in the years ended December 31, 2019, 2018 and 2017 primarily represents the Company’s share of the net profits and net losses on the sale of LINZESS in the U.S. The following table presents the amounts recorded by the Company for commercial efforts related to LINZESS in the U.S. in the years ended December 31, 2019, 2018 and 2017 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Collaborative arrangements revenue related to sales of LINZESS in the U.S. (1)(2) ​ $ 325,429 ​ $ 264,243 ​ $ 256,238 ​ Selling, general and administrative costs incurred by the Company (1) ​ (38,123) ​ (42,435) ​ ​ (41,252) ​ The Company’s share of net profit ​ $ 287,306 ​ $ 221,808 ​ $ 214,986 ​ (1) Includes only collaborative arrangements revenue or selling, general and administrative costs attributable to the cost-sharing arrangement with Allergan. Excludes approximately $2.4 million, approximately $2.2 million, and approximately $0.9 million for the years ended December 31, 2019, 2018 and 2017, respectively, related to patent prosecution and patent litigation costs recognized in connection with the collaboration agreement with Allergan. (2) Certain of the unfavorable adjustments to the Company’s share of the LINZESS net profits were reduced or eliminated in connection with the co-promotion activities under the Company’s agreement with Allergan to co-promote VIBERZI in the U.S., as described below in Agreement with Allergan for VIBERZI . In May 2014, CONSTELLA ® License Agreement with Allergan (All countries other than the countries and territories of North America, China (including Hong Kong and Macau), and Japan) In April 2009, the Company entered into a license agreement with Almirall, S.A. (“Almirall”) to develop and commercialize linaclotide in Europe (including the Commonwealth of Independent States and Turkey) for the treatment of IBS-C, CIC and other GI conditions (the “European License Agreement”). In accordance with the European License Agreement, the Company granted Almirall a right to access its U.S. Phase III clinical trial data for the purposes of supporting European regulatory approval. Additionally, the Company was required to participate on a joint development committee during linaclotide’s development period and is required to participate in a joint commercialization committee while linaclotide is commercially available. In October 2015, Almirall transferred its exclusive license to develop and commercialize linaclotide in Europe to Allergan. Additionally, in October 2015, the Company and Allergan separately entered into an amendment to the European License Agreement relating to the development and commercialization of linaclotide in Europe. Pursuant to the terms of the amendment, (i) certain sales-based milestones payable to the Company under the European License Agreement were modified to increase the total milestone payments such that, when aggregated with certain commercial launch milestones, they could total up to $42.5 million, (ii) the royalties payable to the Company during the term of the European License Agreement were modified such that the royalties based on sales volume in Europe begin in the mid-single digit percent and escalate to the upper-teens percent by calendar year 2019, and (iii) Allergan assumed responsibility for the manufacturing of linaclotide API for Europe from the Company, as well as the associated costs. The Company concluded that the 2015 amendment to the European License Agreement was not a modification to the linaclotide collaboration agreement with Allergan for North America. In January 2017, concurrently with entering into the commercial agreement as described below in Commercial Agreement with Allergan , the Company and Allergan entered into an amendment to the European License Agreement (the “2017 Amendment”). The 2017 Amendment extended the license to develop and commercialize linaclotide in all countries other than China (including Hong Kong and Macau), Japan, and the countries and territories of North America. On a country-by-country and product-by-product basis in such additional territory, Allergan is obligated to pay the Company a royalty as a percentage of net sales of products containing linaclotide as an active ingredient in the upper-single digits for five years following the first commercial sale of a linaclotide product in a country, and in the low-double digits thereafter. The royalty rate for products in the expanded territory will decrease, on a country-by-country basis, to the lower-single digits , or cease entirely, following the occurrence of certain events. Allergan is obligated to assume certain purchase commitments for quantities of linaclotide API under the Company’s agreements with third-party API suppliers. The 2017 Amendment did not modify any of the milestones or royalty terms related to Europe. Prior to the adoption of ASC 606, the Company concluded that the 2017 Amendment was a material modification to the European License Agreement; however, this modification did not have a material impact on the Company's consolidated financial statements as there was no deferred revenue associated with the Amended European License Agreement. The Company also concluded that the 2017 Amendment was not a material modification to the linaclotide collaboration agreement with Allergan for North America. The Company’s conclusions on deliverables under ASC 605-25 are described below in Commercial Agreement with Allergan The Company evaluated the European License Agreement under ASC 606. In evaluating the terms of the European License Agreement under ASC 606, the Company determined that there are no remaining performance obligations as of September 2012. However, the Company continues to be eligible to receive consideration in the form of commercial launch milestones, sales-based milestones, and royalties. The commercial launch milestones, sales-based milestones and royalties under the European License Agreement have historically been recognized as revenue as earned. Under ASC 606, the Company applied the sales-based royalty exception to royalties and sales-based milestones, as these payments relate predominantly to the license granted to Allergan (formerly Almirall). Accordingly, the royalties and sales-based milestones are recorded as revenue in the period earned. The Company records royalties on sales of CONSTELLA in Europe in the period earned based on royalty reports from its partner, if available, or the projected sales and historical trends. The commercial launch milestones are recognized as revenue when it is probable that a significant reversal of revenue would not occur, and the associated constraint has been lifted. Additionally, the Company evaluated the terms of the 2017 Amendment under ASC 606 and determined that it would be treated as a separate contract given that it adds a distinct good or service at an amount that reflects standalone selling price. The Company determined that all performance obligations in the 2017 Amendment were satisfied in January 2017 when the license for the additional territory was transferred. The Company continues to receive royalties under this agreement, which are recorded in the period earned pursuant to the sales-based royalty exception, as they related predominantly to the license granted to Allergan. The Company recognized approximately $1.7 million, approximately $1.1 million and approximately $0.6 million of royalty revenue from the Amended European License Agreement during the years ended December 31, 2019, 2018 and 2017, respectively. License Agreement for Japan with Astellas In November 2009, the Company entered into a license agreement with Astellas, as amended, to develop and commercialize linaclotide for the treatment of IBS-C, CIC and other GI conditions in Japan (the “2009 License Agreement with Astellas”). Astellas is responsible for all activities relating to development, regulatory approval and commercialization in Japan as well as funding the associated costs and the Company was required to participate on a joint development committee over linaclotide’s development period. Under the 2009 License Agreement with Astellas, the Company received an up-front licensing fee of $30.0 million, which was recognized as collaborative arrangements revenue on a straight-line basis over the Company’s estimate of the period over which linaclotide was to be developed under the 2009 License Agreement with Astellas in accordance with ASC 605. The development period was completed in December 2016 upon approval of LINZESS by the Japanese Ministry of Health, Labor and Welfare, at which point all previously deferred revenue under the agreement was recognized. The 2009 License Agreement with Astellas also includes three development milestone payments that totaled up to $45.0 million, all of which were achieved and recognized as revenue through December 31, 2016 in accordance with ASC 605. The Company had evaluated the terms of the 2009 License Agreement with Astellas under ASC 606 and determined that there were no remaining performance obligations as of December 2016. However, there continued to be consideration in the form of royalties on sales of LINZESS in Japan under the 2009 License Agreement with Astellas. Upon adoption of ASC 606, the Company concluded that the royalties on sales of LINZESS in Japan related predominantly to the license granted to Astellas. Accordingly, the Company applied the sales-based royalty exception and recorded royalties on sales of LINZESS in Japan in the period earned based on royalty reports from Astellas, if available, or the projected sales and historical trends. Additionally, under the terms of the Astellas Commercial Supply Agreement, the Company determined it had an ongoing performance obligation to supply API. Upon adoption of ASC 606, product revenue is recognized when the customer obtains control of the Company’s product, which occurs at a point in time, typically upon shipment of the product to the customer. This resulted in earlier revenue recognition than the Company’s historical accounting. During the years ended December 31, 2019, 2018, and 2017, the Company recognized approximately $27.5 In August 2019, the Company and Astellas amended and restated the 2009 License Agreement with Astellas (the “Amended Astellas License Agreement”). This amendment is considered a modification to the 2009 License Agreement with Astellas and is accounted for as a new and separate contract. Under the terms of the Amended Astellas License Agreement, the Company will no longer be responsible for the supply of linaclotide API to Astellas, and Astellas will be responsible for its own supply of linaclotide API in Japan, beginning in 2020. Astellas committed to purchase certain quantities of linaclotide API from the Company in 2019. ​ In connection with the execution of the Amended Astellas License Agreement, Astellas paid the Company a non-refundable upfront payment of $10.0 million in August 2019. Further, beginning in 2020, Astellas will, in lieu of the royalty payment terms set forth in the 2009 License Agreement with Astellas, pay royalties to the Company at rates beginning in the mid-single digit percent and escalating to low-double-digit percent, based on aggregate annual net sales in Japan of products containing linaclotide API. These royalty payments will be subject to reduction following the expiration of certain licensed patents and the occurrence of generic competition in Japan. The Company continued to supply linaclotide API for Japan during 2019 at a contractually defined rate. Additionally, Astellas will reimburse the Company for the Company’s performance of adverse event reporting services at a fixed monthly rate until such services are terminated. ​ The Company identified the following performance obligations under the Amended Astellas License Agreement: ● delivery of the expanded license of intellectual property, including the applicable manufacturing know-how; ● obligation to supply linaclotide API for 2019; and ● adverse event reporting services. ​ The Company allocated the $10.0 million upfront payment to the delivery of the expanded license of intellectual property and recognized it as collaborative arrangements revenue at contract inception. The Company allocated the approximately $20.4 million in remaining purchase orders for API to the obligation to supply linaclotide API to Astellas for 2019. Consideration for the supply of linaclotide API is recognized over the performance period as linaclotide API is shipped to Astellas using an output method. Consideration allocated to the adverse event reporting services is recognized as such services are provided over the performance period based on the amount to which the Company has a right to invoice using an output method. ​ Royalties on sales of LINZESS in Japan relate predominantly to the license granted to Astellas. Accordingly, the Company applies the sales-based royalty exception and records royalties on sales of LINZESS in Japan in the period earned based on royalty reports from its partner, if available, or the projected sales and historical trends. ​ The Company recognized $10.0 million in collaborative arrangements revenue during the year ended December 31, 2019 related to the upfront fee associated with the execution of the Amended Astellas License Agreement. The Company recognized approximately $18.3 million from the sale of API to Astellas under the Amended License Agreement during the year ended December 31, 2019. The Company recognized an insignificant amount of collaborative arrangements revenue related to adverse event reporting services for the year ended December 31, 2019. ​ Collaboration Agreement for China (including Hong Kong and Macau) with AstraZeneca In October 2012, the Company entered into a collaboration agreement with AstraZeneca to co-develop and co-commercialize linaclotide in the AstraZeneca License Territory (the “AstraZeneca Collaboration Agreement”). The collaboration provided AstraZeneca with an exclusive nontransferable license to exploit the underlying technology in the AstraZeneca License Territory. The parties shared responsibility for continued development and commercialization of linaclotide under a joint development plan and a joint commercialization plan, respectively, with AstraZeneca having primary responsibility for the local operational execution. The parties agreed to an Initial Development Plan (“IDP”), which included the planned development of linaclotide in China, including the lead responsibility for each activity and the related internal and external costs. The IDP indicated that AstraZeneca was responsible for a multinational Phase III clinical trial (the “Phase III Trial”), the Company was responsible for nonclinical development and supplying clinical trial material and both parties were responsible for the regulatory submission process. The IDP indicated that the party specifically designated as being responsible for a particular development activity under the IDP should implement and conduct such activities. The activities were governed by a Joint Development Committee (“JDC”), with equal representation from each party. The JDC was responsible for approving, by unanimous consent, the joint development plan and development budget, as well as approving protocols for clinical studies, reviewing and commenting on regulatory submissions, and providing an exchange of data and information. There were no refund provisions in the AstraZeneca Collaboration Agreement. Under the terms of the AstraZeneca Collaboration Agreement, the Company received a $25.0 million non-refundable up-front payment upon execution. The Company was also eligible for $125.0 million in additional commercial milestone payments contingent on the achievement of certain sales targets. The parties also shared in the net profits and losses associated with the development and commercialization of linaclotide in the AstraZeneca License Territory, with AstraZeneca receiving 55% of the net profits or incurring 55% of the net losses until a certain specified commercial milestone was achieved, at which time profits and losses would be shared equally thereafter. Activities under the AstraZeneca Collaboration Agreement were evaluated in accordance with ASC 605-25 to determine if they represented a multiple element revenue arrangement. The Company identified the following deliverables in the AstraZeneca Collaboration Agreement: ● an exclusive license to develop and commercialize linaclotide in the AstraZeneca License Territory (the “License Deliverable”) (the deliverable was completed upon execution and all associated revenue was recognized as of December 31, 2016); ● research, development and regulatory services pursuant to the IDP, as modified from time to time (the “R&D Services”); ● JDC services; ● obligation to supply clinical trial material; and ● co-promotion services for NEXIUM (the “Co-Promotion Deliverable”) (the deliverable was completed and all associated revenue was recognized as of December 31, 2013). Under ASC 605, the License Deliverable was nontransferable and had certain sublicense restrictions. The Company determined that the License Deliverable had standalone value as a result of AstraZeneca’s internal product development and commercialization capabilities, which would enable it to use the License Deliverable for its intended purposes without the involvement of the Company. The remaining deliverables were deemed to have standalone value based on their nature and all deliverables met the criteria to be accounted for as separate units of accounting under ASC 605-25. The Company performed R&D services and JDC services and supplied clinical trial materials during the estimated development period. All consideration allocated to such services was being recognized as a reduction of research and development costs, using the proportional performance method, by which the amounts were recognized in proportion to the costs incurred in accordance with ASC 605. In August 2014, the Company and AstraZeneca, through the JDC, modified the IDP and development budget to include approximately $14.0 million in additional activities over the remaining development period, to be shared by the Company and AstraZeneca under the terms of the AstraZeneca Collaboration Agreement. The total amount of the non-contingent consideration allocable to the AstraZeneca Collaboration Agreement was approximately $34.0 million (“Arrangement Consideration”), which included the $25.0 million non-refundable up-front payment and approximately $9.0 million representing 55% of the costs for clinical trial material supply services and research, development and regulatory activities allocated to the Company in the IDP or as approved by the JDC in subsequent periods. The Company allocated the Arrangement Consideration to the non-contingent deliverables based on management’s best estimated selling price (“BESP”) of each deliverable using the relative selling price method, as the Company did not have vendor-specific objective evidence or third-party evidence of selling price for such deliverables. Of the total Arrangement Consideration, approximately $29.7 million was allocated to the License Deliverable, approximately $1.8 million to the R&D Services, approximately $0.1 million to the JDC services, approximately $0.3 million to the clinical trial material supply services, and approximately $2.1 million to the Co-Promotion Deliverable in the relative selling price model. Because the Company shared development costs with AstraZeneca, payments from AstraZeneca with respect to both research and development and selling, general and administrative costs incurred by the Company prior to the commercialization of linaclotide in the AstraZeneca License Territory were recorded as a reduction in expense, in accordance with the Company’s policy, which was consistent with the nature of the cost reimbursement. Development costs incurred by the Company that pertain to the joint development plan and subsequent amendments to the joint development plan, as approved by the JDC, were recorded as research and development expense as incurred. Payments to AstraZeneca were recorded as incremental research and development expense. As a result of the cost-sharing arrangements under the collaboration, the Company recognized approximately $0.3 million in incremental research and development costs during the year ended December 31, 2017. In March 2017, the Company began providing supply of linaclotide finished drug product and certain commercialization-related services pursuant to the AstraZeneca Collaboration Agreement. During the year ended December 31, 2017, the Company recognized approximately $0.2 million as collaborative arrangements revenue related to linaclotide finished drug product, as this deliverable was no longer contingent. Upon the adoption of ASC 606, the Company reevaluated the AstraZeneca Collaboration Agreement and, consistent with its conclusions under ASC 605, identified six performance obligations including the license, R&D services, JDC services, supply of clinical trial material, co-promotion services for NEXIUM, and the Joint Commercialization Committee (“JCC”) services. The Company determined that the supply of linaclotide finished drug product for commercial requirements was an optional service at inception of the arrangement and did not provide a material right to AstraZeneca. At the ASC 606 adoption date, the Company had fully satisfied its obligation to transfer the license and NEXIUM co-promotion services to AstraZeneca. The following remaining performance obligations were ongoing as of the adoption date: ● R&D Services ● JDC services; ● obligation to supply clinical trial material; and ● JCC services. Under ASC 606, the Company applied the contract modification practical expedient to the August 2014 amendment, which expanded the scope of the Company’s activities under the IDP and increased the development budget. This practical expedient allows an entity to reflect the aggregate effect of all modifications that occur before the beginning of the earliest period presented. The application of this practical expedient resulted in a total transaction price of approximately $34.0 million, which was allocable to the Company’s performance obligations on a relative standalone selling price basis. Under ASC 606, amounts of consideration allocated to the license and NEXIUM co-promotion services would have been recognized in full prior to adoption as these performance obligations were satisfied in October 2012 and December 2013, respectively. Consideration allocated to the R&D Services was

Fair Value of Financial Instrum

Fair Value of Financial Instruments	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Fair Value of Financial Instruments	7. Fair Value of Financial Instruments The tables below present information about the Company’s assets that are measured at fair value on a recurring basis as of December 31, 2019 and 2018 and indicate the fair value hierarchy of the valuation techniques the Company utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize observable inputs such as quoted prices in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are either directly or indirectly observable, such as quoted prices for similar instruments in active markets, interest rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points in which there is little or no market data, which require the Company to develop its own assumptions for the asset or liability. The Company’s investment portfolio may include fixed income securities that do not always trade on a daily basis. As a result, the pricing services used by the Company apply other available information as applicable through processes such as benchmark yields, benchmarking of like securities, sector groupings and matrix pricing to prepare valuations. In addition, model processes are used to assess interest rate impact and develop prepayment scenarios. These models take into consideration relevant credit information, perceived market movements, sector news and economic events. The inputs into these models may include benchmark yields, reported trades, broker-dealer quotes, issuer spreads and other relevant data. The Company validates the prices provided by its third party pricing services by obtaining market values from other pricing sources and analyzing pricing data in certain instances. The Company also invests in certain reverse repurchase agreements which are collateralized by Government Securities and Obligations for an amount not less than 102% of their principal amount. The Company does not record an asset or liability for the collateral as the Company is not permitted to sell or re-pledge the collateral. The collateral has at least the prevailing credit rating of U.S. Government Treasuries and Agencies. The Company utilizes a third party custodian to manage the exchange of funds and ensure the collateral received is maintained at 102% of the reverse repurchase agreements principal amount on a daily basis. The following tables present the assets and liabilities the Company has measured at fair value on a recurring basis (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements at Reporting Date Using ​ ​ ​ Quoted Prices in Significant Other Significant ​ ​ ​ ​ ​ Active Markets for ​ Observable ​ Unobservable ​ ​ December 31, ​ Identical Assets ​ Inputs ​ Inputs ​ ​ 2019 ​ (Level 1) ​ (Level 2) ​ (Level 3) ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 139,190 ​ $ 139,190 ​ $ — ​ $ — ​ Repurchase agreements ​ ​ 37,800 ​ ​ 37,800 ​ ​ — ​ ​ — ​ Restricted cash: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ ​ 2,221 ​ ​ 2,221 ​ ​ — ​ ​ — ​ Convertible Note Hedges ​ ​ 31,366 ​ ​ — ​ ​ — ​ ​ 31,366 ​ Total assets measured at fair value ​ $ 210,577 ​ $ 179,211 ​ $ — ​ $ 31,366 ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Note Hedge Warrants ​ $ 24,260 ​ $ — ​ $ — ​ $ 24,260 ​ Total liabilities measured at fair value ​ $ 24,260 ​ $ — ​ $ — ​ $ 24,260 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements at Reporting Date Using ​ ​ ​ Quoted Prices in Significant Other Significant ​ ​ ​ ​ ​ Active Markets for ​ Observable ​ Unobservable ​ ​ December 31, ​ Identical Assets ​ Inputs ​ Inputs ​ ​ 2018 ​ (Level 1) ​ (Level 2) ​ (Level 3) ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 142,218 ​ $ 142,218 ​ $ — ​ $ — ​ Repurchase agreements ​ ​ 30,875 ​ ​ 30,875 ​ ​ — ​ ​ — ​ Convertible Note Hedges ​ ​ 41,020 ​ ​ — ​ ​ — ​ ​ 41,020 ​ Total assets measured at fair value ​ $ 214,113 ​ $ 173,093 ​ $ — ​ $ 41,020 ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Note Hedge Warrants ​ $ 33,763 ​ $ — ​ $ — ​ $ 33,763 ​ Contingent Consideration ​ ​ 51 ​ ​ — ​ ​ — ​ ​ 51 ​ Total liabilities measured at fair value ​ $ 33,814 ​ $ — ​ $ — ​ $ 33,814 ​ ​ There were no transfers between fair value measurement levels during each of the years ended December 31, 2019 or 2018. Cash equivalents, accounts receivable, related party accounts receivable, prepaid expenses and other current assets, accounts payable, related party accounts payable, accrued research and development costs, accrued expenses and other current liabilities, the current portion of capital lease obligations, deferred rent, deferred revenue and operating lease obligations at December 31, 2019 and 2018 are carried at amounts that approximate fair value due to their short-term maturities. Convertible Note Hedges and Note Hedge Warrants The Company’s Convertible Note Hedges and the Note Hedge Warrants are recorded as derivative assets and liabilities, respectively, and are classified as Level 3 measurements under the fair value hierarchy. These derivatives are not actively traded and are valued using the Black-Scholes option-pricing model, which requires the use of subjective assumptions. Significant inputs used to determine the fair value as of December 31, 2019 included the price per share of the Company’s Class A Common Stock, expected terms of the derivative instruments, strike prices of the derivative instruments, risk-free interest rate, and expected volatility of the Company’s Class A Common Stock. Changes to these inputs could materially affect the valuation of the Convertible Note Hedges and Note Hedge Warrants . The following inputs were used in the fair market valuation of the Convertible Note Hedges and Note Hedge Warrants as of December 31, 2019 and 2018: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended ​ Year Ended ​ ​ ​ December 31, ​ December 31, ​ ​ 2019 ​ 2018 ​ ​ ​ Convertible Note Hedge ​ Convertible Note Hedge ​ ​ Note Hedges ​ Warrants Note Hedges ​ Warrants Risk-free interest rate (1) ​ ​ 1.6 % ​ 1.6 % ​ 2.5 % ​ 2.5 % Expected term ​ 2.5 ​ 3.0 ​ ​ 3.5 ​ 4.1 ​ Stock price (2) ​ $ 13.31 ​ $ 13.31 ​ $ 10.36 ​ $ 10.36 ​ Strike price (3) ​ $ 14.51 ​ $ 18.82 ​ $ 16.58 ​ $ 21.50 ​ Common stock volatility (4) ​ ​ 49.1 % ​ 46.5 % ​ 43.8 % ​ 43.6 % Dividend yield (5) ​ — % — % — % — % (1) Based on U.S. Treasury yield curve, with terms commensurate with the terms of the Convertible Note Hedges and the Note Hedge Warrants. (2) The closing price of the Company’s Class A Common Stock on the last trading days of the years ended December 31, 2019 and 2018, respectively. (3) As per the respective agreements for the Convertible Note Hedges and Note Hedge Warrants. The strike prices for the Convertible Note Hedges and Note Hedge Warrants were adjusted in conjunction with the conversion rate adjustment in April 2019 (Note 12). (4) Expected volatility based on historical volatility of the Company’s Class A Common Stock. (5) The Company has not paid and does not anticipate paying cash dividends on its shares of common stock in the foreseeable future; therefore, the expected dividend yield is assumed to be zero . ​ The Convertible Note Hedges and the Note Hedge Warrants are recorded at fair value at each reporting date and changes in fair value are recorded in other (expense) income, net within the Company's consolidated statements of operations. Gains and losses for these derivative financial instruments are presented separately in the Company's consolidated statements of cash flows. The following table reflects the change in the Company's Level 3 Convertible Note Hedges and Note Hedge Warrants from December 31, 2017 through December 31, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Convertible ​ Note Hedge ​ ​ Note Hedges Warrants Balance at December 31, 2017 ​ $ 108,188 ​ $ (92,188) ​ Change in fair value, recorded as a component of gain (loss) on derivatives ​ ​ (67,168) ​ ​ 58,425 ​ Balance at December 31, 2018 ​ $ 41,020 ​ $ (33,763) ​ Cash settlement (received) paid upon early termination of derivatives ​ ​ (28,909) ​ ​ 25,735 ​ Change in fair value, recorded as a component of gain (loss) on derivatives ​ ​ 19,255 ​ ​ (16,232) ​ Balance at December 31, 2019 ​ $ 31,366 ​ $ (24,260) ​ ​ In August 2019, the Company repurchased $215.0 million aggregate principal amount of the 2022 Convertible Notes, which triggered a partial termination of the outstanding Convertible Note Hedges and Note Hedge Warrants (Note 12). During the year ended December 31, 2019, the Company recorded a gain of approximately $3.0 million on derivatives as a result of the partial termination of the Convertible Note Hedges and Note Hedge Warrants and the change in fair value of the remaining Convertible Note Hedges and Note Hedge Warrants during the year. ​ Contingent Consideration ​ In connection with the Lesinurad Transaction, the Company recorded a liability of $67.9 million as of the Acquisition Date for contingent payments due to AstraZeneca. This valuation was based on a Monte-Carlo simulation, which includes significant estimates related to probability weighted net cash outflow projections, primarily comprised of estimated future royalty and milestone payments to AstraZeneca, discounted using a yield curve equivalent to the Company’s credit risk, which was the estimated cost of debt financing for market participants. During the three months ended September 30, 2018, the Company reduced its projected revenue assumptions associated with the sales of ZURAMPIC and DUZALLO and delivered to AstraZeneca a notice of termination of the lesinurad license agreement. The Company recognized a gain on fair value remeasurement of contingent consideration of approximately $31.0 million during the year ended December 31, 2018. The contingent consideration was fully settled during the year ended December 31, 2019 and no liability remains as of December 31, 2019. ​ The following table reflects the change in the Company’s Level 3 contingent consideration payable from December 31, 2017 through December 31, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ Contingent ​ Consideration Fair Value at December 31, 2017 $ 31,258 ​ Changes in fair value ​ (31,045) ​ Payments/transfers to accrued expenses and other current liabilities ​ (162) ​ Fair Value at December 31, 2018 ​ ​ 51 ​ Payments ​ ​ (51) ​ Fair value at December 31, 2019 $ — ​ ​ Convertible Senior Notes In June 2015, the Company issued approximately $335.7 million aggregate principal amount of its 2022 Convertible Notes. In August 2019, the Company issued $200.0 million aggregate principal amount of its 2024 Convertible Notes and $200.0 million aggregate principal amount of its 2026 Convertible Notes, and used a portion of the proceeds from such issuance to repurchase $215.0 million aggregate principal amount of its 2022 Convertible Notes. The Company separately accounted for the liability and equity components of each of the 2022 Convertible Notes, 2024 Convertible Notes, and 2026 Convertible Notes, by allocating the proceeds between the liability component and equity component (Note 12). The fair value of the respective convertible senior notes, which differs from their carrying value, is influenced by interest rates, the price of the Company’s Class A Common Stock and the volatility thereof, and the prices for the respective convertible senior notes observed in market trading, which are Level 2 inputs. The estimated fair value of the 2022 Convertible Notes as of December 31, 2019 and 2018 was approximately $141.3 million and approximately $315.0 million, respectively. The estimated fair value of the 2024 Convertible Notes was approximately $235.7 million as of December 31, 2019. The estimated fair value of the 2026 Convertible Notes was approximately $240.1 million as of December 31, 2019. Capped Calls ​ In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into the Capped Calls with certain financial institutions. The Capped Calls cover 29,867,480 shares of Class A Common Stock (subject to anti-dilution and certain other adjustments), which is the same number of shares of Class A Common Stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes. The Capped Calls have an initial strike price of approximately $13.39 per share, which corresponds to the initial conversion price of the 2024 Convertible Notes and the 2026 Convertible Notes, and have a cap price of approximately $17.05 per share (Note 12). The strike price and cap price are subject to anti-dilution adjustments generally similar to those applicable to the 2024 Convertible Notes and the 2026 Convertible Notes. These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met (Note 12). ​ 8.375% Notes Due 2026 In September 2016, the Company closed a direct private placement pursuant to which the Company issued $150.0 million in aggregate principal amount of the 2026 Notes in January 2017. The outstanding principal balance of the 2026 Notes was redeemed in September 2019 (Note 12). The estimated fair value of the 2026 Notes was approximately $148.2 million as of December 31, 2018. This valuation was calculated using a discounted cash flow estimate of expected interest and principal payments and was determined using Level 3 inputs, including significant estimates related to expected LINZESS sales and a discount rate equivalent to market participant interest rates. Nonrecurring fair value measurements – Intangible Assets On August 2, 2018, the Company delivered to AstraZeneca a notice of termination of the lesinurad license agreement. During the three months ended September 30, 2018, the Company recorded an approximately $151.8 million impairment charge related to its acquired intangible assets. The impairment assessment performed utilized the revised projected revenue and net cash flows assumed through the termination of the lesinurad license agreement, resulting in an impairment of the full carrying value of the intangible assets (Note 5).

Inventory

Inventory	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Inventory	​ 8. Inventory Inventory consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ 2019 2018 ​ Raw Materials ​ $ 65 ​ $ — ​ Work in Progress ​ ​ 392 ​ ​ — ​ Finished Goods ​ $ 191 ​ $ — ​ ​ ​ $ 648 ​ $ — ​ ​ The Company’s inventory represents linaclotide API, finished drug product, and finished goods. The Company evaluates inventory levels at each quarterly reporting date and any inventory that has a cost basis in excess of its expected net realizable value, inventory that becomes obsolete, inventory in excess of expected sales requirements, inventory that fails to meet commercial sale specifications or is otherwise impaired is written down with a corresponding charge to the statement of operations in the period that the impairment is first identified. No impairment of linaclotide API inventory was recorded during the years ended December 31, 2019 or 2018. The Company has entered into multiple commercial supply agreements for the purchase of linaclotide API. Two of the Company’s linaclotide API supply agreements for supplying API to its collaboration and license partners outside of North America historically contained minimum purchase commitments. The determination of the net realizable value of inventory and non-cancelable purchase commitments is based on demand forecasts from the Company’s partners, which are received quarterly, and the Company’s internal forecast for projected demand in subsequent years. During the year ended December 31, 2015, the Company wrote down approximately $10.1 million related to excess non-cancelable purchase commitments for linaclotide API. During the three months ended September 30, 2018, the Company assigned to Allergan certain of these linaclotide excess non-cancelable purchase commitments that the Company had previously accrued for. Accordingly, the Company relieved the previous accrual of approximately $2.5 million, which was recorded as write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancelable purchase commitments on the Company’s consolidated statement of operations. As of December 31, 2018, the accrual for excess linaclotide purchase commitments was recorded as approximately $2.5 million in accrued expenses and approximately $2.5 million in other liabilities, in the Company's consolidated balance sheet. In connection with the Amended AstraZeneca Agreement, certain of the Company’s previously written-down linaclotide excess purchase commitments were assumed by AstraZeneca and resulted in a settlement of approximately $2.5 million. Additionally, certain previously written-down linaclotide purchase commitments were satisfied through API purchases at pricing terms favorable to the pricing estimates at the time of the write-down, resulting in a gain of approximately $0.7 million upon purchase. Accordingly, the Company recorded a settlement of approximately $3.5 million as write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancelable purchase commitments related to certain of the aforementioned reversals during the year ended December 31, 2019. As of December 31, 2019, the Company had no remaining accruals for excess purchase commitments on its consolidated balance sheet. The Company relied exclusively on AstraZeneca for the commercial manufacture and supply of ZURAMPIC and DUZALLO under the Lesinurad Commercial Supply Agreement (the “Lesinurad CSA”) through the termination of the lesinurad license agreement. As part of the Company's net realizable value assessment of its inventory, the Company assesses whether it has any excess non-cancelable purchase commitments resulting from its minimum supply agreements with its suppliers. During the lesinurad transition service agreement (“Lesinurad TSA”) period, title for ZURAMPIC commercial supply and samples did not pass to the Company. Accordingly, the Company recorded purchases of ZURAMPIC commercial supply and samples from AstraZeneca as prepaid assets until they were sold or used. Purchases of DUZALLO commercial supply and samples were not within the scope of the Lesinurad TSA. As of October 1, 2017, in connection with the expiration of the Lesinurad TSA period, the Company was no longer operating under this agreement for the warehousing and distribution of commercial supply and samples of ZURAMPIC. During the year ended December 31, 2017, the Company wrote down approximately $0.3 million of lesinurad commercial supply purchase commitments as a result of revised demand forecasts and recorded in write-downs of commercial supply and inventory to net realizable value and (settlement) loss on non-cancelable inventory purchase commitments in the Company's consolidated statement of operations. Further, during the year ended December 31, 2017, the Company wrote-down approximately $1.7 million of ZURAMPIC sample supply purchase commitments as a result of a reduction in near-term forecasted demand. These write-downs were recorded in selling, general and administrative expenses in the Company's consolidated statement of operations. The Company wrote down approximately $2.5 million related to lesinurad inventory and commercial supply purchase commitments during the year ended December 31, 2018, as a result of revised demand forecasts and the notice of termination of the Lesinurad License. The adjustment was recorded as write-down of commercial supply and inventory to net realizable value and loss on non-cancelable purchase commitments. Further, during the year ended December 31, 2018, the Company wrote-down approximately $0.4 million of DUZALLO sample supply purchase commitments as a result of the notice of termination of the lesinurad license agreement. These write-downs were recorded in selling, general and administrative expenses in the Company's consolidated statement of operations.

Leases

Leases	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Leases	9. Leases Effective January 1, 2019, the Company adopted ASC 842 using the optional transition method. The Company’s lease portfolio for the year ended December 31, 2019 includes: leases for its prior and current headquarters locations, a data center colocation lease, vehicle leases for its salesforce representatives, and leases for computer and office equipment. ​ Lease cost is recognized on a straight-line basis over the lease term. The components of lease cost for the year ended December 31, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ Year Ended ​ ​ December 31, ​ ​ 2019 Operating lease cost during period, net (1) ​ $ 16,452 Variable lease payments ​ ​ 1,526 Short-term lease cost ​ ​ 1,512 Total lease cost ​ $ 19,490 ​ (1) Operating lease cost is presented net of approximately $0.3 million of sublease income for the year ended December 31, 2019. Sublease income related to a sublease agreement between Ironwood and Cyclerion executed upon Separation. The sublease agreement terminated in May 2019. ​ Supplemental cash flow information related to leases for the periods reported is as follows: ​ ​ ​ ​ ​ ​ ​ ​ Year Ended ​ ​ December 31, ​ ​ 2019 Right-of-use assets obtained in exchange for new operating lease upon adoption of ASC 842 (in thousands) ​ $ 88,299 ​ Adjustment to right-of-use assets as a result of the lease modification at the Separation date (in thousands) ​ ​ (40,427) ​ Adjustment to right-of-use assets as a result of the termination of the Binney Street Lease (in thousands) ​ ​ (34,440) ​ Right-of-use assets obtained in exchange for new operating lease liabilities (1) ​ ​ 18,452 ​ Cash paid for amounts included in the measurement of lease liabilities (in thousands) ​ ​ 18,598 ​ Weighted-average remaining lease term of operating leases (in years) ​ ​ 10.2 ​ Weighted-average discount rate of operating leases ​ ​ 5.8 % (1) Relates to right-of-use assets and operating lease liabilities for the Summer Street Lease. ​ Future minimum lease payments under non-cancelable operating leases under ASC 842 as of December 31, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ Operating ​ Lease ​ ​ Payments 2020 ​ $ 1,146 2021 ​ ​ 3,128 2022 ​ ​ 3,129 2023 ​ ​ 3,065 2024 ​ 3,126 2025 and thereafter ​ 18,044 Total future minimum lease payments ​ ​ 31,638 Less: present value adjustment ​ ​ 8,410 Operating lease liabilities at December 31, 2019 ​ ​ 23,228 Less: current portion of operating lease liabilities ​ ​ 1,146 Operating lease liabilities, net of current portion ​ $ 22,082 ​ At December 31, 2018, future minimum lease payments under non-cancelable leases under ASC 840 were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ Operating ​ Lease ​ ​ Payments 2019 ​ $ 18,736 2020 ​ ​ 18,312 2021 ​ ​ 18,863 2022 ​ ​ 19,365 2023 ​ ​ 19,818 2024 and thereafter ​ 22,118 Total future minimum lease payments ​ $ 117,212 ​ Summer Street Lease (current headquarters) ​ On June 11, 2019, the Company entered into the Summer Street Lease, a non-cancelable operating lease with MA-100 Summer Street Owner, L.L.C. (the “Summer Street Landlord”) for the Summer Street Property. The Summer Street Property began serving as the Company’s headquarters in October 2019, replacing its prior headquarters at 301 Binney Street in Cambridge, Massachusetts. The Summer Street Lease terminates on June 11, 2030 and includes an option to extend the term of the lease for an additional five years at a market base rental rate, a 2% annual rent escalation, free rent periods, and a tenant improvement allowance. The rent expense for the Summer Street Property, inclusive of the escalating rent payments and lease incentives, is recognized on a straight-line basis over the lease term. Additionally, the Summer Street Lease requires a letter of credit to secure the Company’s obligations under the lease agreement of approximately $1.0 million, which is collateralized by a money market account recorded as restricted cash on the Company’s consolidated balance sheet as of December 31, 2019. ​ At lease inception, the Company recorded a right-of-use asset and a lease liability associated with the Summer Street Lease using an incremental borrowing rate of approximately 5.8%. At December 31, 2019, the balances of the right-of-use asset and operating lease liability were approximately $17.7 million and approximately $22.8 million, respectively. ​ The Company recorded an asset retirement obligation in connection with the estimated future costs related to the removal of certain leasehold improvements at the Summer Street Property upon termination of the lease. The balance of the Company’s asset retirement obligation for the Summer Street Lease was approximately $0.5 million as of December 31, 2019. ​ Lease cost related to the Summer Street Lease recorded during the year ended December 31, 2019 was approximately $1.5 million. ​ Binney Street Lease (prior headquarters) ​ The Company rented office space at 301 Binney Street, Cambridge, Massachusetts (“Binney Street Property”) under a non-cancelable operating lease, entered into in January 2007, as amended (“Binney Street Lease”) through October 2019. The Binney Street Property previously served as the Company’s headquarters and was replaced by the Summer Street Property in October 2019, as discussed above. ​ Prior to the modifications discussed below, the term of the Binney Street Lease was through January 31, 2025 for approximately 223,000 square feet of laboratory and office space. The Binney Street Lease included an option to extend the term of the lease for an additional five years at a market base rental rate, a 3% annual rent escalation, free rent periods, and a tenant improvement allowance. The rent expense for the Binney Street Lease, inclusive of the escalating rent payments and lease incentives, was to be recognized on a straight-line basis over the lease term through January 2025. Additionally, the Binney Street Lease required a letter of credit to secure the Company’s obligations under the lease agreement of approximately $6.4 million, which was collateralized by a certificate of deposit recorded as restricted cash and released during the year ended December 31, 2019. ​ As of January 1, 2019, in conjunction with the adoption of ASC 842, the Company recorded a right-of-use asset of approximately $87.7 million and a lease liability of approximately $94.3 million associated with the Binney Street Lease. ​ On April 1, 2019, the Company modified its lease with BMR-Rogers Street LLC (“Binney Street Landlord”), to reduce its leased premises to approximately 108,000 rentable square feet of office space on the first and third floors. The surrendered portion of approximately 114,000 rentable square feet on the first and second floor of the building became occupied by Cyclerion under a direct lease between Cyclerion and the Binney Street Landlord. As a result of the modification, the Company adjusted the value of its right-of-use asset and operating lease liability using an incremental borrowing rate of approximately 5.1%, and recognized a gain of approximately $3.2 million, recorded as operating expenses on its consolidated statement of operations. The Company elected to determine the proportionate reduction in the right-of-use asset based on the reduction to the lease liability and will apply that methodology consistently to all comparable modifications that decrease the scope of the lease. ​ On June 11, 2019, the Company entered into a lease termination agreement (the “Lease Termination”) with the Binney Street Landlord to terminate the Company’s existing lease for approximately 108,000 square feet of office space. The Lease Termination was effective during the fourth quarter of 2019 in exchange for an approximately $9.0 million payment to the Binney Street Landlord. The Company determined that the Lease Termination would be accounted for as a lease modification that reduces the term of the existing lease. As a result of this modification, the Company adjusted the value of its right-of-use asset and operating lease liability using an incremental borrowing rate of approximately 4.0%. ​ Lease cost related to the Binney Street Lease recorded during the year ended December 31, 2019 was approximately $16.3 million, net of sublease income of approximately $0.3 million. Under ASC 840, rent expense related to the Binney Street Lease recorded during the years ended December 31, 2018 and 2017 was approximately $10.0 million and approximately $7.6 million, respectively. ​ Data center colocation lease ​ The Company rents space for its data center at a colocation in Boston, Massachusetts under a non-cancelable operating lease (the “Data Center Lease”). The Data Center Lease contains various provisions, including a 4% annual rent escalation. The rent expense, inclusive of the escalating rent payments, is recognized on a straight-line basis over the lease term through August 2022. The Company recorded a right-of-use asset of approximately $0.6 million and a lease liability of approximately $0.6 million associated with the Data Center Lease upon adoption of ASC 842. The incremental borrowing rate for the outstanding Data Center Lease obligation upon adoption of ASC 842 was approximately 6.0%. During the three months ended March 31, 2019, the Company migrated its data management process to a cloud-based services system, rendering its current data center technology and assets obsolete. As a result, the Company considered the right-of-use asset associated with the Data Center Lease to be impaired. The Company recorded a charge of approximately $0.5 million to selling, general, and administrative expenses on its consolidated statement of operations as a result of the impairment during the three months ended March 31, 2019. ​ At December 31, 2019, the lease liability associated with the Data Center Lease was approximately $0.4 million, and the right-of-use asset remained fully impaired . ​ Lease costs related to the Data Center Lease was approximately $0.2 million for the year ended December 31, 2019. Under ASC 840, rent expenses related to the Data Center Lease were approximately $0.2 million and an insignificant amount for the years ended December 31, 2018 and 2017, respectively. ​ Vehicle fleet leases ​ During April 2018, the Company entered into a master services agreement containing 12-month leases (the “2018 Vehicle Leases”) for certain vehicles within its fleet for its field-based sales force and medical science liaisons. These leases are classified as short-term in accordance with the practical expedient in ASC 842. The 2018 Vehicle Leases expire at varying times beginning in June 2019, with a monthly renewal provision. In accordance with the terms of the 2018 Vehicle Leases, the Company maintains a letter of credit securing its obligation under the lease agreements of $1.3 million, which is collateralized by a money market account recorded as restricted cash on the Company’s consolidated balance sheets. ​ Lease cost related to the 2018 Vehicle Leases was approximately $1.5 million for the year ended December 31, 2019. Under ASC 840, lease cost related to the 2018 Vehicle Leases was approximately $0.8 million for the year ended December 31, 2018. ​ Prior to the adoption of ASC 842, during 2018, the Company had certain ongoing vehicle leases for its field-based sales force and medical science liaisons (the “2015 Vehicle Leases”). These leases were classified as capital leases under ASC 840. The 2015 Vehicle Leases expired at varying times through December 2018. In connection with entering into the 2018 Vehicle Leases, all of the 2015 Vehicle Leases were terminated through December 31, 2018. At December 31, 2018, the Company had no remaining capital lease obligations related to the 2015 Vehicle Leases. ​ Other leases ​ Prior to the adoption of ASC 842, the Company entered into leases for certain computer and office equipment certain of which expired in 2018. These leases were classified as capital leases under ASC 840. At December 31, 2018, the Company had approximately $0.2 million in capital lease obligations. At December 31, 2018, the weighted average interest rate on the outstanding capital lease obligations was approximately

Property and Equipment

Property and Equipment	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Property and Equipment	10. Property and Equipment Property and equipment, net consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 2019 2018 Software ​ $ 9,568 ​ $ 10,976 ​ Leasehold improvements ​ 7,318 ​ 12,472 ​ Laboratory equipment ​ 2,193 ​ 1,597 ​ Furniture and fixtures ​ 1,508 ​ 1,845 ​ Computer and office equipment ​ 1,293 ​ 2,737 ​ Construction in process ​ 631 ​ 115 ​ Manufacturing equipment ​ ​ — ​ ​ 3,748 ​ ​ ​ 22,511 ​ 33,490 ​ Less accumulated depreciation and amortization ​ (10,082) ​ (25,838) ​ ​ ​ $ 12,429 ​ $ 7,652 ​ ​ As of December 31, 2018, certain of the Company’s manufacturing equipment was located in the United Kingdom at one of the Company’s contract manufacturers. During the year ended December 31, 2019, the Company ceased use of its manufacturing equipment that was previously located in the United Kingdom at one of its contract manufacturers in connection with the restructuring of certain of its agreements with its partners outside of the U.S. As of December 31, 2018, the Company had approximately $0.2 million of assets under capital leases and recorded an insignificant amount of accumulated amortization. Depreciation expense of property and equipment for the year ended December 31, 2019 was approximately $5.6 million. Depreciation and amortization expense of property and equipment, including amounts recorded under capital leases under ASC 840, was approximately $3.9 million, and approximately $6.4 million for the years ended December 31, 2018 and 2017, respectively.

Accrued Expenses and Other Curr

Accrued Expenses and Other Current Liabilities	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Accrued Expenses and Other Current Liabilities	11. Accrued Expenses and Other Current Liabilities Accrued expenses and other current liabilities consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 2019 2018 Salaries ​ $ 2,973 ​ $ 3,054 ​ Accrued vacation ​ ​ 2,540 ​ ​ 3,493 ​ Accrued incentive compensation ​ ​ 11,760 ​ ​ 13,867 ​ Other employee benefits ​ ​ 1,260 ​ ​ 1,883 ​ Professional fees ​ 1,421 ​ 1,735 ​ Accrued interest ​ 301 ​ 873 ​ Restructuring liabilities ​ ​ 179 ​ ​ 2,885 ​ Other ​ 10,031 ​ 10,211 ​ ​ ​ $ 30,465 ​ $ 38,001 ​ ​ As of December 31, 2019, other accrued expenses of approximately $10.0 million included approximately $4.1 million related to API batches yet to be invoiced, approximately $0.9 million related to activities associated with the Company’s move to the 100 Summer Street headquarters, approximately $0.6 million related to unbilled inventory, and approximately $0.2 million related to equipment for clinical studies. ​ As of December 31, 2018, other accrued expenses of approximately $10.2 million included approximately $2.5 million related to linaclotide excess purchase commitments and, approximately $1.4 million related to excess non-cancelable Lesinurad Products commercial supply and sample purchase commitments.

Notes Payable

Notes Payable	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Notes Payable	12. Notes Payable 8.375% Notes due 2026 ​ On September 23, 2016, the Company closed a direct private placement, pursuant to which the Company issued $150.0 million in aggregate principal amount of the 2026 Notes on January 5, 2017 (the “Funding Date”). The Company received net proceeds of approximately $11.2 million from the 2026 Notes, which were used to redeem the outstanding principal balance of the 11% PhaRMA Notes due 2024 (the “PhaRMA Notes”) on the Funding Date. The Company capitalized approximately $0.5 million of debt issuance costs, which were netted against the carrying value of the 2026 Notes. Proceeds from the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes were used, in part, to redeem the outstanding principal balance of the 2026 Notes in September 2019. The Company retired the 2026 Notes, which had an outstanding aggregate principal balance of approximately $116.5 million, for a redemption price of approximately $123.0 million. The redemption of the 2026 Notes resulted in a loss on extinguishment of debt of approximately $7.6 million related to the prepayment premium and write-off of the unamortized debt issuance costs and unamortized debt discount. ​ The 2026 Notes had an annual interest rate of 8.375%, with interest payable March 15, June 15, September 15 and December 15 of each year (each an “8.375% Payment Date”), which began June 15, 2017. Principal of the 2026 Notes was payable on the 8.375% Payment Dates beginning March 15, 2019 through the redemption of the 2026 Notes. From March 15, 2019, the Company made quarterly payments on the 2026 Notes equal to the greater of (i) 7.5% of net sales of linaclotide in the U.S. for the preceding quarter (the “8.375% Synthetic Royalty Amount”) and (ii) accrued and unpaid interest on the 2026 Notes (the “8.375% Required Interest Amount”). Principal on the 2026 Notes was due to be repaid in an amount equal to the 8.375% Synthetic Royalty Amount minus the 8.375% Required Interest Amount, when this was a positive number, until the principal had been paid in full. ​ Convertible Senior Notes 2.25% Convertible Senior Notes due 2022 In June 2015, the Company issued approximately $335.7 million aggregate principal amount of the 2022 Convertible Notes. The Company received net proceeds of approximately $324.0 million from the sale of the 2022 Convertible Notes, after deducting fees and expenses of approximately $11.7 million. The Company used approximately $21.1 million of the net proceeds from the sale of the 2022 Convertible Notes to pay the net cost of the Convertible Note Hedges (after such cost was partially offset by the proceeds to the Company from the sale of the Note Hedge Warrants), as described below. The 2022 Convertible Notes are governed by an indenture (the “2022 Indenture”) between the Company and U.S. Bank National Association, as trustee (the “Trustee”). The 2022 Convertible Notes are senior unsecured obligations and bear cash interest at the annual rate of 2.25%, payable on June 15 and December 15 of each year, which began on December 15, 2015. The 2022 Convertible Notes will mature on June 15, 2022, unless earlier converted or repurchased. The Company may settle conversions of the 2022 Convertible Notes through payment or delivery, as the case may be, of cash, shares of Class A Common Stock of the Company or a combination of cash and shares of Class A Common Stock, at the Company’s option (subject to, and in accordance with, the settlement provisions of the 2022 Indenture). The initial conversion rate for the 2022 Convertible Notes was 60.3209 shares of Class A Common Stock (subject to adjustment as provided for in the 2022 Indenture) per $1,000 principal amount of the 2022 Convertible Notes, which was equal to an initial conversion price of approximately $16.58 per share and 20,249,665 shares. In connection with the Separation of the Company’s sGC business, in April 2019, the conversion rate under the 2022 Indenture was adjusted to equal 68.9172 shares of Ironwood Class A Common Stock per $1,000 principal amount of the 2022 Convertible Notes, which is equal to an adjusted conversion price of approximately $14.51 per share and 23,135,435 shares. ​ Holders of the 2022 Convertible Notes may convert their 2022 Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding December 15, 2021 in multiples of $1,000 principal amount, only under the following circumstances: ● during any calendar quarter commencing after the calendar quarter ending on September 30, 2015 (and only during such calendar quarter), if the last reported sale price of the Company’s Class A Common Stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price for the 2022 Convertible Notes on each applicable trading day; ● during the five business day period after any five consecutive trading day period (the “measurement period”) in which the trading price (as defined in the 2022 Indenture) per $1,000 principal amount of the 2022 Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s Class A Common Stock and the conversion rate for the 2022 Convertible Notes on each such trading day; or ● upon the occurrence of specified corporate events described in the 2022 Indenture. On or after December 15, 2021, until the close of business on the second scheduled trading day immediately preceding June 15, 2022, holders may convert their 2022 Convertible Notes, in multiples of $1,000 principal amount, at the option of the holder regardless of the foregoing circumstances. If a make-whole fundamental change, as described in the 2022 Indenture, occurs and a holder elects to convert its 2022 Convertible Notes in connection with such make-whole fundamental change, such holder may be entitled to an increase in the conversion rate as described in the 2022 Indenture. The Company may not redeem the 2022 Convertible Notes prior to the maturity date and no “sinking fund” is provided for by the 2022 Convertible Notes, which means that the Company is not required to periodically redeem or retire the 2022 Convertible Notes. Upon the occurrence of certain fundamental changes involving the Company, holders of the 2022 Convertible Notes may require the Company to repurchase for cash all or part of their 2022 Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2022 Convertible Notes to be repurchased, plus accrued and unpaid interest. The 2022 Indenture does not contain any financial covenants or restrict the Company's ability to repurchase the Company’s securities, pay dividends or make restricted payments in the event of a transaction that substantially increases the Company’s level of indebtedness. The 2022 Indenture provides for customary events of default. In the case of an event of default with respect to the 2022 Convertible Notes arising from specified events of bankruptcy or insolvency, all outstanding 2022 Convertible Notes will become due and payable immediately without further action or notice. If any other event of default with respect to the 2022 Convertible Notes under the 2022 Indenture occurs or is continuing, the Trustee or holders of at least 25% in aggregate principal amount of the then outstanding 2022 Convertible Notes may declare the principal amount of the 2022 Convertible Notes to be immediately due and payable. Notwithstanding the foregoing, the 2022 Indenture provides that, upon the Company's election, and for up to 180 days , the sole remedy for an event of default relating to certain failures by the Company to comply with certain reporting covenants in the 2022 Indenture consists exclusively of the right to receive additional interest on the 2022 Convertible Notes. In accordance with accounting guidance for debt with conversion and other options, the Company separately accounted for the liability and equity components of the 2022 Convertible Notes by allocating the proceeds between the liability component and the embedded conversion option, or equity component, due to the Company's ability to settle the 2022 Convertible Notes in cash, its Class A Common Stock, or a combination of cash and Class A Common Stock at the option of the Company. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The allocation was performed in a manner that reflected the Company's non-convertible debt borrowing rate for similar debt. The equity component of the 2022 Convertible Notes was recognized as a debt discount and represents the difference between the gross proceeds from the issuance of the 2022 Convertible Notes and the fair value of the liability component of the 2022 Convertible Notes on their respective dates of issuance. The excess of the principal amount of the liability component over its carrying amount, or debt discount, is amortized to interest expense using the effective interest method over seven years , or the expected life of the 2022 Convertible Notes. The equity component is not remeasured as long as it continues to meet the conditions for equity classification. ​ In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes in August 2019, the Company repurchased $215.0 million aggregate principal amount of the 2022 Convertible Notes. The 2022 Convertible Notes were repurchased at a premium totaling approximately $227.3 million. The Company recognized a loss on extinguishment of debt of approximately $23.4 million during the year ended December 31, 2019 related to the premium and proportional write-off of the 2022 Convertible Notes unamortized debt issuance costs and unamortized debt discount. Additionally, the repurchase resulted in a reduction to additional paid-in capital of approximately $27.0 million during the year ended December 31, 2019 related to the equity component of the 2022 Convertible Notes. ​ 0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 ​ In August 2019, the Company issued $200.0 million aggregate principal amount of the 2024 Convertible Notes and $200.0 million aggregate principal amount of the 2026 Convertible Notes. The Company received net proceeds of approximately million of the net proceeds from the sale of the 2024 Convertible Notes and 2026 Convertible Notes to pay the cost of the Capped Calls, as described below. For purposes of this section, “Notes” refer to the 2024 Convertible Notes and the 2026 Convertible Notes, collectively. ​ The 2024 Convertible Notes and 2026 Convertible Notes were issued by the Company on August 12, 2019, pursuant to separate Indentures, each dated as of such date (each an “Indenture” and together the “Indentures”), between the Company and the Trustee. The 2024 Convertible Notes will bear cash interest at the annual rate of 0.75% and the 2026 Convertible Notes will bear cash interest at the annual rate of 1.50% , each payable on June 15 and December 15 of each year, which began on December 15, 2019. The 2024 Convertible Notes will mature on June 15, 2024 and the 2026 Convertible Notes will mature on June 15, 2026, unless earlier converted or repurchased. The Company will settle conversions of the 2024 Convertible Notes and 2026 Convertible Notes through payment or delivery, as the case may be, of cash, shares of Class A Common Stock of the Company or a combination of cash and shares of Class A Common Stock, at the Company’s option (subject to, and in accordance with, the settlement provisions of the applicable Indenture). The initial conversion rate for each of the 2024 Convertible Notes and the 2026 Convertible Notes is 74.6687 shares of Class A Common Stock (subject to adjustment as provided for in the applicable Indenture) per $1,000 principal amount of the 2024 Convertible Notes and 2026 Convertible Notes, which is equal to an initial conversion price of approximately $13.39 per share, representing a conversion premium of approximately 37.5% above the last reported sale price of Class A Common Stock of $9.74 per share on August 7, 2019. ​ Holders of the 2024 Convertible Notes and 2026 Convertible Notes may convert their Notes at their option at any time prior to the close of business on the business day immediately preceding December 15, 2023, with respect to the 2024 Convertible Notes, and December 15, 2025, with respect to the 2026 Convertible Notes, in multiples of $1,000 principal amount, only under the following circumstances: ​ ● during any calendar quarter commencing after the calendar quarter ending on December 31, 2019 (and only during such calendar quarter), if the last reported sale price of Class A Common Stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price for the Notes on each applicable trading day; ​ ● during the five business day period after any five consecutive trading day period (the “measurement period”) in which the “trading price” (as defined in each Indenture) per $1,000 principal amount of Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of Class A Common Stock and the conversion rate for the Notes on each such trading day; or ​ ● upon the occurrence of specified corporate events described in each Indenture. ​ On or after December 15, 2023, with respect to the 2024 Convertible Notes, and December 15, 2025, with respect to the 2026 Convertible Notes, until the close of business on the second scheduled trading day immediately preceding the applicable maturity date, the holders of the Notes may convert their Notes, in multiples of $1,000 principal amount, regardless of the foregoing conditions. ​ If the Company experiences a fundamental change, as described in the Indentures, prior to the maturity date of the respective Notes, holders of such Notes will, subject to specified conditions, have the right, at their option, to require the Company to repurchase for cash all or a portion of their Notes at a repurchase price equal to 100% of the principal amount of the Notes to be repurchased, plus accrued and unpaid interest, if any, to, but not including, the fundamental change repurchase date. In addition, following certain corporate events that occur prior to the applicable maturity date of the Notes, the Company will increase the conversion rate for a holder who elects to convert its Notes in connection with such corporate event. ​ The Indentures do not contain any financial covenants or restrict the Company’s ability to repurchase the Company’s securities, pay dividends or make restricted payments in the event of a transaction that substantially increases the Company’s level of indebtedness. The Indentures provide for customary events of default. In the case of an event of default with respect to a series of Notes arising from specified events of bankruptcy or insolvency, all outstanding Notes of such series will become due and payable immediately without further action or notice. If any other event of default with respect to a series of Notes under the relevant Indenture occurs or is continuing, the Trustee or holders of at least 25% in aggregate principal amount of the then outstanding Notes of such series may declare the principal amount of such Notes to be immediately due and payable. ​ In accordance with accounting guidance for debt with conversion and other options, the Company separately accounted for the liability and equity components of the 2024 Convertible Notes and the 2026 Convertible Notes by allocating the proceeds between the liability components and the embedded conversion options, or equity components, due to the Company’s ability to settle the 2024 Convertible Notes and the 2026 Convertible Notes in cash, its Class A Common Stock, or a combination of cash and Class A Common Stock at the option of the Company. The carrying amount of the respective liability components were calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The allocation was performed in a manner that reflected the Company’s non-convertible debt borrowing rate for similar debt. The respective equity components of the 2024 Convertible Notes and the 2026 Convertible Notes were recognized as a debt discount and represent the difference between the gross proceeds from the issuance of the 2024 Convertible Notes and 2026 Convertible Notes and the fair value of the liability of the 2024 Convertible Notes and 2026 Convertible Notes on their respective dates of issuance. The excess of the principal amount of the liability component over its carrying amount, or debt discount, is amortized to interest expense using the effective interest method over approximately five and seven years , or the expected life of the 2024 Convertible Notes and the 2026 Convertible Notes, respectively. The respective equity components are not remeasured as long as they continue to meet the conditions for equity classification. ​ The Company’s outstanding balances for the convertible senior notes as of December 31, 2019 and 2018 consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ ​ 2019 ​ 2018 ​ Liability component: ​ ​ ​ ​ ​ ​ Principal: ​ ​ ​ ​ ​ 2022 Convertible Notes ​ $ 120,699 ​ $ 335,699 ​ 2024 Convertible Notes ​ ​ 200,000 ​ ​ — ​ 2026 Convertible Notes ​ ​ 200,000 ​ ​ — ​ Less: unamortized debt discount ​ ​ (104,700) ​ ​ (65,094) ​ Less: unamortized debt issuance costs ​ ​ (8,005) ​ ​ (5,004) ​ Net carrying amount ​ $ 407,994 ​ $ 265,601 ​ Equity component: ​ ​ ​ ​ ​ ​ ​ 2022 Convertible Notes ​ ​ 19,807 ​ ​ 114,199 ​ 2024 Convertible Notes ​ ​ 41,152 ​ ​ — ​ 2026 Convertible Notes ​ ​ 51,350 ​ ​ — ​ Total equity component ​ $ 112,309 ​ $ 114,199 ​ ​ In connection with the issuance of the 2022 Convertible Notes, the Company incurred approximately $11.7 million of debt issuance costs, which primarily consisted of initial purchasers’ discounts and legal and other professional fees. The Company allocated these costs to the liability and equity components based on the allocation of the proceeds. The portion of these costs allocated to the equity components totaling approximately $4.0 million were recorded as a reduction to additional paid-in capital upon issuance. The portion of these costs allocated to the liability components totaling approximately $7.7 million were recorded as a reduction in the carrying value of the debt on the consolidated balance sheet and are amortized to interest expense using the effective interest method over the expected life of the 2022 Convertible Notes. In connection with the partial repurchase of the 2022 Convertible Notes, the Company recorded a loss on extinguishment of debt of approximately $23.4 million, of which approximately $2.8 million related to the initial debt issuance costs, during the year ended December 31, 2019. The Company determined the expected life of the 2022 Convertible Notes was equal to their seven-year term. The effective interest rate on the liability components of the 2022 Convertible Notes for the period from the date of issuance through June 30, 2019 was 9.34% . From the date of the partial repurchase of the 2022 Convertible Notes in August 2019 through December 31, 2019, the effective interest rate on the liability component of the 2022 Convertible Notes was 7.50% . In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company incurred approximately $9.0 million of debt issuance costs, which primarily consisted of initial purchaser’s discounts and legal and other professional fees. The Company allocated these costs to the liability and equity components based on the allocation of the proceeds. The portion of these costs allocated to the equity components totaling approximately $2.1 million were recorded as a reduction to additional paid-in capital. The portion of these costs allocated to the liability components totaling approximately $6.9 million were recorded as a reduction in the carrying value of the debt on the consolidated balance sheet and are amortized to interest expense using the effective interest method over the expected life of the 2024 Convertible Notes and the 2026 Convertible Notes. ​ The Company determined the expected life of the 2024 Convertible Notes and the 2026 Convertible Notes was equal to their approximately five and seven-year terms, respectively. The effective interest rates on the liability components of the 2024 Convertible Notes and the 2026 Convertible Notes for the period from the date of issuance through December 31, 2019 was 4.73% .and 4.69% , respectively. ​ The following table sets forth total interest expense recognized related to convertible senior notes during the years ended December 31, 2019, 2018, and 2017, (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended ​ ​ December 31, ​ 2019 2018 ​ 2017 Contractual interest expense ​ $ 7,361 ​ $ 7,553 ​ $ 7,553 Amortization of debt issuance costs ​ ​ 1,190 ​ ​ 971 ​ ​ 806 Amortization of debt discount ​ ​ 17,683 ​ ​ 15,437 ​ ​ 14,145 Total interest expense ​ $ 26,234 ​ $ 23,961 ​ $ 22,504 ​ Future minimum payments under the convertible senior notes as of December 31, 2019, are as follows (in thousands): ​ ​ ​ ​ ​ 2020 ​ $ 7,216 2021 ​ ​ 7,216 2022 ​ ​ 126,556 2023 ​ ​ 4,500 2024 ​ ​ 203,750 2025 and Thereafter ​ ​ 204,500 Total future minimum payments under the convertible senior notes ​ 553,738 Less: amounts representing interest ​ ​ (33,039) Less: unamortized debt discount ​ ​ (104,700) Less: unamortized debt issuance costs ​ ​ (8,005) Convertible senior notes balance ​ $ 407,994 ​ Convertible Note Hedge and Note Hedge Warrant Transactions with Respect to 2022 Convertible Notes To minimize the impact of potential dilution to the Company's Class A common stockholders upon conversion of the 2022 Convertible Notes, the Company entered into the Convertible Note Hedges covering 20,249,665 shares of the Company’s Class A Common Stock in connection with the issuance of the 2022 Convertible Notes. The Convertible Note Hedges had an initial exercise price of $16.58 per share, subject to adjustment upon the occurrence of certain corporate events or transactions, and are exercisable if the 2022 Convertible Notes are converted. In connection with the adjustment to the conversion rate of the 2022 Convertible Notes related to the Separation in April 2019, the exercise price of the Convertible Note Hedges was adjusted to $14.51 per share and the number of shares underlying the Convertible Note Hedges was increased to 23,135,435 shares. If upon conversion of the 2022 Convertible Notes, the price of the Company’s Class A Common Stock is above the exercise price of the Convertible Note Hedges, the counterparties are obligated to deliver shares of the Company’s Class A Common Stock and/or cash with an aggregate value approximately equal to the difference between the price of the Company's Class A Common Stock at the conversion date and the exercise price, multiplied by the number of shares of the Company’s Class A Common Stock related to the Convertible Note Hedge being exercised. Concurrently with entering into the Convertible Note Hedges, the Company sold Note Hedge Warrants to the Convertible Note Hedge counterparties to acquire 20,249,665 shares of the Company’s Class A Common Stock, subject to customary anti-dilution adjustments. The strike price of the Note Hedge Warrants was initially $21.50 per share, subject to adjustment, and such warrants are exercisable over the 150 trading day period beginning on September 15, 2022. In connection with the Separation in April 2019, the exercise price was adjusted to $18.82 per share and the number of shares underlying the Note Hedge Warrants was increased to 23,135,435 shares. The Note Hedge Warrants could have a dilutive effect on the Class A Common Stock to the extent that the market price per share of the Company's Class A Common Stock exceeds the applicable strike price of such warrants. The Convertible Note Hedges and the Note Hedge Warrants are separate transactions entered into by the Company and are not part of the terms of the 2022 Convertible Notes. Holders of the 2022 Convertible Notes and the Note Hedge Warrants do not have any rights with respect to the Convertible Note Hedges. The Company paid approximately $91.9 million for the Convertible Note Hedges and recorded this amount as a long-term asset on its consolidated balance sheet. The Company received approximately $70.8 million for the Note Hedge Warrants and recorded this amount as a long-term liability, resulting in a net cost to the Company of approximately $21.1 million. In August 2019, concurrently with the repurchase of $215.0 million aggregate principal amount of the 2022 Convertible Notes, the Company terminated the respective portion of the Convertible Note Hedges and Note Hedge Warrants. The Company received approximately $3.2 million related to net termination payments from the counterparties of the Convertible Note Hedges and Note Hedge Warrants. During the year ended December 31, 2019, the Company recorded approximately $3.0 million in gain on derivatives as a result of the partial termination of the Convertible Note Hedges and Note Hedge Warrants and change in fair value during the period. ​ The Convertible Note Hedges and Note Hedge Warrants are accounted for as derivative assets and liabilities, respectively, in accordance with ASC 815. Capped Calls with Respect to 2024 Convertible Notes and 2026 Convertible Notes ​ To minimize the impact of potential dilution to the Company’s Class A common stockholders upon conversion of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into separate Capped Calls in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes. The Company paid the counterparties approximately $25.2 million to enter into the Capped Calls. ​ The Capped Calls have an initial strike price of approximately $13.39 per share, which corresponds to the initial conversion price of the 2024 Convertible Notes and the 2026 Convertible Notes and is subject to anti-dilution adjustments generally similar to those applicable to the 2024 Convertible Notes and the 2026 Convertible Notes. The Capped Calls have a cap price of approximately $17.05 per share, representing an approximately 75% premium over the last reported sale price of the Class A Common Stock as of August 7, 2019, which cap price is subject to certain adjustments under the terms of the Capped Calls. The Capped Calls cover 29,867,480 shares of Class A Common Stock (subject to anti-dilution and certain other adjustments), which is the same number of shares of Class A Common Stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes. ​ The Capped Calls are expected generally to reduce the potential dilution to the Class A Common Stock upon conversion of the 2024 Convertible Notes and the 2026 Convertible Notes in the event that the market price per share of Class A Common Stock, as measured under the terms of the Capped Calls, is greater than the strike price of the Capped Calls as adjusted pursuant to the anti-dilution adjustments. If, however, the market price per share of Class A Common Stock, as measured under the terms of the Capped Calls, exceeds the cap price of the Capped Calls, there would nevertheless be dilution upon conversion of the 2024 Convertible Notes and the 2026 Convertible Notes to the extent that such market price exceeds the cap price of the Capped Calls. ​ The Capped Calls are separate transactions entered into by and between the Company and the Capped Calls counterparties and are not part of the terms of the 2024 Convertible Notes or the 2026 Convertible Notes. Holders of the 2024 Convertible Notes and the 2026 Convertible Notes do not have any rights with respect to the Capped Calls. These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met. The Company recorded a reduction to additional paid-in capital of approximately $25.0 million during the year ended December 31, 2019 related to the premium payments for the Capped Calls. Additionally, the Company recorded an approximately $0.2 million reduction to equity related to transaction costs incurred in connection with the Capped Calls during the year ended December 31, 2019. ​

Commitments and Contingencies

Commitments and Contingencies	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Commitments and Contingencies	13. Commitments and Contingencies Commercial Supply Commitments The Company has multiple supply agreements for the purchase of linaclotide finished drug product and API. Two of the Company’s API supply agreements for supplying API to its collaboration partners outside of North America have historically contained minimum purchase commitments. During the year ended December 31, 2019, the Company amended its API supply agreements to transfer its minimum purchase commitments to its partners outside of North America beginning in 2020. Under its remaining agreements, the Company had no minimum purchase commitments as of December 31, 2019. In addition, the Company and Allergan are jointly obligated to make minimum purchases of linaclotide API for the territories covered by the Company's collaboration with Allergan for North America. Currently, Allergan fulfills all such minimum purchase commitments. Commitments Related to the Collaboration and License Agreements Under the collaboration agreement with Allergan for North America the Company shares all development and commercialization costs related to linaclotide in the U.S. with Allergan. The actual amounts that the Company pays its partner or that the partner pays to the Company will depend on numerous factors outside of the Company’s control, including the success of certain clinical development efforts with respect to linaclotide, the content and timing of decisions made by the regulators, the reimbursement and competitive landscape around linaclotide and the Company’s other product candidates, and other factors. In addition, the Company has commitments to make potential future milestone payments to third parties under certain of its license and collaboration arrangements. These milestones primarily relate to the initiation and results of clinical trials, obtaining regulatory approval in various jurisdictions and the future commercial success of development programs, the outcome and timing of which are difficult to predict and subject to significant uncertainty. In addition to the milestones discussed above, the Company is obligated to pay royalties on future sales, which are contingent on generating levels of sales of future products that have not been achieved and may never be achieved. These agreements are more fully described in Note 6, Collaboration, License, Co-promotion and Other Commercial Agreements Other Funding Commitments As of December 31, 2019, the Company has several on-going studies in various clinical trial stages. The Company’s most significant clinical trial expenditures are to contract research organizations. These contracts are generally cancellable, with notice, at the Company’s option and do not have any significant cancellation penalties. Guarantees As permitted under Delaware law, the Company indemnifies its directors and certain of its officers for certain events or occurrences while such director or officer is, or was, serving at the Company’s request in such capacity. The maximum potential amount of future payments the Company could be required to make is unlimited; however, the Company has directors’ and officers’ insurance coverage that is intended to limit its exposure and enable it to recover a portion of any future amounts paid. The Company enters into certain agreements with other parties in the ordinary course of business that contain indemnification provisions. These typically include agreements with business partners, contractors, landlords, clinical sites and customers. Under these provisions, the Company generally indemnifies and holds harmless the indemnified party for losses suffered or incurred by the indemnified party as a result of the Company’s activities. These indemnification provisions generally survive termination of the underlying agreements. The maximum potential amount of future payments the Company could be required to make under these indemnification provisions is unlimited. However, to date the Company has not incurred material costs to defend lawsuits or settle claims related to these indemnification provisions. As a result, the estimated fair value of these obligations is minimal. Accordingly, the Company did not have any liabilities recorded for these obligations as of December 31, 2019 and 2018. Litigation From time to time, the Company is involved in various legal proceedings and claims, either asserted or unasserted, which arise in the ordinary course of business. While the outcome of these other claims cannot be predicted with certainty, management does not believe that the outcome of any of these ongoing legal matters, individually and in aggregate, will have a material adverse effect on the Company’s consolidated financial statements. In connection with the settlements the Company entered into in 2018, the Company agreed to pay an aggregate of $4.0 million in avoidance of litigation fees and expenses during the year ended December 31, 2018. For additional information relating to such ANDAs and any resolution of related litigation, see Item 3, Legal Proceedings ​

Stockholders' Equity

Stockholders' Equity	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Stockholders' Equity	14. Stockholders’ Equity Preferred Stock The Company’s preferred stock may be issued from time to time in one or more series, with each such series to consist of such number of shares and to have such terms as adopted by the board of directors. Authority is given to the board of directors to determine and fix such voting powers, full or limited, or no voting powers, and such designations, preferences and relative participating, optional or other special rights, and qualifications, limitation or restrictions thereof, including without limitation, dividend rights, conversion rights, redemption privileges and liquidation preferences. Common Stock Prior to December 31, 2018, the Company had designated two series of common stock, Series A common stock (“Class A Common Stock”) and Series B common stock (“Class B Common Stock”). The holders of Class A Common Stock and Class B Common Stock voted together as a single class. Class A Common Stock is entitled to one vote per share. Class B Common Stock was also entitled to one vote per share with the following exceptions : (1) after the completion of an initial public offering of the Company’s stock, the holders of the Class B Common Stock were entitled to ten votes per share if the matter was an adoption of an agreement of merger or consolidation, an adoption of a resolution with respect to the sale, lease, or exchange of the Company’s assets or an adoption of dissolution or liquidation of the Company, and (2) Class B common stockholders were entitled to ten votes per share on any matter if any individual, entity, or group sought to obtain or had obtained beneficial ownership of 30% or more of the Company’s outstanding shares of common stock. Class B Common Stock could be sold at any time and irrevocably converted to Class A Common Stock, on a one - for-one basis, upon sale or transfer. The Class B Common Stock was also entitled to a separate class vote for the issuance of additional shares of Class B Common Stock (except pursuant to dividends, splits or convertible securities), or any amendment, alteration or repeal of any provision of the Company’s charter. On December 31, 2018, all Class B Common Stock automatically converted into Class A Common Stock. The Company had reserved such number of shares of Class A Common Stock as there were outstanding shares of Class B Common Stock solely for the purpose of effecting the conversion of the Class B Common Stock. Upon conversion, 13,972,688 shares of Class B Common Stock were converted to Class A Common Stock. There are no outstanding shares of Class B Common Stock remaining after the conversion as of December 31, 2018. The Company has reserved, out of its authorized but unissued shares of Class A Common Stock, sufficient shares to effect the conversion of the convertible senior notes and the Note Hedge Warrants pursuant to the terms thereof (Note 12). The Company’s shareholders are entitled to dividends if and when declared by the board of directors.

Employee Stock Benefit Plans

Employee Stock Benefit Plans	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Employee Stock Benefit Plans	15. Employee Stock Benefit Plans The Company has several share-based compensation plans under which stock options, RSAs, RSUs, and other share-based awards are available for grant to employees, officers, directors and consultants of the Company. ​ The following table summarizes share-based compensation expense (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Employee stock options ​ $ 12,526 ​ $ 20,478 ​ $ 19,331 ​ Restricted stock units ​ ​ 15,488 ​ ​ 17,160 ​ ​ 7,646 ​ Restricted stock awards ​ 2,095 ​ 2,330 ​ 2,441 ​ Non-employee stock options ​ — ​ — ​ 301 ​ Employee stock purchase plan ​ 1,115 ​ 1,097 ​ 1,172 ​ Stock award ​ 54 ​ 17 ​ 14 ​ ​ ​ $ 31,278 ​ $ 41,082 ​ $ 30,905 ​ ​ The following table summarizes the expenses reflected in the consolidated statements of operations as follows for the years ended December 31, 2019, 2018 and 2017 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years Ended December 31, ​ 2019 2018 2017 Research and development ​ $ 6,343 ​ $ 11,500 ​ $ 9,853 ​ Selling, general and administrative ​ 24,281 ​ 27,440 ​ 21,052 ​ Restructuring expenses ​ ​ 654 ​ ​ 2,142 ​ ​ — ​ ​ ​ $ 31,278 ​ $ 41,082 ​ $ 30,905 ​ ​ During the three months ended March 31, 2018, the Company reduced its field-based workforce by approximately 60 employees, primarily consisting of field-based sales representatives that promoted DUZALLO or ZURAMPIC in the first position, resulting in modifications to certain share-based payment awards. As a result of the modification, the Company recorded share-based compensation expense of approximately $0.2 million to restructuring expenses during the year ended December 31, 2018. During the three months ended June 30, 2018, the Company initiated a reduction in its headquarter-based workforce by approximately 40 employees associated with the Separation. Certain share-based payment awards were modified in connection with the reduction in workforce. As a result of the modifications, the Company recorded share-based compensation expense of approximately $1.4 million during the year ended December 31, 2018. During the three months ended September 30, 2018, the Company reduced its workforce by approximately 100 employees, primarily consisting of field-based sales representatives, as a result of the termination of the exclusive Lesinurad License. Certain share-based payment awards were modified in connection with the reduction in workforce. As a result of the modifications, the Company recorded share-based compensation expense of approximately $0.6 million to restructuring expenses during the year ended December 31, 2018. In February 2019, following further analysis of the Company’s strategy and core business needs, and in an effort to further strengthen the operational efficiency of the organization, the Company commenced a reduction in workforce by approximately 35 employees, primarily based in the home office. Certain share-based payment awards were modified in connection with the reduction in workforce. As a result of the modifications, the Company recorded share-based compensation expense of approximately $0.7 million to restructuring expenses for the year ended December 31, 2019. ​ In April 2019, in connection with the Separation, all outstanding share-based payment awards were modified in accordance with the equity conversion-related provisions of the employee matters agreement. No share-based compensation expense was recognized in connection with these modifications. Additionally, modifications with respect to the Company’s ESPP were made due to the change in share price as a result of the Separation. As a result of the modification to the ESPP, the Company recorded approximately $0.3 million of share-based compensation expense for the year ended December 31, 2019. ​ In connection with certain other modifications of share-based payment awards for the year ended December 31, 2019, the Company recognized approximately $3.0 million in share-based compensation expense. ​ Stock Benefit Plans As of December 31, 2019, the Company has the following active stock benefit plans pursuant to which awards are currently outstanding: the 2019 Equity Incentive Plan (the “2019 Equity Plan”), the Amended and Restated 2010 Employee Stock Purchase Plan (the “2010 Purchase Plan”), the Amended and Restated 2010 Employee, Director, and Consultant Equity Incentive Plan (the “2010 Equity Plan”), and the Amended and Restated 2005 Stock Incentive Plan (the “2005 Equity Plan”). At December 31, 2019, there were 15,867,625 shares available for future grant under the 2019 Equity Plan and the 2010 Purchase Plan. 2019 Equity Plan During 2019, the Company’s stockholders approved the 2019 Equity Plan under which stock options, RSAs, RSUs, and other stock-based awards may be granted to employees, officers, directors, or consultants of the Company. Under the 2019 Equity Plan, 10,000,000 shares of Class A Common Stock were initially reserved for issuance. Awards that are returned to the 2010 Equity Plan and 2005 Equity Plan as a result of their expiration, cancellation, termination or repurchase are automatically made available for issuance under the 2019 Equity Plan. Awards that expire, cancel, terminate, or are repurchased under the 2019 Equity Plan will no longer be available for future grant. As of December 31, 2019, 10,954,595 shares were available for future grant under the 2019 Equity Plan. 2010 Purchase Plan During 2010, the Company’s stockholders approved the 2010 Purchase Plan, which gives eligible employees the right to purchase shares of common stock at the lower of 85% of the fair market value on the first or last day of an offering period. Each offering period is six months . There were 400,000 shares of common stock initially reserved for issuance pursuant to the 2010 Purchase Plan. The number of shares available for future grant under the 2010 Purchase Plan may be increased on the first day of each fiscal year by an amount equal to the lesser of: (i) 1,000,000 shares, (ii) 1% of the Class A shares of common stock outstanding on the last day of the immediately preceding fiscal year, or (iii) such lesser number of shares as is determined by the board of directors. At December 31, 2019, there were 4,913,030 shares available for future grant under the 2010 Purchase Plan. 2010 Equity Plan & 2005 Equity Plan The 2010 Equity Plan and 2005 Equity Plan provided for the granting of stock options, RSAs, RSUs, and other share-based awards to employees, officers, directors, consultants, or advisors of the Company. At December 31, 2019, there were no shares available for future grant under the 2010 Equity Plan or 2005 Equity Plan. Restricted Stock Awards In 2019, the Company granted an aggregate of 198,523 shares of Class A Common Stock to independent members of the board of directors under restricted stock agreements in accordance with the terms of the 2010 Equity Plan, and either the Company’s director compensation plan, effective in January 2014, or the Company’s non-employee director compensation policy, effective May 2019. These shares of restricted stock vest ratably over the period of service from the Company’s 2019 annual meeting of stockholders through the Company’s 2020 annual meeting of stockholders, provided the individual continues to serve on the Company’s board of directors through each vest date. In 2018, the Company granted an aggregate of 129,784 shares of Class A Common Stock to independent members of the board of directors under restricted stock agreements in accordance with the terms of the 2010 Equity Plan and the Company’s director compensation plan, effective in January 2014. These shares of restricted stock vested ratably over the period of service from the Company’s 2018 annual meeting of stockholders through the Company’s 2019 annual meeting of stockholders, provided the individual continued to serve on the Company’s board of directors through each vesting date. In 2017, the Company granted an aggregate of 134,793 shares of Class A Common Stock to independent members of the board of directors under restricted stock agreements in accordance with the terms of the 2010 Equity Plan and the Company’s director compensation plan, effective in January 2014. These shares of restricted stock vested ratably over the period of service from the Company’s 2017 annual meeting of stockholders through the Company’s 2018 annual meeting of stockholders, provided the individual continued to serve on the Company’s board of directors through each vest date. A summary of restricted stock activity for the year ended December 31, 2019 is presented below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ Average ​ ​ Number of ​ Grant Date ​ ​ Shares ​ Fair Value (1) Unvested as of December 31, 2018 64,896 ​ $ 18.58 ​ Granted 198,523 ​ $ 10.96 ​ Vested (65,547) ​ $ 17.18 ​ Forfeited (16,224) ​ $ 18.58 ​ Unvested as of December 31, 2019 181,648 ​ $ 10.76 ​ (1) Prior period amounts have not been retrospectively adjusted to reflect the effect of the Separation on the Company’s stock price. Restricted Stock Units RSUs granted under the Company’s equity plans represent the right to receive one share of the Company’s Class A Common Stock pursuant to the terms of the applicable award agreement. The RSUs generally vest 25% per year on the approximate anniversary of the date of grant until fully vested, provided the individual remains in continuous service with the Company through each vesting date. Shares of the Company's Class A Common Stock are delivered to the employee upon vesting, subject to payment of applicable withholding taxes. The fair value of all RSUs is based on the market value of the Company's Class A Common Stock on the date of grant. Compensation expense, including the effect of estimated forfeitures, is recognized over the applicable service period. A summary of RSU activity for the year ended December 31, 2019 is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ ​ Average ​ ​ ​ Number ​ Grant Date ​ ​ of Shares Fair Value (1) Unvested as of December 31, 2018 3,057,808 ​ $ 15.53 ​ Granted ​ 3,097,661 ​ ​ 12.11 ​ Vested ​ (1,298,536) ​ ​ 15.38 ​ Forfeited ​ (1,649,844) ​ ​ 13.84 ​ Unvested as of December 31, 2019 3,207,089 ​ $ 12.33 ​ (1) Prior period amounts have not been retrospectively adjusted to reflect the effect of the Separation on the Company’s stock price. Stock Options Stock options granted under the Company’s equity plans generally have a ten-year term and vest over a period of four years , provided the individual continues to serve at the Company through the vesting dates. Options granted under all equity plans are exercisable at a price per share not less than the fair market value of the underlying common stock on the date of grant. The estimated fair value of options, including the effect of estimated forfeitures, is recognized over the requisite service period, which is typically the vesting period of each option. The weighted average assumptions used to estimate the fair value of the stock options using the Black-Scholes option-pricing model were as follows for the years ended December 31, 2019, 2018 and 2017: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended ​ ​ ​ December 31, ​ ​ ​ 2019 ​ 2018 ​ 2017 ​ Expected volatility ​ 46.3 % 43.7 % 45.8 % Expected term (in years) ​ 6.1 ​ 6.0 ​ 6.0 ​ Risk-free interest rate ​ 2.5 % 2.7 % 2.0 % Expected dividend yield ​ — % — % — % ​ Expected volatility is based on the historic volatility of the Company’s Class A Common Stock. The Company estimates the expected term using historical data. The risk-free interest rate used for each grant is based on a zero-coupon U.S. Treasury instrument with a remaining term similar to the expected term of the share-based award. The Company has not paid and does not anticipate paying cash dividends on its shares of common stock in the foreseeable future; therefore, the expected dividend yield is assumed to be zero. The weighted-average grant date fair value per share of options granted during the years ended December 31, 2019, 2018 and 2017 was $6.10, $6.81, and $7.62, respectively. Prior period amounts have not been adjusted to reflect the effect of the Separation on the Company’s stock price. The Company grants to certain employees performance-based options to purchase shares of common stock. These options are subject to performance-based milestone vesting. During the years ended December 31, 2019 and 2018, there were no shares that vested as a result of performance milestone achievements. The Company recorded no share-based compensation expense related to these performance-based options during each of the years ended December 31, 2019, 2018 and 2017. The following table summarizes stock option activity under the Company’s share-based compensation plans, including performance-based options: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Shares of ​ ​ ​ ​ ​ ​ Common ​ Weighted- ​ Weighted- ​ ​ ​ ​ ​ Stock ​ Average ​ Average ​ Aggregate ​ ​ Attributable ​ Exercise ​ Contractual ​ Intrinsic ​ ​ to Options ​ Price (1) ​ Life ​ Value ​ ​ ​ ​ ​ ​ ​ (in years) ​ (in thousands) Outstanding at December 31, 2018 20,457,537 ​ $ 13.47 5.80 ​ $ 4,147 ​ Granted 5,743,167 ​ $ 11.71 ​ — ​ $ — ​ Exercised (1,369,327) ​ $ 8.33 ​ — ​ $ — ​ Cancelled (7,637,138) ​ $ 12.32 ​ — ​ $ — ​ Outstanding at December 31, 2019 17,194,239 ​ $ 12.13 ​ 5.11 ​ $ 25,226 ​ Vested or expected to vest at December 31, 2019 16,729,428 ​ $ 12.13 ​ 5.01 ​ $ 24,590 ​ Exercisable at December 31, 2019 14,030,936 ​ $ 12.07 ​ 4.33 ​ $ 21,423 ​ (1) Prior period amounts have not been retrospectively adjusted to reflect the effect of the Separation on the exercise price of the Company’s stock options. ​ The total intrinsic value of options exercised during the years ended December 31, 2019, 2018 and 2017 was approximately $5.1 million, approximately $20.1 million, and approximately $16.0 million, respectively. The intrinsic value was calculated as the difference between the fair value of the Company’s common stock and the exercise price of the option issued. The following table sets forth the Company's unrecognized share-based compensation expense, net of estimated forfeitures, as of December 31, 2019, by type of award and the weighted-average period over which that expense is expected to be recognized: ​ ​ ​ ​ ​ ​ ​ ​ ​ Unrecognized Weighted-Average ​ ​ Expense, Net ​ Remaining ​ ​ of Estimated ​ Recognition ​ ​ ​ Forfeitures ​ Period ​ ​ (in thousands) ​ (in years) Type of award: ​ ​ ​ ​ ​ ​ Stock options with time-based vesting ​ $ 13,849 2.63 ​ Restricted stock awards ​ ​ 758 0.41 ​ Restricted stock units ​ ​ 24,469 2.45 ​ Stock options with time-based and performance-based vesting (1) ​ ​ 147 — ​ (1) The weighted-average remaining recognition period cannot be determined for performance-based or time-accelerated options due to the nature of such awards, as detailed above. The total unrecognized share-based compensation cost will be adjusted for future changes in estimated forfeitures.

Income Taxes

Income Taxes	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Income Taxes	16. Income Taxes In general, the Company has not recorded a provision for federal or state income taxes as it has had cumulative net operating losses since inception. On December 22, 2017, the Tax Cuts and Jobs Act was enacted. This law substantially amended the Internal Revenue Code, including reducing the U.S. corporate tax rates. Upon enactment, the Company’s deferred tax asset and related valuation allowance decreased by approximately The Company completed its accounting for the tax effects of the Tax Cuts and Job Act as of December 31, 2018 and did not record any material adjustments to its original estimate. A reconciliation of income taxes computed using the U.S. federal statutory rate to that reflected in operations follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Income tax benefit using U.S. federal statutory rate ​ $ 4,517 ​ $ (59,297) ​ $ (39,759) ​ Effect of U.S. tax reform ​ ​ — ​ ​ — ​ ​ 153,894 ​ Permanent differences ​ 65 ​ 218 ​ 34 ​ State income taxes, net of federal benefit ​ (1,902) ​ (17,121) ​ (6,117) ​ Disallowed Separation related costs ​ ​ 4,658 ​ ​ — ​ ​ — ​ Executive compensation - Section 162(m) ​ ​ 662 ​ ​ 8 ​ ​ — ​ Meals and entertainment ​ ​ 495 ​ ​ 995 ​ ​ 1,346 ​ Non-deductible share-based compensation ​ (1,202) ​ (494) ​ 9 ​ Excess tax benefits ​ ​ 3,324 ​ ​ (1,223) ​ ​ (2,626) ​ Fair market valuation of Note Hedge Warrants and Convertible Note Hedges ​ ​ (290) ​ ​ 2,367 ​ ​ 1,289 ​ Tax credits ​ (4,374) ​ (7,863) ​ (12,290) ​ Expiring net operating losses and tax credits ​ 3,764 ​ 250 ​ 276 ​ Effect of change in state tax rate on deferred tax assets and deferred tax liabilities ​ (2,563) ​ 1,476 ​ (232) ​ Change in the valuation allowance ​ (7,154) ​ 80,684 ​ (95,824) ​ ​ ​ $ — ​ $ — ​ $ — ​ ​ Components of the Company’s deferred tax assets and liabilities are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 Deferred tax assets: ​ ​ ​ ​ ​ ​ ​ Net operating loss carryforwards ​ $ 265,494 ​ $ 259,450 ​ Tax credit carryforwards ​ 59,892 ​ 60,115 ​ Capitalized research and development ​ 9,952 ​ 12,113 ​ Contingent consideration ​ ​ — ​ ​ 14 ​ Share-based compensation ​ ​ 24,401 ​ ​ 23,242 ​ Basis difference on North America collaboration agreement ​ ​ 48,594 ​ ​ 36,423 ​ Accruals and reserves ​ ​ 6,415 ​ ​ 10,867 ​ Basis difference on 2022 Convertible Notes ​ ​ 4,322 ​ ​ 7,220 ​ Interest expense ​ ​ 22,020 ​ ​ 5,104 ​ Intangibles ​ ​ — ​ ​ 25,928 ​ Operating lease liability ​ ​ 6,421 ​ ​ — ​ Other ​ 5,295 ​ 18,867 ​ Total deferred tax assets ​ 452,806 ​ 459,343 ​ Deferred tax liabilities: ​ ​ ​ ​ ​ ​ ​ Basis Difference on 2024 Convertible Notes ​ ​ (7,381) ​ ​ — ​ Basis Difference on 2026 Convertible Notes ​ ​ (10,276) ​ ​ — ​ Operating lease right-of-use assets ​ ​ (4,905) ​ ​ — ​ Total deferred tax liabilities ​ ​ (22,562) ​ ​ — ​ Net deferred tax asset ​ ​ 430,244 ​ ​ 459,343 ​ Valuation allowance ​ (430,244) ​ (459,343) ​ Net deferred tax asset ​ $ — ​ $ — ​ ​ Management of the Company has evaluated the positive and negative evidence bearing upon the realizability of its deferred tax assets. Management has considered the Company’s history of operating losses prior to the year ended December 31, 2019 and concluded, in accordance with the applicable accounting standards, that it is more likely than not that the Company will not realize the benefit of its deferred tax assets. Accordingly, the deferred tax assets have been fully reserved at December 31, 2019 and 2018. Management reevaluates the positive and negative evidence on a quarterly basis. The valuation allowance decreased approximately $29.1 million during the year ended December 31, 2019 primarily due to a decrease of the intangible deferred tax asset due to the recognition of a tax loss during the year ended December 31, 2019 related to the termination of the lesinurad license agreement and establishment of a deferred tax liability for a basis difference in the 2024 Convertible Notes and 2026 Convertible Notes, partially offset by an increase in the deferred tax asset for temporarily disallowed interest expense. The valuation allowance increased approximately $80.7 million during the year ended December 31, 2018 primarily due to the 2018 net operating loss and increase in tax credit carryforwards; the establishment of a deferred tax asset for temporarily disallowed interest expense; an increase in the basis difference on the collaboration agreement for North America with Allergan; and an increase in intangible deferred tax assets as a result of the impairment of the lesinurad franchise, partially offset by adjustments to the contingent consideration obligation. Subject to the limitations described below, at each of December 31, 2019 and 2018, the Company had federal net operating loss carryforwards of approximately $1.2 billion to offset future federal taxable income, which expiration began in 2019 and will continue through 2037. The 2019 and 2018 net operating loss of $32.7 million and $89.1 million, respectively, have an indefinite life. As of December 31, 2019 and 2018, the Company had state net operating loss carryforwards of approximately $1.0 billion and approximately $877.1 million, respectively, to offset future state taxable income, which will begin to expire in 2020 and will continue to expire through 2039. The Company also had tax credit carryforwards of approximately $64.6 million and approximately $63.3 million as of December 31, 2019 and 2018, respectively, to offset future federal and state income taxes, which expire at various times through 2039. Utilization of net operating loss carryforwards and research and development credit carryforwards may be subject to a substantial annual limitation due to ownership change limitations that could occur in the future in accordance with Section 382 of the Internal Revenue Code of 1986 (“IRC Section 382”) and with Section 383 of the Internal Revenue Code of 1986, as well as similar state provisions. These ownership changes may limit the amount of net operating loss carryforwards and research and development credit carryforwards that can be utilized annually to offset future taxable income and taxes, respectively. In general, an ownership change, as defined by IRC Section 382, results from transactions increasing the ownership of certain stockholders or public groups in the stock of a corporation by more than 50 percentage points over a three-year period. The Company has completed several financings since its inception which may result in a change in control as defined by IRC Section 382, or could result in a change in control in the future. The following table summarizes the changes in the Company’s unrecognized income tax benefits for the years ended December 31, 2019, 2018 and 2017 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ ​ 2019 ​ 2018 ​ 2017 ​ Balance at the beginning of the period ​ $ 38,551 ​ $ 24,078 ​ $ 26,393 ​ Increases based on tax positions related to the current period ​ ​ 51,699 ​ ​ 38,551 ​ ​ 24,078 ​ Increases for tax positions related to prior periods ​ ​ 1,400 ​ ​ — ​ ​ — ​ Decreases for tax positions in prior periods ​ ​ (38,551) ​ ​ (24,078) ​ ​ (26,393) ​ Balance at the end of the period ​ $ 53,099 ​ $ 38,551 ​ $ 24,078 ​ ​ The Company had gross unrecognized tax benefits of approximately $53.1 million, approximately $38.6 million, and approximately $24.1 million as of December 31, 2019, 2018 and 2017 . total unrecognized tax benefits at December 31, 2019, none of the unrecognized tax positions would, if recognized, affect the Company’s effective tax rate, due to a valuation allowance against deferred tax assets and only impacts the Company’s deferred tax accounting. The Company will recognize interest and penalties, if any, related to uncertain tax positions in income tax expense. As of December 31, 2019, no interest or penalties have been accrued. The statute of limitations for assessment by the Internal Revenue Service (“IRS”) and state tax authorities is open for tax years ended December 31, 2019, 2018, and 2017. There are currently no federal or state income tax audits in progress.

Defined Contribution Plan

Defined Contribution Plan	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Defined Contribution Plan	17. Defined Contribution Plan The Ironwood Pharmaceuticals, Inc. 401(k) Savings Plan is a defined contribution plan in the form of a qualified 401(k) plan in which substantially all employees are eligible to participate upon employment. Subject to certain IRS limits, eligible employees may elect to contribute from 1% to 100% of their compensation. Company contributions to the plan are at the sole discretion of the Company’s board of directors. Currently, the Company provides a matching contribution of 75% of the employee’s contributions, up to $6,000 annually. During the years ended December 31, 2019, 2018 and 2017, the Company recorded approximately $2.2 million, approximately $3.2 million, and approximately $3.5 million of expense related to its 401(k) company match, respectively.

Related Party Transactions

Related Party Transactions	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Related Party Transactions	18. Related Party Transactions Under the collaboration agreement, the Company and Allergan equally support the development and commercialization of linaclotide (Note 6). Amounts due to and due from Allergan are reflected as related party accounts payable and related party accounts receivable, respectively. These balances are reported net of any balances due to or from the related party. As of December 31, 2019 and 2018, the Company had approximately $106.0 million and approximately $60.0 million, respectively, in related party accounts receivable, net of related party accounts payable, associated with Allergan. ​ The Company has and currently obtains health insurance services for its employees from an insurance provider whose President and Chief Executive Officer became a member of the Company’s Board of Directors in April 2016. The Company paid approximately insurance premiums to this insurance provider during the years ended December 31, 2019, 2018, and 2017, respectively. At both December 31, 2019 and 2018, the Company had no accounts payable due to this related party. ​ In connection with the Separation, the Company executed certain contracts with Cyclerion whose President became a member of the Company’s Board of Directors in April 2019 (Note 3). As of December 31, 2019, the Company had an insignificant amount of accounts receivable and approximately $1.5 million of accounts payable due from and to Cyclerion, respectively. ​

Workforce Reduction

Workforce Reduction	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Workforce Reduction	19. Workforce Reduction On January 30, 2018, the Company commenced an initiative to evaluate the optimal mix of investments for the lesinurad franchise. As part of this effort, the Company reduced its field-based workforce by approximately 60 employees, primarily consisting of field-based sales representatives that promoted DUZALLO or ZURAMPIC in the first position. During the three months ended March 31, 2018, the Company substantially completed the implementation of this reduction in field-based workforce and, in accordance with ASC 420, recorded approximately $2.4 million of costs in its consolidated statement of operations as restructuring expenses. ​ On June 27, 2018, the Company determined the initial organizational designs of the two new businesses, including employees’ roles and responsibilities, in connection with the Separation. As part of this process, the Company initiated a reduction in its headquarter-based workforce by approximately 40 employees and substantially completed the reduction in its workforce during the year ended December 31, 2019. During the years ended December 31, 2019 and 2018, the Company recorded an insignificant amount of adjustments and approximately $4.0 million in connection with the reduction in workforce in accordance with ASC 420, respectively. These costs are reflected in the consolidated statement of operations as restructuring expenses. ​ On August 16, 2018, the Company initiated a reduction in its workforce by approximately 100 employees, primarily consisting of field-based sales representatives in connection with the termination of the Lesinurad License and substantially completed the reduction in its workforce and recorded associated costs during the year ended December 31, 2019. During the year ended December 31, 2019, the Company recorded an insignificant amount of adjustments to restructuring costs related to this workforce reduction. During the year ended December 31, 2018, the Company recorded approximately $8.3 million of costs, including approximately $5.4 million of severance, benefits and related costs and approximately $2.9 million of contract-related costs, including the write-down of certain prepaid assets and deposits, in accordance with ASC 420 in connection with the reduction in workforce. These costs are reflected in the consolidated statement of operations as restructuring expenses. ​ On February 7, 2019, following further analysis of the Company’s strategy and core business needs, and in an effort to further strengthen the operational efficiency of the organization, the Company commenced a reduction in workforce by approximately 35 employees, primarily based in the home office. During the year ended December 31, 2019, the Company recorded approximately $3.7 million of costs that are reflected in the consolidated statement of operations as restructuring expenses. ​ The following table summarizes the accrued liabilities activity recorded in connection with the reduction in workforce for the year ended December 31, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ Accrued at ​ ​ ​ ​ ​ ​ ​ ​ ​ Accrued at ​ ​ December 31, 2018 Charges ​ Amount Paid ​ Adjustments ​ December 31, 2019 ​ Employee severance, benefits and related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 2018 Reduction $ 696 ​ $ 16 ​ $ (689) ​ $ (23) ​ $ — ​ August 2018 Reduction ​ 1,756 ​ ​ — ​ ​ (1,708) ​ ​ (48) ​ ​ — ​ February 2019 Reduction ​ — ​ ​ 3,182 ​ ​ (2,968) ​ ​ (139) ​ ​ 75 ​ Total $ 2,452 ​ $ 3,198 ​ $ (5,365) ​ $ (210) ​ $ 75 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contract related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ August 2018 Reduction $ 433 ​ $ — ​ $ (287) ​ $ (42) ​ $ 104 ​ Total $ 433 ​ $ — ​ $ (287) ​ $ (42) ​ $ 104 ​ ​ The following table summarizes the accrued liabilities activity recorded in connection with the reduction in workforce for the year ended December 31, 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ Accrued at ​ ​ ​ ​ ​ ​ ​ ​ ​ Accrued at ​ ​ December 31, 2017 Charges ​ Amount Paid ​ Adjustments ​ December 31, 2018 ​ Employee severance, benefits and related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ January 2018 Reduction $ — ​ $ 2,228 ​ $ (2,215) ​ $ (13) ​ $ — ​ June 2018 Reduction ​ — ​ ​ 2,881 ​ ​ (2,074) ​ ​ (111) ​ ​ 696 ​ August 2018 Reduction ​ — ​ ​ 5,383 ​ ​ (3,522) ​ ​ (105) ​ ​ 1,756 ​ Total $ — ​ $ 10,492 ​ $ (7,811) ​ $ (229) ​ $ 2,452 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contract related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ August 2018 Reduction $ — ​ $ 1,265 ​ $ (614) ​ $ (218) ​ $ 433 ​ Total $ — ​ $ 1,265 ​ $ (614) ​ $ (218) ​ $ 433 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ During the years ended December 31, 2019 and 2018, the Company recorded approximately $3.6 million and approximately $14.7 million in restructuring expenses, respectively.

Selected Quarterly Financial Da

Selected Quarterly Financial Data (Unaudited)	12 Months Ended
	Dec. 31, 2018
Disclosure Text Block
Selected Quarterly Financial Data (Unaudited)	20. Selected Quarterly Financial Data (Unaudited) The following table contains quarterly financial information for the years ended December 31, 2019 and 2018. The Company believes that the following information reflects all normal recurring adjustments necessary for a fair presentation of the information for the periods presented. The operating results for any quarter are not necessarily indicative of results for any future period. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ First ​ Second ​ Third ​ Fourth ​ Total ​ ​ Quarter ​ Quarter ​ Quarter ​ Quarter ​ Year ​ ​ (in thousands, except per share data) 2019 ​ ​ ​ ​ ​ Total revenues (1) ​ $ 68,730 ​ $ 102,215 ​ $ 131,167 ​ $ 126,301 ​ $ 428,413 ​ Total cost and expenses (2) ​ 85,663 ​ 80,638 ​ 65,280 ​ 76,709 ​ 308,290 ​ Other expense, net (3) ​ (4,912) ​ (9,294) ​ (45,239) ​ (1,735) ​ (61,180) ​ Net (loss) income from continuing operations ​ ​ (21,846) ​ ​ 12,283 ​ ​ 20,648 ​ ​ 47,858 ​ 58,943 ​ Net loss from discontinued operations (4) ​ ​ (37,438) ​ ​ — ​ ​ — ​ ​ — ​ (37,438) ​ Net (loss) income ​ (59,284) ​ 12,283 ​ 20,648 ​ 47,858 ​ 21,505 ​ Net (loss) income per share from continuing operations—basic ​ $ (0.14) ​ $ 0.08 ​ $ 0.13 ​ $ 0.31 ​ $ 0.38 ​ Net (loss) income per share from continuing operations—diluted ​ ​ (0.14) ​ ​ 0.08 ​ ​ 0.13 ​ ​ 0.30 ​ ​ 0.38 ​ Net loss per share from discontinued operations—basic and diluted ​ ​ (0.24) ​ ​ — ​ ​ — ​ ​ — ​ ​ (0.24) ​ Net (loss) income per share--basic ​ ​ (0.38) ​ ​ 0.08 ​ ​ 0.13 ​ ​ 0.31 ​ ​ 0.14 ​ Net (loss) income per share—diluted (5) ​ ​ (0.38) ​ ​ 0.08 ​ ​ 0.13 ​ ​ 0.30 ​ ​ 0.14 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ First ​ Second ​ Third ​ Fourth ​ Total ​ ​ Quarter ​ Quarter ​ Quarter ​ Quarter ​ Year ​ ​ (in thousands, except per share data) 2018 ​ ​ ​ ​ ​ Total revenues (6) ​ $ 69,155 ​ $ 81,106 ​ $ 65,686 ​ $ 130,692 ​ $ 346,639 ​ Total cost and expenses (7) ​ 88,438 ​ 95,783 ​ 212,257 ​ 100,831 ​ 497,309 ​ Other expense, net (8) ​ (7,276) ​ (9,460) ​ (5,252) ​ (21,488) ​ (43,476) ​ Net (loss) income from continuing operations ​ ​ (26,559) ​ ​ (24,137) ​ ​ (151,823) ​ ​ 8,373 ​ ​ (194,146) ​ Net loss from discontinued operations (4) ​ ​ (16,585) ​ ​ (25,243) ​ ​ (22,528) ​ ​ (23,866) ​ ​ (88,222) ​ Net loss ​ (43,144) ​ (49,380) ​ (174,351) ​ (15,493) ​ (282,368) ​ Net (loss) income per share from continuing operations—basic and diluted ​ ​ (0.18) ​ ​ (0.16) ​ ​ (0.99) ​ ​ 0.05 ​ ​ (1.27) ​ Net loss per share from discontinued operations—basic and diluted ​ ​ (0.11) ​ ​ (0.17) ​ ​ (0.15) ​ ​ (0.15) ​ ​ (0.58) ​ Net loss per share--basic and diluted ​ $ (0.29) ​ $ (0.32) ​ $ (1.14) ​ $ (0.10) ​ $ (1.85) ​ (1) Total revenues includes approximately $48.8 million of revenue from sales of linaclotide API to our linaclotide partners, primarily driven by the commercialization of linaclotide in Japan for the year ended December 31, 2019, as well as approximately $32.4 million related to the non-contingent payments from the Amended AstraZeneca Agreement and a $10.0 million upfront fee from the Amended Astellas License Agreement, both executed during the third quarter of 2019. (2) Total costs and expenses includes approximately $3.6 . million in restructuring expenses for the year ended December 31, 2019, as well as approximately $3.2 million related to the gain on lease modification in April 2019. (3) Other expense, net includes approximately $31.0 million in loss on extinguishment of debt related to the partial repurchase of the 2022 Convertible Notes and the redemption of the 2026 Notes, and approximately $3.0 million gain on fair value remeasurement of derivatives for the year ended December 31, 2019. (4) During the year ended December 31, 2019, the Company completed the Separation. Certain amounts related to Cyclerion have been reclassified as discontinued operations for the years ended December 31, 2019 and 2018. (5) Diluted earnings per share is equivalent to basic earnings per share for the year ended December 31, 2019. (6) Total revenue includes approximately $70.4 million of revenue from sales of linaclotide API to our linaclotide partners, primarily driven by the commercialization of linaclotide in Japan for the year ended December 31, 2018. (7) Total costs and expenses includes approximately $14.7 million in restructuring expenses for the year ended December 31, 2018, as well as approximately $151.8 million related to the impairment of intangible assets and approximately $31.0 million related to a gain on remeasurement of contingent consideration incurred during the third quarter of 2018 in connection with the exit of the Lesinurad License. (8) Other expense, net includes approximately $8.7 million loss on fair value remeasurement of derivatives for the year ended December 31, 2018.

Subsequent Events

Subsequent Events	12 Months Ended
	Dec. 31, 2019
Disclosure Text Block
Subsequent Events	21. Subsequent Events ​ In January 2020, the Company and Allergan entered into settlement agreements with Sandoz Inc. (“Sandoz”) and Teva Pharmaceuticals, USA (“Teva”) resolving patent litigation brought in response to Sandoz’s and Teva’s abbreviated new drug applications seeking approval to market generic versions of LINZESS prior to the expiration of the Company and Allergan’s applicable patents. For additional information relating to the resolution of such litigation, see Item 3, Legal Proceedings ​ ​ ​

Nature of Business (Policies)

Nature of Business (Policies)	12 Months Ended
	Dec. 31, 2019
Policy Text Blocks
Principles of Consolidation	Principles of Consolidation The accompanying consolidated financial statements include the accounts of Ironwood and its wholly-owned subsidiaries, as of December 31, 2019, Ironwood Pharmaceuticals Securities Corporation and Ironwood Pharmaceuticals GmbH. Cyclerion was a wholly-owned subsidiary until it became an independent publicly-traded company on April 1, 2019. All intercompany transactions and balances are eliminated in consolidation.
Segment Information	Segment Information Operating segments are components of an enterprise for which separate financial information is available and is evaluated regularly by the Company’s chief operating decision-maker in deciding how to allocate resources and in assessing performance. The Company currently operates in one reportable business segment—human therapeutics.
Reclassifications and Revisions to Prior Period Financial Statements	Reclassifications and Revisions to Prior Period Financial Statements Certain prior period financial statement items have been reclassified to conform to current period presentation. The Company has presented its business as discontinued operations in its consolidated financial statements for all periods presented. The historical financial statements and footnotes have been recast accordingly.
Discontinued Operations	Discontinued Operations ​ During the three months ended June 30, 2019, the Company determined that its sGC business met the criteria for classification as a discontinued operation in accordance with Accounting Standards Codification (“ASC”) Subtopic 205-20, Discontinued Operations Cyclerion Separation
Use of Estimates	Use of Estimates The preparation of consolidated financial statements in accordance with U.S. generally accepted accounting principles requires the Company’s management to make estimates and judgments that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the consolidated financial statements, and the amounts of revenues and expenses during the reported periods. On an ongoing basis, the Company’s management evaluates its estimates, judgments and methodologies. Significant estimates and assumptions in the consolidated financial statements include those related to revenue recognition; accounts receivable; inventory valuation and related reserves; useful lives of long-lived assets, impairment of long-lived assets, including its acquired intangible assets and goodwill; valuation procedures for right-of-use assets and operating lease liabilities; valuation procedures for the issuance and repurchase of convertible notes; valuation of assets and liabilities held for disposition and losses related to discontinued operations; fair value of derivatives; balance sheet classification of notes payable and convertible notes; income taxes, including the valuation allowance for deferred tax assets; research and development expenses; contingencies and share-based compensation. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results may differ materially from these estimates under different assumptions or conditions. Changes in estimates are reflected in reported results in the period in which they become known.
Cash and Cash Equivalents	Cash and Cash Equivalents The Company considers all highly liquid investment instruments with a remaining maturity when purchased of three months or less to be cash equivalents. Investments qualifying as cash equivalents primarily consist of money market funds, U.S. government-sponsored securities, and repurchase agreements. The carrying amount of cash equivalents approximates fair value. The amount of cash equivalents included in cash and cash equivalents was approximately $177.0 million and approximately $173.1 million at December 31, 2019 and 2018, respectively.
Restricted Cash	Restricted Cash The Company is contingently liable under unused letters of credit with a bank, related to the Company’s facility lease and vehicle lease agreements, in the amount of approximately $2.2 million and approximately $7.7 million as of December 31, 2019 and 2018, respectively. The Company records as restricted cash the collateral used to secure these letters of credit. During the year ended December 31, 2019, approximately $6.4 million of the Company’s restricted cash related to the termination of its former headquarters lease in Cambridge, Massachusetts was released. The amount of restricted cash in current assets and non-current assets was approximately $1.2 million and $1.0 million at December 31, 2019, respectively.
Inventory	Inventory Inventory is stated at the lower of cost or net realizable value with cost determined under the first-in, first-out basis in accordance with ASC 330, Inventory Inventory (Topic 330): Simplifying the Measurement of Inventory The Company evaluates inventory levels quarterly and any inventory that has a cost basis in excess of its expected net realizable value, inventory that becomes obsolete, inventory in excess of expected sales requirements, inventory that fails to meet commercial sale specifications or is otherwise impaired is written down with a corresponding charge to the statement of operations in the period that the impairment is first identified. The Company also assesses, on a quarterly basis, whether it has any excess non-cancelable purchase commitments resulting from its minimum supply agreements with its suppliers. The Company relies on data from several sources to estimate the net realizable value of inventory and non-cancelable purchase commitments, including partner forecasts of projected inventory purchases that are received quarterly, the Company’s internal forecasts and related process, historical sales by geographic region, and the status of and progress toward commercialization of linaclotide in partnered territories. The Company capitalizes inventories manufactured in preparation for initiating sales of a product candidate when the related product candidate is considered to have a high likelihood of regulatory approval and the related costs are expected to be recoverable through sales of the inventories. In determining whether or not to capitalize such inventories, the Company evaluates, among other factors, information regarding the product candidate’s safety and efficacy, the status of regulatory submissions and communications with regulatory authorities and the outlook for commercial sales, including the existence of current or anticipated competitive drugs and the availability of reimbursement. In addition, the Company evaluates risks associated with manufacturing the product candidate, including the ability of the Company’s third-party suppliers to complete the validation batches, and the remaining shelf life of the inventories. Costs associated with developmental products prior to satisfying the inventory capitalization criteria are charged to research and development expense as incurred.
Concentrations of Suppliers	Concentrations of Suppliers The Company relies on third-party manufacturers and its collaboration partners to manufacture linaclotide API, linaclotide finished drug product, and finished goods. Currently, the Company uses three third-party facilities actively producing linaclotide API and finished drug product. The Company also has an agreement with another independent third party to serve as a redundant linaclotide API manufacturing capacity to support its partnered territories. Beginning in 2020, each of the Company’s partners for linaclotide will be responsible for API, finished drug product and finished goods manufacturing (including bottling and packaging) for its respective territories and distributing the finished goods to wholesalers. If any of the Company’s suppliers were to limit or terminate production or otherwise fail to meet the quality or delivery requirements needed to satisfy the supply commitments, the process of locating and qualifying alternate sources could require up to several months, during which time the Company’s production could be delayed. Such delays could have a material adverse effect on the Company’s business, financial position and results of operations.
Accounts Receivable and Related Valuation Account	Accounts Receivable and Related Valuation Account The Company makes judgments as to its ability to collect outstanding receivables and provides an allowance for receivables when collection becomes doubtful. Provisions are made based upon a specific review of all significant outstanding invoices and the overall quality and age of those invoices not specifically reviewed. The Company’s receivables relate primarily to amounts reimbursed under its collaboration, license and co-promotion agreements, as well as historical amounts due from product sales to wholesalers. The Company believes that credit risks associated with these partners and wholesalers are not significant. To date, the Company has not had any significant write-offs of bad debt, and the Company did not have an allowance for doubtful accounts as of December 31, 2019 or 2018.
Concentrations of Credit Risk	Concentrations of Credit Risk Financial instruments that subject the Company to credit risk primarily consist of cash and cash equivalents, restricted cash, and accounts receivable. The Company maintains its cash and cash equivalent balances with high-quality financial institutions and, consequently, the Company believes that such funds are subject to minimal credit risk. The Company has adopted an investment policy which limits the amounts the Company may invest in certain types of investments, and requires all investments held by the Company to be at least AA- rated, thereby reducing credit risk exposure. Accounts receivable, including related party accounts receivable, primarily consist of amounts due under the linaclotide collaboration agreement with Allergan for North America and linaclotide license agreement with Astellas for Japan (Note 6). The Company does not obtain collateral for its accounts receivable. Accounts receivable or payable to or from Allergan and Cyclerion are presented as related party accounts receivable and related party accounts payable, respectively, on the consolidated balance sheets. The percentages of revenue recognized from significant customers of the Company in the years ended December 31, 2019, 2018 and 2017 as well as the account receivable balances, net of any payables due, at December 31, 2019 and 2018 are included in the following table: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accounts ​ Revenue ​ ​ December 31, ​ Year Ended December 31, ​ 2019 2018 2019 2018 2017 Collaborative Partner: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Allergan (North America and Europe) 90 % 72 % 78 % 77 % 88 % Astellas (Japan) 8 % 26 % 13 % 20 % 10 % ​ For the years ended December 31, 2019, 2018 and 2017, no additional customers accounted for more than 10% of the Company’s revenue.
Property and Equipment	​ Property and Equipment ​ Property and equipment, including leasehold improvements, are recorded at cost, and are depreciated when placed into service using the straight-line method based on their estimated useful lives as follows: ​ ​ ​ ​ ​ ​ Estimated Useful Life Asset Description (In Years) Manufacturing equipment 10 ​ Laboratory equipment 5 ​ Computer and office equipment 3 ​ Furniture and fixtures 7 ​ Software 3 ​ ​ Included in property and equipment are certain costs of software obtained for internal use. Costs incurred during the preliminary project stage are expensed as incurred, while costs incurred during the application development stage are capitalized and amortized over the estimated useful life of the software. The Company also capitalizes costs related to specific upgrades and enhancements when it is probable the expenditures will result in additional functionality. Maintenance and training costs related to software obtained for internal use are expensed as incurred. Leasehold improvements are amortized over the shorter of the estimated useful life of the asset or the lease term. Under ASC Topic 840, Leases Costs for capital assets not yet placed into service have been capitalized as construction in process, and will be depreciated in accordance with the above guidelines once placed into service. Maintenance and repair costs are expensed as incurred.
Finite Lived Intangible Assets	Finite Lived Intangible Assets The Company records the fair value of purchased intangible assets with finite useful lives as of the transaction date of a business combination. Purchased intangible assets with finite useful lives are amortized to their estimated residual values over their estimated useful lives. The value of the Company’s finite-lived intangible assets was based on the future expected net cash flows related to ZURAMPIC and DUZALLO (the “Lesinurad Products”), which included significant assumptions around future net sales and the respective investment to support these products. During the year ended December 31, 2018, the Company recorded an impairment charge of approximately $151.8 million to fully write-off its ZURAMPIC and DUZALLO intangible assets.
Goodwill	Goodwill ​ Goodwill represents the difference between the purchase price and the fair value of the identifiable tangible and intangible net assets when accounting for business combinations. Goodwill is not amortized, but is reviewed for impairment. The Company tests its goodwill for impairment annually as of October 1 st
Impairment of Long-Lived Assets	Impairment of Long-Lived Assets The Company regularly reviews the carrying amount of its long-lived assets to determine whether indicators of impairment may exist, which warrant adjustments to carrying values or estimated useful lives. If indications of impairment exist, projected future undiscounted cash flows associated with the asset are compared to the carrying amount to determine whether the asset’s value is recoverable. If the carrying value of the asset exceeds such projected undiscounted cash flows, the asset will be written down to its estimated fair value. There were no significant impairments of long-lived assets for the years ended December 31, 2019, 2018, or 2017.
Income Taxes	Income Taxes The Company provides for income taxes under the liability method. Deferred tax assets and liabilities are determined based on differences between financial reporting and tax bases of assets and liabilities and are measured using the enacted tax rates in effect when the differences are expected to reverse. Deferred tax assets are reduced by a valuation allowance to reflect the uncertainty associated with their ultimate realization. The Company accounts for uncertain tax positions recognized in the consolidated financial statements in accordance with the provisions of ASC Topic 740, Income Taxes
Financing Costs	Financing Costs Financing costs include costs directly attributable to the Company’s offerings of its equity securities and its debt financings. Costs attributable to equity offerings are charged as a reduction to stockholders’ equity against the proceeds of the offering once the offering is completed. Costs attributable to debt financings are deferred and amortized to interest expense over the term of the debt using the effective interest method. Portions of the financing costs incurred in connection with the 2022 Convertible Notes, 2024 Convertible Notes and 2026 Convertible Notes were deemed to relate to the equity components and were recorded as a reduction to additional paid in capital. In accordance with ASC 835, Interest Notes Payable
Leases	Leases Effective January 1, 2019 , the Company adopted ASC Topic 842, Leases (“ASC 842”), using the optional transition method. The adoption of ASC 842 represents a change in accounting principle that aims to increase transparency and comparability among organizations by requiring the recognition of right-of-use assets and lease liabilities on the balance sheet for both operating and finance leases. In addition, the standard requires enhanced disclosures that meet the objective of enabling financial statement users to assess the amount, timing, and uncertainty of cash flows arising from leases. The reported results for the year ended December 31, 2019 reflect the application of ASC 842 guidance, while the reported results for prior periods were prepared in conjunction with ASC 840. Because there were no material changes to the values of capital leases as a result of adoption of ASC 842, the Company concluded that no cumulative-effect adjustment to the accumulated deficit as of January 1, 2019 was necessary. ​ The recognition of right-of-use assets and lease liabilities related to the Company’s operating leases under ASC 842 has had a material impact on the Company’s consolidated financial statements. ​ As part of the ASC 842 adoption, the Company elected certain practical expedients outlined in the guidance. These practical expedients include: ​ ● Accounting policy election to use the short-term lease exception by asset class; and ● Election of the practical expedient package during transition, which includes: o An entity need not reassess whether any expired or existing contracts are or contain leases. o An entity need not reassess the classification for any expired or existing leases. As a result, all leases that were classified as operating leases in accordance with ASC 840 are classified as operating leases under ASC 842, and all leases that were classified as capital leases in accordance with ASC 840 are classified as finance leases under ASC 842. o An entity need not reassess initial direct costs for any existing leases. ​ Subsequent to the Company’s adoption of ASC 842, the Company elected the post-transition practical expedient, by class of underlying asset, to account for lease components and non-lease components together as a single component for the asset class of operating lease right-of-use real estate assets. ​ The Company’s lease portfolio for year ended December 31, 2019 includes: leases for its prior and current headquarters locations, a data center colocation lease, vehicle leases for its salesforce representatives, and leases for computer and office equipment. The Company determines if an arrangement is a lease at the inception of the contract. The asset component of the Company’s operating leases is recorded as operating lease right-of-use assets, and the liability component is recorded as current portion of operating lease liabilities and operating lease liabilities, net of current portion in the Company’s consolidated balance sheets. As of December 31, 2019, the Company did not record any finance leases. ​ Right-of-use assets and operating lease liabilities are recognized based on the present value of lease payments over the lease term at the lease inception date. Existing leases in the Company’s lease portfolio as of the adoption date were valued as of January 1, 2019. The Company uses an incremental borrowing rate based on the information available at lease inception in determining the present value of lease payments, if an implicit rate of return is not provided with the lease contract. Operating lease right-of-use assets are adjusted for incentives expected to be received. ​ Right-of-use assets and operating lease liabilities are remeasured upon certain modifications to leases using the present value of remaining lease payments and estimated incremental borrowing rate upon lease modification. ​ Lease cost is recognized on a straight-line basis over the lease term, and includes amounts related to short-term leases. The Company recognizes variable lease payments as operating expenses in the period in which the obligation for those payments is incurred. Variable lease payments primarily include common area maintenance, utilities, real estate taxes, insurance, and other operating costs that are passed on from the lessor in proportion to the space leased by the Company.
Derivative Assets and Liabilities	Derivative Assets and Liabilities In June 2015, in connection with the issuance of the 2022 Convertible Notes, the Company entered into convertible note hedge transactions (the “Convertible Note Hedges”). Concurrently with entering into the Convertible Note Hedges, the Company also entered into certain warrant transactions in which it sold note hedge warrants (the “Note Hedge Warrants”) to the Convertible Note Hedge counterparties to acquire shares of the Company’s Class A Common Stock, subject to customary anti-dilution adjustments (Note 12). In connection with the partial repurchase of the 2022 Convertible Notes in August 2019, the Company terminated its Convertible Note Hedges and Note Hedge Warrants proportionately. These instruments are derivative financial instruments under ASC Topic 815, Derivatives and Hedging These derivatives are recorded as assets or liabilities at fair value each reporting date and the fair value is determined using the Black-Scholes option-pricing model. The changes in fair value are recorded as a component of other (expense) income in the consolidated statements of operations. Significant inputs used to determine the fair value include the price per share of the Company’s Class A Common Stock on the date of valuation, expected term of the derivative instruments, strike prices of the derivative instruments, risk-free interest rate, and expected volatility of the Company’s Class A Common Stock. Changes to these inputs could materially affect the valuation of the Convertible Note Hedges and Note Hedge Warrants in future periods. In August 2019, in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into the Capped Calls. The Capped Calls cover the same number of shares of Class A Common Stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes (subject to anti-dilution and certain other adjustments). These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met. ​
Revenue Recognition	Revenue Recognition Effective January 1, 2018 , the Company adopted ASU No. 2014 -09, Revenue from Contracts with Customers (Topic 606) and related amendments (“ASU 2014 -09”) using the modified retrospective transition method. The adoption of ASU 2014-09 represented a change in accounting principle that aimed to more closely align revenue recognition with the delivery of the Company's products or services and provided financial statement readers with enhanced disclosures. ASU 2014-09 also included Subtopic 340-40, Other Assets and Deferred Costs—Contracts with Customers , which required the deferral of incremental costs of obtaining a contract with a customer. In accordance with ASC Topic 606, Revenue from Contracts with Customers (“ASC 606”), the Company recognizes revenue when the customer obtains control of a promised good or service, in an amount that reflects the consideration which the Company expects to receive in exchange for the good or service. Upon adoption of ASC 606, the Company concluded that no cumulative-effect adjustment to the accumulated deficit as of January 1, 2018 was necessary. There were no remaining or ongoing deliverables or unrecognized consideration as of December 31, 2017 that required an adjustment to the accumulated deficit. The adoption of ASC 606 had no impact on the Company’s consolidated statement of operations, balance sheets, or statement of cash flows. The reported results for the years ended December 31, 2019 and 2018 reflect the application of ASC 606 guidance, while the reported results for the year ended December 31, 2017 were prepared in accordance with ASC 605, Revenue Recognition (“ASC 605”). As part of the ASC 606 adoption, the Company has utilized certain practical expedients outlined in the guidance. These practical expedients include: ● Expensing as incurred incremental costs of obtaining a contract, such as sales commissions, if the amortization period of the asset would be less than one year; ● Recognizing revenue in the amount that the Company has the right to invoice, when consideration from the customer corresponds directly with the value to the customer of the Company’s performance completed to date; and ● For contracts that were modified before the beginning of the earliest reporting period presented in accordance with the pending content that links to this paragraph, an entity need not retrospectively restate the contract for those contract modifications in accordance with paragraphs ASC 606-10-25-12 through 25-13. Instead, an entity shall reflect the aggregate effect of all modifications that occur before the beginning of the earliest period presented in accordance with the pending content that links to this paragraph when: (a) Identifying the satisfied and unsatisfied performance obligations, (b) Determining the transaction price, and (c) Allocating the transaction price to the satisfied and unsatisfied performance obligations. Prior to the adoption of ASC 606, the Company recognized revenue when there was persuasive evidence that an arrangement existed, services had been rendered or delivery had occurred, the price was fixed or determinable, and collection was reasonably assured. The Company’s revenues are generated primarily through collaborative arrangements and license agreements related to the research and development and commercialization of linaclotide, as well as co-promotion arrangements in the U.S. The terms of the collaborative research and development, license, co-promotion and other agreements contain multiple performance obligations which may include (i) licenses, (ii) research and development activities, including participation on joint steering committees, (iii) the manufacture of finished drug product, API, or development materials for a partner, which are reimbursed at a contractually determined rate, and (iv) education or co-promotion activities by the Company’s clinical sales specialists. Non-refundable payments to the Company under these agreements may include (i) up-front license fees, (ii) payments for research and development activities, (iii) payments for the manufacture of finished drug product, API, or development materials, (iv) payments based upon the achievement of certain milestones, (v) payments for sales detailing, promotional support services and medical education initiatives, and (vi) royalties on product sales. The Company receives its share of the net profits or bears its share of the net losses from the sale of linaclotide in the U.S. through its collaboration agreement with Allergan for North America. Prior to the execution of the amended and restated collaboration agreement with AstraZeneca (the “Amended AstraZeneca Agreement”) on September 16, 2019, the Company received its share of the net profits and bore its share of the net losses from the sale of linaclotide in the China (including Hong Kong and Macau), through its collaboration with AstraZeneca. The Company has adopted a policy to recognize revenue net of tax withholdings, as applicable. Revenue recognition under ASC 606 Upon executing a revenue generating arrangement, the Company assesses whether it is probable the Company will collect consideration in exchange for the good or service it transfers to the customer. To determine revenue recognition for arrangements that the Company determines are within the scope of ASC 606, it performs the following five steps: (i) identify the contract(s) with a customer; (ii) identify the performance obligations in the contract; (iii) determine the transaction price; (iv) allocate the transaction price to the performance obligations in the contract; and (v) recognize revenue when (or as) the Company satisfies the performance obligations. The Company must develop assumptions that require significant judgment to determine the standalone selling price for each performance obligation identified in the contract. The assumptions that are used to determine the standalone selling price may include forecasted revenues, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success. Collaboration, License, Co-Promotion and Other Commercial Agreements Upon licensing intellectual property to a customer, the Company determines if the license is distinct from the other performance obligations identified in the arrangement. The Company recognizes revenues from the transaction price, including non-refundable, up-front fees allocated to the license when the license is transferred to the customer if the license has distinct benefit to the customer. For licenses that are combined with other promises, the Company assesses the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time. For performance obligations that are satisfied over time, the Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. The Company’s license and collaboration agreements include milestone payments, such as development and other milestones. The Company evaluates whether the milestones are considered probable of being reached and estimates the amount to be included in the transaction price using the most likely amount method at the inception of the agreement. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within the control of the Company, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. The transaction price is then allocated to each performance obligation on a relative standalone selling price basis, for which the Company recognizes revenue as or when the performance obligations under the contract are satisfied. The Company re-evaluates the probability of achievement of such milestones and any related constraint at each reporting period, and any adjustments are recorded on a cumulative catch-up basis. Agreements that include the supply of API or drug product for either clinical development or commercial supply at the customer’s discretion are generally considered as options. The Company assesses if these options provide a material right to its partner, and if so, they are accounted for as separate performance obligations. If the Company is entitled to additional payments when the customer exercises these options, any additional payments are recorded as revenue when the customer obtains control of the goods, which is typically upon shipment for sales of API and finished drug product. For agreements that include sales-based royalties, including milestone payments based on the level of sales, and the license is deemed to be the predominant item to which the royalties relate, the Company recognizes revenue when the related sales occur in accordance with the sales-based royalty exception under ASC 606-10-55-65. Net Profit or Net Loss Sharing In accordance with ASC 808 Topic, Collaborative Arrangements (“ASC 808”), the Company considered the nature and contractual terms of the arrangement and the nature of the Company’s business operations to determine the classification of payments under the Company’s collaboration agreements. While ASC 808 provides guidance on classification, the standard is silent on matters of separation, initial measurement, and recognition. Therefore, the Company, consistent with its accounting policies prior to the adoption of ASC 606, applies the separation, initial measurement, and recognition principles of ASC 606 to its collaboration agreements. The Company adopted ASU No. 2018-18, Collaborative Arrangements (Topic 808): Clarifying the Interaction between Topic 808 and Topic 606, The Company’s collaborative arrangements revenues generated from sales of LINZESS in the U.S. are considered akin to sales-based royalties. In accordance with the sales-based royalty exception, the Company recognizes its share of the pre-tax commercial net profit or net loss generated from the sales of LINZESS in the U.S. in the period the product sales are earned, as reported by Allergan, and related cost of goods sold and selling, general and administrative expenses are incurred by the Company and its collaboration partner. These amounts are partially determined based on amounts provided by Allergan and involve the use of estimates and judgments, such as product sales allowances and accruals related to prompt payment discounts, chargebacks, governmental and contractual rebates, wholesaler fees, product returns, and co-payment assistance costs, which could be adjusted based on actual results in the future. The Company is highly dependent on Allergan for timely and accurate information regarding any net revenues realized from sales of LINZESS in the U.S. in accordance with both ASC 808 and ASC 606, and the costs incurred in selling it, in order to accurately report its results of operations. If the Company does not receive timely and accurate information or incorrectly estimates activity levels associated with the collaboration at a given point in time, the Company could be required to record adjustments in future periods. In accordance with ASC 606-10-55, Principal Agent Considerations basis and presents the settlement payments to and from Allergan as collaboration expense or collaborative arrangements revenue, as applicable. The Company and Allergan settle the cost sharing quarterly, such that the Company’s statements of operations reflects 50% of the pre-tax net profit or loss generated from sales of LINZESS in the U.S. Product revenue, net Product revenue consisted of sales of the Lesinurad Products, in the U.S. until the termination of the exclusive license to develop, manufacture, and commercialize in the U.S. products containing lesinurad as an active ingredient (the “Lesinurad License”) in January 2019. The Company sold the Lesinurad Products principally to a limited number of national wholesalers and selected regional wholesalers (the “Distributors”). The Distributors resold the Lesinurad Products to retail pharmacies and healthcare providers, who then sold to patients. Net product revenue was recognized when the Distributor obtained control of the Company’s product, which occurred at a point in time, typically upon shipment of Lesinurad Products to the Distributor. When the Company performed shipping and handling activities after the transfer of control to the Distributor (e.g., when control transfers prior to delivery), they were considered fulfillment activities, and accordingly, the costs were accrued for when the related revenue was recognized. The Company expensed incremental costs of obtaining a contract as and when incurred if the expected amortization period of the asset that the Company would have recognized was one year or less. The Company evaluated the creditworthiness of each of its Distributors to determine whether it was probable that a significant reversal in the amount of the cumulative revenue recognized would not occur. The Company calculated its net product revenue based on the wholesale acquisition cost that the Company charged its Distributors for the Lesinurad Products less variable consideration. The product revenue variable consideration consisted of estimates relating to (i) trade discounts and allowances, such as invoice discounts for prompt payment and distributor fees, (ii) estimated government and private payor rebates, chargebacks and discounts, such as Medicaid reimbursements, (iii) reserves for expected product returns and (iv) estimated costs of incentives offered to certain indirect customers including patients. These estimates would be adjusted based on actual results in the period such variances became known. Product revenue was recorded net of the trade discounts, allowances, rebates, chargebacks, discounts, product returns, and other incentives. Certain of these adjustments were recorded as an accounts receivable reserve, while certain of these adjustments were recorded as accrued expenses. ​ Other The Company produced linaclotide finished drug product, API and development materials for certain of its partners. The Company recognizes revenue on linaclotide finished drug product, API and development materials when control has transferred to the partner, which generally occurs upon shipment for sales of API and finished drug product, after the material has passed all quality testing required for collaborator acceptance. As it relates to development materials and API produced for Astellas, the Company is reimbursed at a contracted rate. Such reimbursements are considered as part of revenue generated pursuant to the Astellas license agreement and are presented as collaborative arrangements revenue. Any linaclotide finished drug product, API and development materials currently produced for Allergan for the U.S. are recognized in accordance with the cost-sharing provisions of the collaboration agreement with Allergan for North America. Prior to the execution of the Amended AstraZeneca Agreement in September 2019, any linaclotide finished drug product, API and development materials produced for AstraZeneca for China (including Hong Kong and Macau) were recognized in accordance with the cost-sharing provisions of the AstraZeneca collaboration agreement. Beginning in 2020, the Company will no longer be responsible for the supply of linaclotide finished drug product or API to its partners. The Company’s deferred revenue balance consists of advance billings and payments received from customers in excess of revenue recognized. Revenue recognition prior to the adoption of ASC 606 Agreements Entered into Prior to January 1, 2011 For arrangements that include multiple deliverables and were entered into prior to January 1, 2011, the Company followed the provisions of ASC Topic 605-25, Revenue Recognition—Multiple-Element Arrangements ● Delivered element(s) had value to the collaborator on a standalone basis; ● There was objective and reliable evidence of the fair value of the undelivered obligation(s); and ● If the arrangement included a general right of return relative to the delivered item(s), delivery or performance of the undelivered item(s) was considered probable and substantially within the Company’s control. The Company allocated arrangement consideration among the separate units of accounting either on the basis of each unit’s respective fair value or using the residual method, and applied the applicable revenue recognition criteria to each of the separate units. If the separation criteria were not met, revenue of the combined unit of accounting was recorded based on the method appropriate for the last delivered item. Agreements Entered into or Materially Modified on or after January 1, 2011 and prior to January 1, 2018 The Company evaluated revenue from multiple element agreements entered into on or after January 1, 2011 under ASC 605 or ASU No. 2009-13, Multiple-Deliverable Revenue Arrangements 13”) until the adoption of ASC 606. The Company also evaluated whether amendments to its multiple element arrangements were considered material modifications that were subject to the application of ASU 2009-13. This evaluation required management to assess all relevant facts and circumstances and to make subjective determinations and judgments. When evaluating multiple element arrangements under ASU 2009-13, the Company considered whether the deliverables under the arrangement represented separate units of accounting. This evaluation required subjective determinations and required management to make judgments about the individual deliverables and whether such deliverables were separable from the other aspects of the contractual relationship. In determining the units of accounting, management evaluated certain criteria, including whether the deliverables had standalone value, based on the consideration of the relevant facts and circumstances for each arrangement. Factors considered in this determination included the research, manufacturing and commercialization capabilities of the partner and the availability of relevant research and manufacturing expertise in the general marketplace. In addition, the Company considered whether the collaborator can use the license or other deliverables for their intended purpose without the receipt of the remaining elements, and whether the value of the deliverable was dependent on the undelivered items and whether there were other vendors that could provide the undelivered items. The consideration received was allocated among the separate units of accounting using the relative selling price method, and the applicable revenue recognition criteria were applied to each of the separate units. The Company determined the estimated selling price for deliverables using vendor-specific objective evidence (“VSOE”) of selling price, if available, third-party evidence (“TPE”) of selling price if VSOE was not available, or best estimate of selling price (“BESP”) if neither VSOE nor TPE was available. Up-Front License Fees prior to January 1, 2018 When management believed the license to its intellectual property had standalone value, the Company generally recognized revenue attributed to the license upon delivery. When management believed the license to its intellectual property did not have standalone value from the other deliverables to be provided in the arrangement, it was combined with other deliverables and the revenue of the combined unit of accounting was recorded based on the method appropriate for the last delivered item. Milestones prior to January 1, 2018 At the inception of each arrangement that included pre-commercial milestone payments, the Company evaluated whether each pre-commercial milestone was substantive, in accordance with ASU No. 2010-17, Revenue Recognition—Milestone Method Commercial milestones were accounted for as royalties and are recorded as revenue upon achievement of the milestone, assuming all other revenue recognition criteria are met. Net Profit or Net Loss Sharing prior to January 1, 2018 In accordance with ASC 808 and ASC 605-45, Principal Agent Considerations The Company recognized its share of the pre-tax commercial net profit or net loss generated from the sales of LINZESS in the U.S. in the period the product sales are reported by Allergan and related cost of goods sold and selling, general and administrative expenses are incurred by the Company and its collaboration partner. These amounts were partially determined based on amounts provided by Allergan and involve the use of estimates and judgments, such as product sales allowances and accruals related to prompt payment discounts, chargebacks, governmental and contractual rebates, wholesaler fees, product returns, and co-payment assistance costs, which could be adjusted based on actual results. For the periods covered in the consolidated financial statements presented, there have been no material changes to prior period estimates of revenues, cost of goods sold or selling, general and administrative expenses associated with the sales of LINZESS in the U.S. The Company recorded its share of the net profits or net losses from the sales of LINZESS in the U.S. on a net basis and presented the settlement payments to and from Allergan as collaboration expense or collaborative arrangements revenue, as applicable, as the Company was not the primary obligor and did not have the risks and rewards of ownership in the collaboration agreement with Allergan for North America. The Company and Allergan settle the cost sharing quarterly, such that the Company’s consolidated statements of operations reflect 50% of the pre-tax net profit or loss generated from sales of LINZESS in the U.S. Royalties on Product Sales prior to January 1, 2018 The Company received royalty revenues under certain of the Company’s license or collaboration agreements. The Company recorded these revenues as earned. Product Revenue, Net prior to January 1, 2018 ​ As noted above, net product revenue was derived from sales of the Lesinurad Products in the U.S. The Company recognized net product revenue from sales of the Lesinurad Products in accordance with ASC 605, when persuasive evidence of an arrangement existed, delivery had occurred and title of the product and associated risk of loss had passed to the customer, the price was fixed or determinable, and collection from the customer was reasonably assured. ASC 605 required, among other criteria, that future returns could be reasonably estimated in order to recognize revenue. The Company began commercializing ZURAMPIC in October 2016 and DUZALLO in October 2017 in the U.S. Initially, upon the product launch of each of the Lesinurad Products, the Company determined that it was not able to reliably make certain estimates, including returns, necessary to recognize product revenue upon delivery to Distributors. As a result, through September 30, 2017, the Company recorded net product revenue for the Lesinurad Products using a deferred revenue recognition model (sell-through). Accordingly, the Company recognized net product revenue when the Lesinurad Products were prescribed to the end-user, using estimated prescription demand and pharmacy demand from third party sources and the Company’s analysis of third party market research data, as well as other third-party information through September 30, 2017. During the three months ended December 31, 2017, the Company concluded it had sufficient volume of historical activity and visibility into the distribution channel in order to reasonably make all estimates required under ASC 605 to recognize product revenue upon delivery to the Distributor. During the three months and year ended December 31, 2017, product revenue was recognized upon delivery of the Lesinurad Products to the Distributors. The Company evaluated the creditworthiness of each of its Distributors to determine whether revenue could be recognized upon delivery, subject to satisfaction of the other requirements, or whether recognition was required to be delayed until receipt of payment. In order to conclude that the price is fixed or determinable, the Company must be able to (i) calculate its gross product revenue from the sales to Distributors and (ii) reasonably estimate its net product revenue. The Company calculated gross product revenue based on the wholesale acquisition cost that the Company charged its Distributors for ZURAMPIC and DUZALLO. The Company estimated its net product revenue by deducting from its gross product revenue (i) trade discounts and allowances, such as invoice discounts for prompt payment and distributor fees, (ii) estimated government and private payor rebates, chargebacks and discounts, such as Medicaid reimbursements, (iii) reserves for expected product returns and (iv) estimated costs of incentives offered to certain indirect customers including patients. These estimates could be adjusted based on actual results in the period such variances become known. Other The Company supplied linaclotide finished drug product, API and development materials for certain of its partners. The Company recognized revenue on linaclotide finished drug product, API and development materials when the material had passed all quality testing required for collaborator acceptance, delivery had occurred, title and risk of loss had transferred to the partner, the price was fixed or determinable, and collection was reasonably assured.
Cost of Revenues	Cost of Revenues Cost of revenues includes cost related to the sales of linaclotide API and finished drug product, as well as the cost of product revenue related to sales of the Lesinurad Products in the U.S. Cost related to the sales of linaclotide API and finished drug product are recognized upon shipment of linaclotide API and finished drug product to certain of the Company’s partners outside of the U.S. The Company’s cost of revenues for linaclotide consists of the internal and external costs of producing such API and finished drug product. Cost of product revenue related to the sales of the Lesinurad Products in the U.S. includes the cost of producing finished goods that correspond with product revenue for the reporting period, such as third-party supply and overhead costs, as well as certain period costs related to freight, packaging, stability and quality testing, and customer acquisition.
Research and Development Costs	Research and Development Costs The Company generally expenses research and development costs to operations as incurred. The Company capitalizes nonrefundable advance payments made by the Company for research and development activities and defers expense recognition until the related goods are received or the related services are performed. Research and development expenses are comprised of costs incurred in performing research and development activities, including salary, benefits, share-based compensation, and other employee-related expenses; laboratory supplies and other direct expenses; facilities expenses; overhead expenses; third-party contractual costs relating to nonclinical studies and clinical trial activities and related contract manufacturing expenses, development of manufacturing processes and regulatory registration of third-party manufacturing facilities; licensing fees for the Company’s product candidates; and other outside expenses. The Company has certain collaboration agreements pursuant to which it shares or has shared research and development expenses related to linaclotide. The Company records expenses incurred under such linaclotide collaboration arrangements as research and development expense. Prior to the execution of the Amended AstraZeneca Agreement in September 2019, under the Company’s collaboration agreement with AstraZeneca for China (including Hong Kong and Macau), the Company was reimbursed for certain research and development expenses and it netted these reimbursements against its research and development expenses as incurred. Under the Company’s collaboration agreement with Allergan for North America, the Company is reimbursed for certain research and development expenses and nets these reimbursements against its research and development expenses as incurred. Amounts owed to Allergan or AstraZeneca under the Company’s respective collaboration agreements were recorded as incremental research and development expense. Nonrefundable advance payments for research and development activities are capitalized and expensed over the related service period or as goods are received. In connection with the execution of the Amended AstraZeneca Agreement, AstraZeneca is fully responsible for all research and development costs incurred related to the development, manufacture, and commercialization of linaclotide in ​
Restructuring Expenses	Restructuring Expenses The Company records costs and liabilities associated with exit and disposal activities in accordance with ASC 420, Exit or Disposal Cost Obligations . Such costs are based on estimates of fair value in the period liabilities are incurred. The Company evaluates and adjusts these costs as appropriate for changes in circumstances as additional information becomes available.
Selling, General and Administrative Expenses	Selling, General and Administrative Expenses The Company expenses selling, general and administrative costs to operations as incurred. Selling, general and administrative expenses consist primarily of compensation, benefits and other employee-related expenses for personnel in the Company’s administrative, finance, legal, information technology, business development, commercial, sales, marketing, communications and human resource functions. Other costs include the legal costs of pursuing patent protection of the Company’s intellectual property, general and administrative related facility costs, insurance costs and professional fees for accounting, tax, consulting, legal and other services. Prior to the execution of the Amended AstraZeneca Agreement, the Company was reimbursed for certain selling, general and administrative expenses and the Company netted these reimbursements against the Company’s selling, general and administrative expenses as incurred. In connection with the Amended AstraZeneca Agreement, effective in September 2019, AstraZeneca will be fully responsible for all costs related to the development, manufacture, and commercialization of linaclotide in China (including Hong Kong and Macau). The Company includes Allergan’s selling, general and administrative cost-sharing payments in the calculation of the net profits and net losses from the sale of LINZESS in the U.S. and presents the net payment to or from Allergan as collaboration expense or collaborative arrangements revenue, respectively.
Share-Based Compensation Expense	Share-Based Compensation Expense The Company grants awards under its share-based compensation programs, including stock awards, restricted stock awards (“RSAs”), restricted stock units (“RSUs”), stock options, and shares issued under the Company’s employee stock purchase plan (“ESPP”). Share-based compensation is recognized as expense in the consolidated statements of operations based on the grant date fair value over the requisite service period, net of estimated forfeitures. The Company estimates the fair value of the stock option and ESPP shares using the Black-Scholes option-pricing model, which requires the use of subjective assumptions including volatility and expected term, among others. The fair value of stock awards, RSAs, and RSUs is based on the market value of the Company’s Class A Common Stock on the date of grant. For awards that vest based on service conditions, the Company uses a straight-line method to allocate compensation expense to reporting periods. For awards that contain performance conditions, the Company determines the appropriate amount to expense based on the anticipated achievement of performance targets, which requires judgement, including forecasting the achievement of future specified targets. The Company makes certain assumptions in order to value and record expense associated with awards made to employees and non-employees under our share-based compensation arrangements. Changes in these assumptions may lead to variability with respect to the amount of expense the Company recognizes in connection with share-based payments. The Company estimates forfeitures at the time of grant and revises those estimates in subsequent periods if actual forfeitures differ from those estimates. The Company estimates forfeitures over the requisite service period using historical forfeiture activity and records share-based compensation expense only for those awards that are expected to vest. Compensation expense related to modified awards is measured based on the fair value for the awards as of the modification date. Any incremental compensation expense arising from the excess of the fair value of the awards on the modification date compared to the fair value of the awards immediately before the modification date is recognized at the modification date or ratably over the requisite remaining service period, as appropriate. The Company records the expense for stock option grants subject to performance-based milestone vesting using the accelerated attribution method over the remaining service period when management determines that achievement of the milestone is probable. Management evaluates when the achievement of a performance-based milestone is probable based on the relative satisfaction of the performance conditions as of the reporting date. Compensation expense for discounted purchases under the ESPP is measured using the Black-Scholes model to compute the fair value of the lookback provision plus the purchase discount and is recognized as compensation expense over the offering period. While the assumptions used to calculate and account for share-based compensation awards represent management’s best estimates, these estimates involve inherent uncertainties and the application of management’s judgment. As a result, if revisions are made to the Company’s underlying assumptions and estimates, the Company’s share-based compensation expense could vary significantly from period to period.
Patent Costs	Patent Costs The Company incurred and recorded as operating expense legal and other fees related to patents of approximately $7.8 million, approximately $5.0 million, and approximately $3.5 million for the years ended December 31, 2019, 2018 and 2017, respectively. These costs were charged to selling, general and administrative expenses as incurred.
Contingent Consideration	Contingent Consideration In accordance with ASC Topic 805, Business Combinations
Net Income (Loss) Per Share	Net Income (Loss) Per Share The Company calculates basic net income (loss) per common share and diluted net income (loss) per common share by dividing the net income (loss) by the weighted average number of common shares outstanding during the period. Diluted net income (loss) per common share is computed by dividing net income (loss) by the diluted number of shares outstanding during the period. Except where the result would be antidilutive to net income (loss), diluted net income (loss) per common share is computed assuming the conversion of the 2022 Convertible Notes, the 2024 Convertible Notes and the 2026 Convertible Notes, the exercise of outstanding common stock options and the vesting of RSUs and RSAs (using the treasury stock method), as well as their related income tax effects. As of December 31, 2018, there were no longer any Class B common shares outstanding as all Class B common shares converted on a one-to-one basis to Class A common shares. Historically, the Company allocated undistributed earnings between the classes of common stock on a one-to-one basis when computing net income (loss) per share. As a result, historically, basic and diluted net income (loss) per Class A and Class B shares were equivalent.
Comprehensive Income (Loss)	Comprehensive Income (Loss) Comprehensive income (loss) is defined as the change in equity of a business enterprise during a period from transactions, and other events and circumstances from non-owner sources and consists of net income (loss) and changes in unrealized gains and losses on available-for-sale debt securities in the periods presented in the Company’s consolidated statements of comprehensive income (loss).
Subsequent Events	Subsequent Events The Company considers events or transactions that have occurred after the balance sheet date of December 31, 2019, but prior to the filing of the financial statements with the Securities and Exchange Commission (“SEC”) to provide additional evidence relative to certain estimates or to identify matters that require additional recognition or disclosure. Subsequent events have been evaluated through the filing of the financial statements accompanying this Annual Report on Form 10-K.
New Accounting Pronouncements	New Accounting Pronouncements From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (the “FASB”) or other standard setting bodies that are adopted by the Company as of the specified effective date. Except as set forth below, the Company did not adopt any new accounting pronouncements during the year ended December 31, 2019 that had a material effect on its consolidated financial statements. In June 2018, the FASB issued ASU No. 2018-07, Compensation—Stock Compensation (Topic 718) : Improvements to Nonemployee Share-Based Payment Accounting (“ASU 2018-07”) . ASU 2018-07 expands the scope of Topic 718 to include share-based payment transactions for acquiring goods and services from non-employees, and as a result, the accounting for share-based payments to non-employees will be substantially aligned. ASU 2018-07 is effective for fiscal years beginning after December 15, 2018, including interim periods within that fiscal year. Early adoption is permitted but not earlier than an entity’s adoption date of Topic 606. The Company adopted this standard during the three months ended March 31, 2019 . The adoption of ASU 2018-07 did not have a material impact on the Company’s financial position and results of operations. ​ In July 2018, the FASB issued ASU 2018-09, Codification Improvements (“ASU 2018-09”). The amendments in ASU 2018-09 affect a wide variety of Topics in the FASB codification and apply to all reporting entities within the scope of the affected accounting guidance. The Company has evaluated ASU 2018- 09 in its entirety and determined that the amendments related to Topic 718-740, Compensation—Stock Compensation—Income Taxes , are the only provisions that currently apply to the Company. The amendments in ASU 2018- 09 related to Topic 718-740, Compensation—Stock Compensation—Income Taxes , clarify that an entity should recognize excess tax benefits related to stock compensation transactions in the period in which the amount of the deduction is determined. The amendments in ASU 2018- 09 related to Topic 718-740 are effective for fiscal years beginning after December 15, 2018, with early adoption permitted. The Company adopted this standard during the three months ended March 31, 2019 . The adoption of this standard did not have a material impact on the Company’s financial position and results of operations. The Company adopted ASC 842 using the optional transition method outlined in ASU 2018-11 as of January 1, 2019. The adoption of ASC 842 resulted in the recognition of operating lease right-of-use assets of approximately $88.3 million and corresponding lease liabilities of approximately $94.9 million. In July 2019, the FASB issued ASU No. 2019-07, Disclosure Update and Simplification and Investment Company Reporting Modernization (“ASU 2019-07”). The update is intended to simplify disclosure requirements to reflect the amendments of various SEC disclosure requirements that the SEC determined were redundant, duplicative, overlapping, outdated or superseded and is effective upon issuance. The adoption of ASU 2019-07 did not have a material impact on the Company’s financial position, results of operations, or financial statement disclosures. ​ In June 2016, the FASB issued ASU No. 2016 -13, Measurement of Credit Losses on Financial Instruments (“ASU 2016-13”). ASU 2016-13 will change how companies account for credit losses for most financial assets and certain other instruments. For trade receivables, loans and held-to-maturity debt securities, companies will be required to recognize an allowance for credit losses rather than reducing the carrying value of the asset. Subsequent to the issuance of ASU 2016-13, the FASB issued ASU No. 2019-04, Codification Improvements to Topic 326, Financial Instruments—Credit Losses, Topic 815, Derivatives and Hedging, and Topic 825, Financial Instruments (“ASU 2019-04”), ASU No. 2019-05, Financial Instruments—Credit Losses (Topic 326): Targeted Transition Relief (“ASU 2019-05”), ASU No. 2019-10, Financial Instruments—Credit Losses (Topic 326), Derivatives and Hedging (Topic 815), and Leases (Topic 842): Effective Date (“ASU 2019-10”), and ASU No. 2019-11, Codification Improvements to Topic 326, Financial Instruments—Credit Losses (“ASU 2019-11”) to provide additional guidance on the adoption of ASU 2016-13. ASU 2019-04 added Topic 326, Financial Instruments—Credit Losses , and made several amendments to the codification, including modifying the accounting for available-for-sale debt securities. ASU 2019-05 provides targeted transition relief by providing an option to irrevocably elect the fair value option for certain financial assets previously measured at amortized cost basis. ASU 2016-13, ASU 2019-04, ASU 2019-05, ASU 2019-10, and ASU 2019-11 are effective for fiscal years beginning after December 15, 2019, including interim periods within those fiscal years. Early adoption is permitted. The Company does not expect the adoption of ASU 2016-13 and related amendments to have a material impact on the Company’s financial position and results of operations. ​ In January 2017, the FASB issued ASU No. 2017 -04, Intangibles—Goodwill and Other (Topic 350) (“ASU 2017-04”) to simplify the accounting for goodwill impairment by removing Step 2 of the goodwill impairment test. ASU 2017-04 is effective for fiscal years beginning after December 15, 2019. Early adoption is permitted. The Company does not expect the adoption of ASU 2017-04 to have a material impact on the Company’s financial position and results of operations. In August 2018, the FASB issued ASU No. 2018 -13, Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirement for Fair Value Measurement (“ASU 2018-13”) which amends the disclosure requirements for fair value measurements. The amendments in ASU 2018-13 are effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-13 may have on the Company’s financial position and results of operations. In August 2018, the FASB issued ASU No. 2018 -15, Intangibles—Goodwill and Other—Internal Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement that is a Service Contract (a consensus of the FASB Emerging Issues Task Force) (“ASU 2018-15”) which provides additional guidance on the accounting for costs of implementation activities performed in a cloud computing arrangement that is a service contract. ASU 2015-18 requires a customer in a cloud computing arrangement that is a service contract to follow the new internal-use software guidance to determine which implementation costs to capitalize as assets or expense as incurred. The new internal-use software guidance requires that certain costs incurred during the application development stage be capitalized and other costs incurred during the preliminary project and post-implementation stages be expensed as they are incurred. A customer’s accounting for the hosting component of the arrangement is not affected by this guidance. The amendments in ASU 2018-15 are effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-15 may have on the Company’s financial position and results of operations. In October 2018, the FASB issued ASU No. 2018 -17, Consolidation (Topic 810): Targeted Improvements to Related Party Guidance for Variable Interest Entities (“ASU 2018-17”). The update is intended to improve general purpose financial reporting by considering indirect interests held through related parties in common control arrangements on a proportional basis for determining whether fees paid to decision makers and service providers are variable interests. The amendments in ASU 2018-17 will be effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-17 may have on the Company’s financial position and results of operations. In December 2019, the FASB issued ASU No. 2019-12, Income Taxes (Topic 740): Simplifying the Accounting for Income Taxes , No other accounting standards known by the Company to be applicable to it that have been issued by the FASB or other standard-setting bodies and that do not require adoption until a future date are expected to have a material impact on the Company’s consolidated financial statements upon adoption.

Summary of Significant Accoun_2

Summary of Significant Accounting Policies (Tables)	12 Months Ended
	Dec. 31, 2019
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Schedule of percentages of revenue and accounts receivable recognized from significant customers	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accounts ​ Revenue ​ ​ December 31, ​ Year Ended December 31, ​ 2019 2018 2019 2018 2017 Collaborative Partner: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Allergan (North America and Europe) 90 % 72 % 78 % 77 % 88 % Astellas (Japan) 8 % 26 % 13 % 20 % 10 %
Schedule of estimated useful life	​ ​ ​ ​ ​ ​ Estimated Useful Life Asset Description (In Years) Manufacturing equipment 10 ​ Laboratory equipment 5 ​ Computer and office equipment 3 ​ Furniture and fixtures 7 ​ Software 3 ​

Cyclerion Separation (Tables)

Cyclerion Separation (Tables)	12 Months Ended
	Dec. 31, 2019
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Summary of assets and liabilities transferred in separation	​ ​ ​ ​ ​ ​ ​ ​ ​ As of April 1, 2019 ​ Assets: ​ ​ ​ ​ Prepaid expenses and other current assets ​ $ 1,169 ​ Property and equipment, net ​ ​ 10,241 ​ Other assets ​ ​ 21 ​ ​ ​ $ 11,431 ​ Liabilities: ​ ​ ​ ​ Accrued research and development costs ​ $ 5,673 ​ Accrued expenses and other current liabilities ​ ​ 3,149 ​ ​ ​ $ 8,822 ​ Net Assets Transferred to Cyclerion ​ $ 2,609 ​
Summary of the discontinued operations	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Costs and expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Research and development ​ ​ 21,792 ​ 65,443 ​ 60,083 ​ Selling, general and administrative ​ ​ 15,646 ​ 21,615 ​ 1,939 ​ Restructuring expenses ​ ​ — ​ ​ 1,164 ​ ​ — ​ Net loss from discontinued operations ​ $ 37,438 ​ $ 88,222 ​ $ 62,022 ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ Prepaid expenses and other current assets ​ $ 847 Property and equipment, net ​ ​ 9,618 Other assets ​ ​ 25 ​ ​ $ 10,490 Liabilities: ​ ​ ​ Accounts payable ​ $ 3,232 Accrued research and development costs ​ ​ 5,256 Accrued expenses and other current liabilities ​ ​ 7,251 ​ ​ $ 15,739

Net Income (Loss) Per Share (Ta

Net Income (Loss) Per Share (Tables)	12 Months Ended
	Dec. 31, 2019
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Schedule of computation of basic and diluted net loss per common share	The following table sets forth the computation of basic and diluted net income (loss) per common share (in thousands, except per share amounts), which is computed by dividing net (income) loss by the weighted average number of common shares outstanding during the period: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Numerator: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Net income (loss) ​ $ 21,505 ​ $ (282,368) ​ $ (116,937) ​ Denominator: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average number of common shares outstanding used in net income (loss) per share — basic and diluted ​ 156,023 ​ 152,634 ​ 148,993 ​ Net income (loss) per share — basic and diluted ​ $ 0.14 ​ $ (1.85) ​ $ (0.78) ​
Schedule of potentially dilutive securities that have been excluded from computation of diluted weighted average shares outstanding	The following potentially dilutive securities have been excluded from the computation of diluted weighted average shares outstanding, as applicable, as their effect would be anti-dilutive (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Options to purchase Class A Common Stock 17,194 20,457 21,086 ​ Shares subject to repurchase 182 65 62 ​ Restricted stock units ​ 3,207 ​ 3,058 ​ 2,277 ​ Note Hedge Warrants ​ 8,318 ​ 20,250 ​ 20,250 ​ 2022 Convertible Notes ​ 8,318 ​ 20,250 ​ 20,250 ​ 2024 Convertible Notes ​ 14,934 ​ — ​ — ​ 2026 Convertible Notes ​ 14,934 ​ — ​ — ​ ​ 67,087 64,080 63,925 ​

Collaboration, License, Co-Pr_2

Collaboration, License, Co-Promotion and Other Commercial Agreements (Tables)	12 Months Ended
	Dec. 31, 2019
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Schedule of revenue attributable to transactions from collaboration and license arrangements	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, Collaborative Arrangements Revenue 2019 2018 2017 Linaclotide Collaboration Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Allergan (North America) ​ $ 327,591 $ 266,177 $ 260,210 ​ Allergan (Europe and other) ​ ​ 1,718 ​ ​ 1,146 ​ ​ 617 ​ AstraZeneca (China, including Hong Kong and Macau) ​ ​ 32,628 ​ — ​ 208 ​ Astellas (Japan) ​ ​ 10,147 ​ — ​ — ​ Co-Promotion and Other Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Exact Sciences (COLOGUARD) (1) ​ ​ — ​ ​ — ​ ​ 2,544 ​ Allergan (VIBERZI) ​ ​ 3,723 ​ ​ 4,290 ​ ​ 1,535 ​ Alnylam (GIVLAARI) ​ ​ 2,000 ​ ​ — ​ ​ — ​ Other ​ ​ 1,845 ​ ​ 1,226 ​ ​ 419 ​ Total collaborative arrangements revenue ​ $ 379,652 ​ $ 272,839 ​ $ 265,533 ​ Sale of API ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Linaclotide License Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Astellas (Japan) ​ $ 45,788 ​ $ 69,599 ​ $ 29,682 ​ AstraZeneca (China, including Hong Kong and Macau) ​ ​ 2,973 ​ ​ — ​ ​ — ​ Other (2) ​ ​ — ​ ​ 756 ​ ​ — ​ Total sale of API ​ $ 48,761 ​ $ 70,355 ​ $ 29,682 ​ (1) In August 2016, the Company terminated the Co-Promotion Agreement for COLOGUARD with Exact Sciences Corp. Under the terms of the agreement, the Company continued to receive royalty payments through July 2017. (2) During the year ended December 31, 2018, the Company recorded approximately $0.8 million in revenue related to the sale of API to Allergan, separate from its existing revenue agreements.
Allergan
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Schedule of revenue attributable to transactions from collaboration and license arrangements	The Company recognized collaborative arrangements revenue from the Allergan collaboration agreement for North America during the years ended December 31, 2019, 2018 and 2017 as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Collaborative arrangements revenue related to sales of LINZESS in the U.S. ​ $ 325,429 ​ $ 264,243 $ 256,238 ​ Royalty revenue ​ 2,162 ​ 1,934 ​ 2,295 ​ Other (1) ​ ​ — ​ ​ — ​ ​ 1,677 ​ Total collaborative arrangements revenue ​ $ 327,591 ​ $ 266,177 ​ $ 260,210 ​ (1) Includes net profit share adjustments of approximately $1.7 million recorded during the year ended December 31, 2017 related to a change in estimated selling expenses previously recorded.
Schedule of amount recorded by the Company for share of net loss related to collaborative arrangement	The following table presents the amounts recorded by the Company for commercial efforts related to LINZESS in the U.S. in the years ended December 31, 2019, 2018 and 2017 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Collaborative arrangements revenue related to sales of LINZESS in the U.S. (1)(2) ​ $ 325,429 ​ $ 264,243 ​ $ 256,238 ​ Selling, general and administrative costs incurred by the Company (1) ​ (38,123) ​ (42,435) ​ ​ (41,252) ​ The Company’s share of net profit ​ $ 287,306 ​ $ 221,808 ​ $ 214,986 ​ (1) Includes only collaborative arrangements revenue or selling, general and administrative costs attributable to the cost-sharing arrangement with Allergan. Excludes approximately $2.4 million, approximately $2.2 million, and approximately $0.9 million for the years ended December 31, 2019, 2018 and 2017, respectively, related to patent prosecution and patent litigation costs recognized in connection with the collaboration agreement with Allergan. (2) Certain of the unfavorable adjustments to the Company’s share of the LINZESS net profits were reduced or eliminated in connection with the co-promotion activities under the Company’s agreement with Allergan to co-promote VIBERZI in the U.S., as described below in Agreement with Allergan for VIBERZI .

Fair Value of Financial Instr_2

Fair Value of Financial Instruments (Tables)	12 Months Ended
	Dec. 31, 2019
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Schedule of assets and liabilities measured at fair value on a recurring basis	The following tables present the assets and liabilities the Company has measured at fair value on a recurring basis (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements at Reporting Date Using ​ ​ ​ Quoted Prices in Significant Other Significant ​ ​ ​ ​ ​ Active Markets for ​ Observable ​ Unobservable ​ ​ December 31, ​ Identical Assets ​ Inputs ​ Inputs ​ ​ 2019 ​ (Level 1) ​ (Level 2) ​ (Level 3) ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 139,190 ​ $ 139,190 ​ $ — ​ $ — ​ Repurchase agreements ​ ​ 37,800 ​ ​ 37,800 ​ ​ — ​ ​ — ​ Restricted cash: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ ​ 2,221 ​ ​ 2,221 ​ ​ — ​ ​ — ​ Convertible Note Hedges ​ ​ 31,366 ​ ​ — ​ ​ — ​ ​ 31,366 ​ Total assets measured at fair value ​ $ 210,577 ​ $ 179,211 ​ $ — ​ $ 31,366 ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Note Hedge Warrants ​ $ 24,260 ​ $ — ​ $ — ​ $ 24,260 ​ Total liabilities measured at fair value ​ $ 24,260 ​ $ — ​ $ — ​ $ 24,260 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements at Reporting Date Using ​ ​ ​ Quoted Prices in Significant Other Significant ​ ​ ​ ​ ​ Active Markets for ​ Observable ​ Unobservable ​ ​ December 31, ​ Identical Assets ​ Inputs ​ Inputs ​ ​ 2018 ​ (Level 1) ​ (Level 2) ​ (Level 3) ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 142,218 ​ $ 142,218 ​ $ — ​ $ — ​ Repurchase agreements ​ ​ 30,875 ​ ​ 30,875 ​ ​ — ​ ​ — ​ Convertible Note Hedges ​ ​ 41,020 ​ ​ — ​ ​ — ​ ​ 41,020 ​ Total assets measured at fair value ​ $ 214,113 ​ $ 173,093 ​ $ — ​ $ 41,020 ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Note Hedge Warrants ​ $ 33,763 ​ $ — ​ $ — ​ $ 33,763 ​ Contingent Consideration ​ ​ 51 ​ ​ — ​ ​ — ​ ​ 51 ​ Total liabilities measured at fair value ​ $ 33,814 ​ $ — ​ $ — ​ $ 33,814 ​
Schedule of assumptions used in fair market valuations	The following inputs were used in the fair market valuation of the Convertible Note Hedges and Note Hedge Warrants as of December 31, 2019 and 2018: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended ​ Year Ended ​ ​ ​ December 31, ​ December 31, ​ ​ 2019 ​ 2018 ​ ​ ​ Convertible Note Hedge ​ Convertible Note Hedge ​ ​ Note Hedges ​ Warrants Note Hedges ​ Warrants Risk-free interest rate (1) ​ ​ 1.6 % ​ 1.6 % ​ 2.5 % ​ 2.5 % Expected term ​ 2.5 ​ 3.0 ​ ​ 3.5 ​ 4.1 ​ Stock price (2) ​ $ 13.31 ​ $ 13.31 ​ $ 10.36 ​ $ 10.36 ​ Strike price (3) ​ $ 14.51 ​ $ 18.82 ​ $ 16.58 ​ $ 21.50 ​ Common stock volatility (4) ​ ​ 49.1 % ​ 46.5 % ​ 43.8 % ​ 43.6 % Dividend yield (5) ​ — % — % — % — % (1) Based on U.S. Treasury yield curve, with terms commensurate with the terms of the Convertible Note Hedges and the Note Hedge Warrants. (2) The closing price of the Company’s Class A Common Stock on the last trading days of the years ended December 31, 2019 and 2018, respectively. (3) As per the respective agreements for the Convertible Note Hedges and Note Hedge Warrants. The strike prices for the Convertible Note Hedges and Note Hedge Warrants were adjusted in conjunction with the conversion rate adjustment in April 2019 (Note 12). (4) Expected volatility based on historical volatility of the Company’s Class A Common Stock. (5) The Company has not paid and does not anticipate paying cash dividends on its shares of common stock in the foreseeable future; therefore, the expected dividend yield is assumed to be zero . ​
Schedule of the change in Level 3 convertible note derivatives	The following table reflects the change in the Company's Level 3 Convertible Note Hedges and Note Hedge Warrants from December 31, 2017 through December 31, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Convertible ​ Note Hedge ​ ​ Note Hedges Warrants Balance at December 31, 2017 ​ $ 108,188 ​ $ (92,188) ​ Change in fair value, recorded as a component of gain (loss) on derivatives ​ ​ (67,168) ​ ​ 58,425 ​ Balance at December 31, 2018 ​ $ 41,020 ​ $ (33,763) ​ Cash settlement (received) paid upon early termination of derivatives ​ ​ (28,909) ​ ​ 25,735 ​ Change in fair value, recorded as a component of gain (loss) on derivatives ​ ​ 19,255 ​ ​ (16,232) ​ Balance at December 31, 2019 ​ $ 31,366 ​ $ (24,260) ​
Schedule of changes in contingent consideration payable	The following table reflects the change in the Company’s Level 3 contingent consideration payable from December 31, 2017 through December 31, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ Contingent ​ Consideration Fair Value at December 31, 2017 $ 31,258 ​ Changes in fair value ​ (31,045) ​ Payments/transfers to accrued expenses and other current liabilities ​ (162) ​ Fair Value at December 31, 2018 ​ ​ 51 ​ Payments ​ ​ (51) ​ Fair value at December 31, 2019 $ — ​

Inventory (Tables)

Inventory (Tables)	12 Months Ended
	Dec. 31, 2019
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Schedule of Inventory	Inventory consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ 2019 2018 ​ Raw Materials ​ $ 65 ​ $ — ​ Work in Progress ​ ​ 392 ​ ​ — ​ Finished Goods ​ $ 191 ​ $ — ​ ​ ​ $ 648 ​ $ — ​

Leases (Tables)

Leases (Tables)	12 Months Ended
	Dec. 31, 2019
Table Text Blocks
Schedule of components of lease cost and supplemental cash flow information	Lease cost is recognized on a straight-line basis over the lease term. The components of lease cost for the year ended December 31, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ Year Ended ​ ​ December 31, ​ ​ 2019 Operating lease cost during period, net (1) ​ $ 16,452 Variable lease payments ​ ​ 1,526 Short-term lease cost ​ ​ 1,512 Total lease cost ​ $ 19,490 ​ (1) Operating lease cost is presented net of approximately $0.3 million of sublease income for the year ended December 31, 2019. Sublease income related to a sublease agreement between Ironwood and Cyclerion executed upon Separation. The sublease agreement terminated in May 2019. ​ Supplemental cash flow information related to leases for the periods reported is as follows: ​ ​ ​ ​ ​ ​ ​ ​ Year Ended ​ ​ December 31, ​ ​ 2019 Right-of-use assets obtained in exchange for new operating lease upon adoption of ASC 842 (in thousands) ​ $ 88,299 ​ Adjustment to right-of-use assets as a result of the lease modification at the Separation date (in thousands) ​ ​ (40,427) ​ Adjustment to right-of-use assets as a result of the termination of the Binney Street Lease (in thousands) ​ ​ (34,440) ​ Right-of-use assets obtained in exchange for new operating lease liabilities (1) ​ ​ 18,452 ​ Cash paid for amounts included in the measurement of lease liabilities (in thousands) ​ ​ 18,598 ​ Weighted-average remaining lease term of operating leases (in years) ​ ​ 10.2 ​ Weighted-average discount rate of operating leases ​ ​ 5.8 % (1) Relates to right-of-use assets and operating lease liabilities for the Summer Street Lease. ​
Schedule of future minimum lease payments under non-cancelable operating leases - ASC 842	Future minimum lease payments under non-cancelable operating leases under ASC 842 as of December 31, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ Operating ​ Lease ​ ​ Payments 2020 ​ $ 1,146 2021 ​ ​ 3,128 2022 ​ ​ 3,129 2023 ​ ​ 3,065 2024 ​ 3,126 2025 and thereafter ​ 18,044 Total future minimum lease payments ​ ​ 31,638 Less: present value adjustment ​ ​ 8,410 Operating lease liabilities at December 31, 2019 ​ ​ 23,228 Less: current portion of operating lease liabilities ​ ​ 1,146 Operating lease liabilities, net of current portion ​ $ 22,082
Schedule of future minimum lease payments under non-cancelable operating leases - ASC 840	At December 31, 2018, future minimum lease payments under non-cancelable leases under ASC 840 were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ Operating ​ Lease ​ ​ Payments 2019 ​ $ 18,736 2020 ​ ​ 18,312 2021 ​ ​ 18,863 2022 ​ ​ 19,365 2023 ​ ​ 19,818 2024 and thereafter ​ 22,118 Total future minimum lease payments ​ $ 117,212

Property and Equipment (Tables)

Property and Equipment (Tables)	12 Months Ended
	Dec. 31, 2019
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Schedule of property and equipment	Property and equipment, net consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 2019 2018 Software ​ $ 9,568 ​ $ 10,976 ​ Leasehold improvements ​ 7,318 ​ 12,472 ​ Laboratory equipment ​ 2,193 ​ 1,597 ​ Furniture and fixtures ​ 1,508 ​ 1,845 ​ Computer and office equipment ​ 1,293 ​ 2,737 ​ Construction in process ​ 631 ​ 115 ​ Manufacturing equipment ​ ​ — ​ ​ 3,748 ​ ​ ​ 22,511 ​ 33,490 ​ Less accumulated depreciation and amortization ​ (10,082) ​ (25,838) ​ ​ ​ $ 12,429 ​ $ 7,652 ​

Accrued Expenses and Other Cu_2

Accrued Expenses and Other Current Liabilities (Tables)	12 Months Ended
	Dec. 31, 2019
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Schedule of accrued expenses and other current liabilities	Accrued expenses and other current liabilities consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 2019 2018 Salaries ​ $ 2,973 ​ $ 3,054 ​ Accrued vacation ​ ​ 2,540 ​ ​ 3,493 ​ Accrued incentive compensation ​ ​ 11,760 ​ ​ 13,867 ​ Other employee benefits ​ ​ 1,260 ​ ​ 1,883 ​ Professional fees ​ 1,421 ​ 1,735 ​ Accrued interest ​ 301 ​ 873 ​ Restructuring liabilities ​ ​ 179 ​ ​ 2,885 ​ Other ​ 10,031 ​ 10,211 ​ ​ ​ $ 30,465 ​ $ 38,001 ​

Notes Payable (Tables)

Notes Payable (Tables)	12 Months Ended
	Dec. 31, 2019
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Schedule of outstanding Convertible Note	The Company’s outstanding balances for the convertible senior notes as of December 31, 2019 and 2018 consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ ​ 2019 ​ 2018 ​ Liability component: ​ ​ ​ ​ ​ ​ Principal: ​ ​ ​ ​ ​ 2022 Convertible Notes ​ $ 120,699 ​ $ 335,699 ​ 2024 Convertible Notes ​ ​ 200,000 ​ ​ — ​ 2026 Convertible Notes ​ ​ 200,000 ​ ​ — ​ Less: unamortized debt discount ​ ​ (104,700) ​ ​ (65,094) ​ Less: unamortized debt issuance costs ​ ​ (8,005) ​ ​ (5,004) ​ Net carrying amount ​ $ 407,994 ​ $ 265,601 ​ Equity component: ​ ​ ​ ​ ​ ​ ​ 2022 Convertible Notes ​ ​ 19,807 ​ ​ 114,199 ​ 2024 Convertible Notes ​ ​ 41,152 ​ ​ — ​ 2026 Convertible Notes ​ ​ 51,350 ​ ​ — ​ Total equity component ​ $ 112,309 ​ $ 114,199 ​
Schedule of interest expense related to Convertible Notes	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended ​ ​ December 31, ​ 2019 2018 ​ 2017 Contractual interest expense ​ $ 7,361 ​ $ 7,553 ​ $ 7,553 Amortization of debt issuance costs ​ ​ 1,190 ​ ​ 971 ​ ​ 806 Amortization of debt discount ​ ​ 17,683 ​ ​ 15,437 ​ ​ 14,145 Total interest expense ​ $ 26,234 ​ $ 23,961 ​ $ 22,504
Schedule of future minimum payments details of debt	​ ​ ​ ​ ​ 2020 ​ $ 7,216 2021 ​ ​ 7,216 2022 ​ ​ 126,556 2023 ​ ​ 4,500 2024 ​ ​ 203,750 2025 and Thereafter ​ ​ 204,500 Total future minimum payments under the convertible senior notes ​ 553,738 Less: amounts representing interest ​ ​ (33,039) Less: unamortized debt discount ​ ​ (104,700) Less: unamortized debt issuance costs ​ ​ (8,005) Convertible senior notes balance ​ $ 407,994 ​

Employee Stock Benefit Plans (T

Employee Stock Benefit Plans (Tables)	12 Months Ended
	Dec. 31, 2019
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Summary of expense recognized for share-based compensation arrangements	The following table summarizes share-based compensation expense (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Employee stock options ​ $ 12,526 ​ $ 20,478 ​ $ 19,331 ​ Restricted stock units ​ ​ 15,488 ​ ​ 17,160 ​ ​ 7,646 ​ Restricted stock awards ​ 2,095 ​ 2,330 ​ 2,441 ​ Non-employee stock options ​ — ​ — ​ 301 ​ Employee stock purchase plan ​ 1,115 ​ 1,097 ​ 1,172 ​ Stock award ​ 54 ​ 17 ​ 14 ​ ​ ​ $ 31,278 ​ $ 41,082 ​ $ 30,905 ​
Share-based compensation expense reflected in the condensed consolidated statements of operations	The following table summarizes the expenses reflected in the consolidated statements of operations as follows for the years ended December 31, 2019, 2018 and 2017 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years Ended December 31, ​ 2019 2018 2017 Research and development ​ $ 6,343 ​ $ 11,500 ​ $ 9,853 ​ Selling, general and administrative ​ 24,281 ​ 27,440 ​ 21,052 ​ Restructuring expenses ​ ​ 654 ​ ​ 2,142 ​ ​ — ​ ​ ​ $ 31,278 ​ $ 41,082 ​ $ 30,905 ​
Summary of the unvested shares of restricted stock	A summary of restricted stock activity for the year ended December 31, 2019 is presented below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ Average ​ ​ Number of ​ Grant Date ​ ​ Shares ​ Fair Value (1) Unvested as of December 31, 2018 64,896 ​ $ 18.58 ​ Granted 198,523 ​ $ 10.96 ​ Vested (65,547) ​ $ 17.18 ​ Forfeited (16,224) ​ $ 18.58 ​ Unvested as of December 31, 2019 181,648 ​ $ 10.76 ​ (1) Prior period amounts have not been retrospectively adjusted to reflect the effect of the Separation on the Company’s stock price.
Schedule of weighted-average assumptions used to estimate the fair value of the stock options using the Black-Scholes option-pricing model	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended ​ ​ ​ December 31, ​ ​ ​ 2019 ​ 2018 ​ 2017 ​ Expected volatility ​ 46.3 % 43.7 % 45.8 % Expected term (in years) ​ 6.1 ​ 6.0 ​ 6.0 ​ Risk-free interest rate ​ 2.5 % 2.7 % 2.0 % Expected dividend yield ​ — % — % — %
Summary of RSU activity	A summary of RSU activity for the year ended December 31, 2019 is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ ​ Average ​ ​ ​ Number ​ Grant Date ​ ​ of Shares Fair Value (1) Unvested as of December 31, 2018 3,057,808 ​ $ 15.53 ​ Granted ​ 3,097,661 ​ ​ 12.11 ​ Vested ​ (1,298,536) ​ ​ 15.38 ​ Forfeited ​ (1,649,844) ​ ​ 13.84 ​ Unvested as of December 31, 2019 3,207,089 ​ $ 12.33 ​ (1) Prior period amounts have not been retrospectively adjusted to reflect the effect of the Separation on the Company’s stock price.
Summary of stock option activity	The following table summarizes stock option activity under the Company’s share-based compensation plans, including performance-based options: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Shares of ​ ​ ​ ​ ​ ​ Common ​ Weighted- ​ Weighted- ​ ​ ​ ​ ​ Stock ​ Average ​ Average ​ Aggregate ​ ​ Attributable ​ Exercise ​ Contractual ​ Intrinsic ​ ​ to Options ​ Price (1) ​ Life ​ Value ​ ​ ​ ​ ​ ​ ​ (in years) ​ (in thousands) Outstanding at December 31, 2018 20,457,537 ​ $ 13.47 5.80 ​ $ 4,147 ​ Granted 5,743,167 ​ $ 11.71 ​ — ​ $ — ​ Exercised (1,369,327) ​ $ 8.33 ​ — ​ $ — ​ Cancelled (7,637,138) ​ $ 12.32 ​ — ​ $ — ​ Outstanding at December 31, 2019 17,194,239 ​ $ 12.13 ​ 5.11 ​ $ 25,226 ​ Vested or expected to vest at December 31, 2019 16,729,428 ​ $ 12.13 ​ 5.01 ​ $ 24,590 ​ Exercisable at December 31, 2019 14,030,936 ​ $ 12.07 ​ 4.33 ​ $ 21,423 ​ (1) Prior period amounts have not been retrospectively adjusted to reflect the effect of the Separation on the exercise price of the Company’s stock options.
Schedule of unrecognized share-based compensation expense, net of estimated forfeitures by type of awards and weighted-average period	​ ​ ​ ​ ​ ​ ​ ​ ​ Unrecognized Weighted-Average ​ ​ Expense, Net ​ Remaining ​ ​ of Estimated ​ Recognition ​ ​ ​ Forfeitures ​ Period ​ ​ (in thousands) ​ (in years) Type of award: ​ ​ ​ ​ ​ ​ Stock options with time-based vesting ​ $ 13,849 2.63 ​ Restricted stock awards ​ ​ 758 0.41 ​ Restricted stock units ​ ​ 24,469 2.45 ​ Stock options with time-based and performance-based vesting (1) ​ ​ 147 — ​ (1) The weighted-average remaining recognition period cannot be determined for performance-based or time-accelerated options due to the nature of such awards, as detailed above.

Income Taxes (Tables)

Income Taxes (Tables)	12 Months Ended
	Dec. 31, 2019
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Reconciliation of income taxes from continuing operations computed using U.S. federal statutory rate to that reflected in operations	A reconciliation of income taxes computed using the U.S. federal statutory rate to that reflected in operations follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 2017 Income tax benefit using U.S. federal statutory rate ​ $ 4,517 ​ $ (59,297) ​ $ (39,759) ​ Effect of U.S. tax reform ​ ​ — ​ ​ — ​ ​ 153,894 ​ Permanent differences ​ 65 ​ 218 ​ 34 ​ State income taxes, net of federal benefit ​ (1,902) ​ (17,121) ​ (6,117) ​ Disallowed Separation related costs ​ ​ 4,658 ​ ​ — ​ ​ — ​ Executive compensation - Section 162(m) ​ ​ 662 ​ ​ 8 ​ ​ — ​ Meals and entertainment ​ ​ 495 ​ ​ 995 ​ ​ 1,346 ​ Non-deductible share-based compensation ​ (1,202) ​ (494) ​ 9 ​ Excess tax benefits ​ ​ 3,324 ​ ​ (1,223) ​ ​ (2,626) ​ Fair market valuation of Note Hedge Warrants and Convertible Note Hedges ​ ​ (290) ​ ​ 2,367 ​ ​ 1,289 ​ Tax credits ​ (4,374) ​ (7,863) ​ (12,290) ​ Expiring net operating losses and tax credits ​ 3,764 ​ 250 ​ 276 ​ Effect of change in state tax rate on deferred tax assets and deferred tax liabilities ​ (2,563) ​ 1,476 ​ (232) ​ Change in the valuation allowance ​ (7,154) ​ 80,684 ​ (95,824) ​ ​ ​ $ — ​ $ — ​ $ — ​
Schedule of components of deferred tax assets and liabilities	Components of the Company’s deferred tax assets and liabilities are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2019 2018 Deferred tax assets: ​ ​ ​ ​ ​ ​ ​ Net operating loss carryforwards ​ $ 265,494 ​ $ 259,450 ​ Tax credit carryforwards ​ 59,892 ​ 60,115 ​ Capitalized research and development ​ 9,952 ​ 12,113 ​ Contingent consideration ​ ​ — ​ ​ 14 ​ Share-based compensation ​ ​ 24,401 ​ ​ 23,242 ​ Basis difference on North America collaboration agreement ​ ​ 48,594 ​ ​ 36,423 ​ Accruals and reserves ​ ​ 6,415 ​ ​ 10,867 ​ Basis difference on 2022 Convertible Notes ​ ​ 4,322 ​ ​ 7,220 ​ Interest expense ​ ​ 22,020 ​ ​ 5,104 ​ Intangibles ​ ​ — ​ ​ 25,928 ​ Operating lease liability ​ ​ 6,421 ​ ​ — ​ Other ​ 5,295 ​ 18,867 ​ Total deferred tax assets ​ 452,806 ​ 459,343 ​ Deferred tax liabilities: ​ ​ ​ ​ ​ ​ ​ Basis Difference on 2024 Convertible Notes ​ ​ (7,381) ​ ​ — ​ Basis Difference on 2026 Convertible Notes ​ ​ (10,276) ​ ​ — ​ Operating lease right-of-use assets ​ ​ (4,905) ​ ​ — ​ Total deferred tax liabilities ​ ​ (22,562) ​ ​ — ​ Net deferred tax asset ​ ​ 430,244 ​ ​ 459,343 ​ Valuation allowance ​ (430,244) ​ (459,343) ​ Net deferred tax asset ​ $ — ​ $ — ​
Summary of changes in the unrecognized tax benefits	The following table summarizes the changes in the Company’s unrecognized income tax benefits for the years ended December 31, 2019, 2018 and 2017 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ ​ 2019 ​ 2018 ​ 2017 ​ Balance at the beginning of the period ​ $ 38,551 ​ $ 24,078 ​ $ 26,393 ​ Increases based on tax positions related to the current period ​ ​ 51,699 ​ ​ 38,551 ​ ​ 24,078 ​ Increases for tax positions related to prior periods ​ ​ 1,400 ​ ​ — ​ ​ — ​ Decreases for tax positions in prior periods ​ ​ (38,551) ​ ​ (24,078) ​ ​ (26,393) ​ Balance at the end of the period ​ $ 53,099 ​ $ 38,551 ​ $ 24,078 ​

Workforce Reduction (Tables)

Workforce Reduction (Tables)	12 Months Ended
	Dec. 31, 2019
Table Text Blocks
Schedule of charges made to the reduction in field-based workforce	The following table summarizes the accrued liabilities activity recorded in connection with the reduction in workforce for the year ended December 31, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ Accrued at ​ ​ ​ ​ ​ ​ ​ ​ ​ Accrued at ​ ​ December 31, 2018 Charges ​ Amount Paid ​ Adjustments ​ December 31, 2019 ​ Employee severance, benefits and related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 2018 Reduction $ 696 ​ $ 16 ​ $ (689) ​ $ (23) ​ $ — ​ August 2018 Reduction ​ 1,756 ​ ​ — ​ ​ (1,708) ​ ​ (48) ​ ​ — ​ February 2019 Reduction ​ — ​ ​ 3,182 ​ ​ (2,968) ​ ​ (139) ​ ​ 75 ​ Total $ 2,452 ​ $ 3,198 ​ $ (5,365) ​ $ (210) ​ $ 75 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contract related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ August 2018 Reduction $ 433 ​ $ — ​ $ (287) ​ $ (42) ​ $ 104 ​ Total $ 433 ​ $ — ​ $ (287) ​ $ (42) ​ $ 104 ​ ​ The following table summarizes the accrued liabilities activity recorded in connection with the reduction in workforce for the year ended December 31, 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ Accrued at ​ ​ ​ ​ ​ ​ ​ ​ ​ Accrued at ​ ​ December 31, 2017 Charges ​ Amount Paid ​ Adjustments ​ December 31, 2018 ​ Employee severance, benefits and related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ January 2018 Reduction $ — ​ $ 2,228 ​ $ (2,215) ​ $ (13) ​ $ — ​ June 2018 Reduction ​ — ​ ​ 2,881 ​ ​ (2,074) ​ ​ (111) ​ ​ 696 ​ August 2018 Reduction ​ — ​ ​ 5,383 ​ ​ (3,522) ​ ​ (105) ​ ​ 1,756 ​ Total $ — ​ $ 10,492 ​ $ (7,811) ​ $ (229) ​ $ 2,452 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contract related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ August 2018 Reduction $ — ​ $ 1,265 ​ $ (614) ​ $ (218) ​ $ 433 ​ Total $ — ​ $ 1,265 ​ $ (614) ​ $ (218) ​ $ 433 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​

Selected Quarterly Financial _2

Selected Quarterly Financial Data (Unaudited) (Tables)	12 Months Ended
	Dec. 31, 2019
Table Text Blocks
Selected Quarterly Financial Data (Unaudited)	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ First ​ Second ​ Third ​ Fourth ​ Total ​ ​ Quarter ​ Quarter ​ Quarter ​ Quarter ​ Year ​ ​ (in thousands, except per share data) 2019 ​ ​ ​ ​ ​ Total revenues (1) ​ $ 68,730 ​ $ 102,215 ​ $ 131,167 ​ $ 126,301 ​ $ 428,413 ​ Total cost and expenses (2) ​ 85,663 ​ 80,638 ​ 65,280 ​ 76,709 ​ 308,290 ​ Other expense, net (3) ​ (4,912) ​ (9,294) ​ (45,239) ​ (1,735) ​ (61,180) ​ Net (loss) income from continuing operations ​ ​ (21,846) ​ ​ 12,283 ​ ​ 20,648 ​ ​ 47,858 ​ 58,943 ​ Net loss from discontinued operations (4) ​ ​ (37,438) ​ ​ — ​ ​ — ​ ​ — ​ (37,438) ​ Net (loss) income ​ (59,284) ​ 12,283 ​ 20,648 ​ 47,858 ​ 21,505 ​ Net (loss) income per share from continuing operations—basic ​ $ (0.14) ​ $ 0.08 ​ $ 0.13 ​ $ 0.31 ​ $ 0.38 ​ Net (loss) income per share from continuing operations—diluted ​ ​ (0.14) ​ ​ 0.08 ​ ​ 0.13 ​ ​ 0.30 ​ ​ 0.38 ​ Net loss per share from discontinued operations—basic and diluted ​ ​ (0.24) ​ ​ — ​ ​ — ​ ​ — ​ ​ (0.24) ​ Net (loss) income per share--basic ​ ​ (0.38) ​ ​ 0.08 ​ ​ 0.13 ​ ​ 0.31 ​ ​ 0.14 ​ Net (loss) income per share—diluted (5) ​ ​ (0.38) ​ ​ 0.08 ​ ​ 0.13 ​ ​ 0.30 ​ ​ 0.14 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ First ​ Second ​ Third ​ Fourth ​ Total ​ ​ Quarter ​ Quarter ​ Quarter ​ Quarter ​ Year ​ ​ (in thousands, except per share data) 2018 ​ ​ ​ ​ ​ Total revenues (6) ​ $ 69,155 ​ $ 81,106 ​ $ 65,686 ​ $ 130,692 ​ $ 346,639 ​ Total cost and expenses (7) ​ 88,438 ​ 95,783 ​ 212,257 ​ 100,831 ​ 497,309 ​ Other expense, net (8) ​ (7,276) ​ (9,460) ​ (5,252) ​ (21,488) ​ (43,476) ​ Net (loss) income from continuing operations ​ ​ (26,559) ​ ​ (24,137) ​ ​ (151,823) ​ ​ 8,373 ​ ​ (194,146) ​ Net loss from discontinued operations (4) ​ ​ (16,585) ​ ​ (25,243) ​ ​ (22,528) ​ ​ (23,866) ​ ​ (88,222) ​ Net loss ​ (43,144) ​ (49,380) ​ (174,351) ​ (15,493) ​ (282,368) ​ Net (loss) income per share from continuing operations—basic and diluted ​ ​ (0.18) ​ ​ (0.16) ​ ​ (0.99) ​ ​ 0.05 ​ ​ (1.27) ​ Net loss per share from discontinued operations—basic and diluted ​ ​ (0.11) ​ ​ (0.17) ​ ​ (0.15) ​ ​ (0.15) ​ ​ (0.58) ​ Net loss per share--basic and diluted ​ $ (0.29) ​ $ (0.32) ​ $ (1.14) ​ $ (0.10) ​ $ (1.85) ​ (1) Total revenues includes approximately $48.8 million of revenue from sales of linaclotide API to our linaclotide partners, primarily driven by the commercialization of linaclotide in Japan for the year ended December 31, 2019, as well as approximately $32.4 million related to the non-contingent payments from the Amended AstraZeneca Agreement and a $10.0 million upfront fee from the Amended Astellas License Agreement, both executed during the third quarter of 2019. (2) Total costs and expenses includes approximately $3.6 . million in restructuring expenses for the year ended December 31, 2019, as well as approximately $3.2 million related to the gain on lease modification in April 2019. (3) Other expense, net includes approximately $31.0 million in loss on extinguishment of debt related to the partial repurchase of the 2022 Convertible Notes and the redemption of the 2026 Notes, and approximately $3.0 million gain on fair value remeasurement of derivatives for the year ended December 31, 2019. (4) During the year ended December 31, 2019, the Company completed the Separation. Certain amounts related to Cyclerion have been reclassified as discontinued operations for the years ended December 31, 2019 and 2018. (5) Diluted earnings per share is equivalent to basic earnings per share for the year ended December 31, 2019. (6) Total revenue includes approximately $70.4 million of revenue from sales of linaclotide API to our linaclotide partners, primarily driven by the commercialization of linaclotide in Japan for the year ended December 31, 2018. (7) Total costs and expenses includes approximately $14.7 million in restructuring expenses for the year ended December 31, 2018, as well as approximately $151.8 million related to the impairment of intangible assets and approximately $31.0 million related to a gain on remeasurement of contingent consideration incurred during the third quarter of 2018 in connection with the exit of the Lesinurad License. (8) Other expense, net includes approximately $8.7 million loss on fair value remeasurement of derivatives for the year ended December 31, 2018.

Nature of Business - Non-cancel

Nature of Business - Non-cancelable Operating Lease (Details) ft² in Thousands	Jun. 11, 2019ft²
Summer Street Lease
Operating leases
Rentable area leased (in square feet)	39

Nature of Business - Notes Paya

Nature of Business - Notes Payable (Details) - USD ($) $ in Thousands	Aug. 31, 2019	Sep. 23, 2016	Aug. 31, 2019	Dec. 31, 2019	Dec. 31, 2017	Sep. 16, 2019	Aug. 12, 2019	Dec. 31, 2018	Jun. 30, 2015
Notes Payable
Loss on extinguishment of debt				$ 30,977	$ 2,009
Equity component of the partial repurchase of the 2022 Convertible Notes				(26,959)
Convertible Senior Notes
Notes Payable
Net proceed received			$ 391,000
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued				120,699				$ 335,699	$ 335,700
Stated interest rate (as a percent)						2.25%			2.25%
Fees and expenses									$ 11,700
Debt redeemed/repurchased	$ 215,000		215,000			$ 215,000
Debt redemption/repurchase price	227,300		227,300
Loss on extinguishment of debt	23,400		23,400
Initial debt issuance costs			2,800
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes
Notes Payable
Fees and expenses	9,000		9,000
0.75% Convertible Senior Notes due 2024 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued	200,000		200,000	200,000			$ 200,000
Stated interest rate (as a percent)							0.75%
1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued	200,000		200,000	200,000			$ 200,000
Stated interest rate (as a percent)							1.50%
8.375% Notes due 2026 | Notes Payable
Notes Payable
Aggregate principal amount of notes issued		$ 150,000		$ 150,000
Stated interest rate (as a percent)		8.375%		8.375%
Debt redeemed/repurchased	$ 116,500		$ 116,500			116,500
Debt redemption/repurchase price						$ 123,000
Loss on extinguishment of debt		$ 7,600		$ 31,000

Nature of Business - Accumulate

Nature of Business - Accumulated Deficit (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Accumulated deficit
Net income	$ 47,858	$ 20,648	$ 12,283	$ (59,284)	$ (15,493)	$ (174,351)	$ (49,380)	$ (43,144)	$ 21,505	$ (282,368)	$ (116,937)
Accumulated deficit since inception	$ 1,572,232				$ 1,591,128				$ 1,572,232	$ 1,591,128

Summary of Significant Accoun_3

Summary of Significant Accounting Policies - Segment Information (Details)	12 Months Ended
	Dec. 31, 2019segment
Segment Information
Number of reportable segments	1

Summary of Significant Accoun_4

Summary of Significant Accounting Policies - Cash and Cash Equivalents (Details) - USD ($) $ in Millions	Dec. 31, 2019	Dec. 31, 2018
Cash and Cash Equivalents
Cash Equivalent included in cash and cash equivalent	$ 177	$ 173.1

Summary of Significant Accoun_5

Summary of Significant Accounting Policies - Restricted Cash (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Restricted Cash [Abstract]
Restricted cash	$ 2,221	$ 7,676	$ 7,056
Withdrawal of Restricted cash	6,400
Restricted cash, current	1,250	1,250
Restricted cash, noncurrent	$ 971	$ 6,426

Summary of Significant Accoun_6

Summary of Significant Accounting Policies - Concentrations of Suppliers (Details)	12 Months Ended
	Dec. 31, 2019item
Supplier concentration
Concentrations
Number of third-party facilities	3

Summary of Significant Accoun_7

Summary of Significant Accounting Policies - Concentrations of Credit Risk (Details)	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Accounts receivable | Accounts receivable balances | Allergan
Concentrations
Concentration risk percentage (as a percent)	90.00%	72.00%
Accounts receivable | Accounts receivable balances | Astellas Pharma Inc.
Concentrations
Concentration risk percentage (as a percent)	8.00%	26.00%
Revenue | Revenue | Allergan
Concentrations
Concentration risk percentage (as a percent)	78.00%	77.00%	88.00%
Revenue | Revenue | Astellas Pharma Inc.
Concentrations
Concentration risk percentage (as a percent)	13.00%	20.00%	10.00%

Summary of Significant Accoun_8

Summary of Significant Accounting Policies - Property and Equipment (Details)	12 Months Ended
	Dec. 31, 2019
Manufacturing equipment
Property and Equipment
Estimated useful life	10 years
Laboratory equipment
Property and Equipment
Estimated useful life	5 years
Computer and office equipment
Property and Equipment
Estimated useful life	3 years
Furniture and fixtures
Property and Equipment
Estimated useful life	7 years
Software
Property and Equipment
Estimated useful life	3 years

Summary of Significant Accoun_9

Summary of Significant Accounting Policies - Finite Lived Intangible Assets (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2018USD ($)
Finite Lived Intangible Assets
Impairment of intangible assets	$ 151,794

Summary of Significant Accou_10

Summary of Significant Accounting Policies - Goodwill (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Goodwill
Impairment of goodwill	$ 0	$ 0	$ 0

Summary of Significant Accou_11

Summary of Significant Accounting Policies - Impairment of Long-Lived Assets (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Impairment of Long-Lived Assets
Significant impairment of long-lived assets	$ 0	$ 0	$ 0

Summary of Significant Accou_12

Summary of Significant Accounting Policies - Lease Cumulative Adjustment (Details) $ in Millions	Jan. 01, 2019USD ($)
Accounting Standards Update 2016-02
New Accounting Pronouncements
Cumulative effect of adoption of accounting standard	$ 0

Summary of Significant Accou_13

Summary of Significant Accounting Policies - Practical Expedients (Details)	12 Months Ended
	Dec. 31, 2019
Leases
Lease, Practical Expedients, Package	true
Lease, Practical Expedient, Lessor Single Lease Component	true

Summary of Significant Accou_14

Summary of Significant Accounting Policies - Revenue Recognition - Practical Expedients (Details)	12 Months Ended
	Dec. 31, 2019
Practical expedients
Practical Expedient, Incremental Cost	true
Practical Expedient, Use of Transaction Price	true
Practical Expedient, Nonrestatement of Modified Contract	true

Summary of Significant Accou_15

Summary of Significant Accounting Policies - Revenue Cumulative Adjustment (Details) $ in Millions	Dec. 31, 2019USD ($)
Accounting Standards Update 2014-09
New Accounting Pronouncements
Cumulative effect of adoption of accounting standard	$ 0

Summary of Significant Accou_16

Summary of Significant Accounting Policies - Revenue Recognition (Details)	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
U.S. | Allergan
Collaboration agreements
Percentage of the pre-tax net profit or loss (as a percent)	50.00%	50.00%

Summary of Significant Accou_17

Summary of Significant Accounting Policies - Patent Costs (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Patent Costs
Selling, general and administrative	$ 172,450	$ 219,676	$ 231,184
Patents
Patent Costs
Selling, general and administrative	$ 7,800	$ 5,000	$ 3,500

Summary of Significant Accou_18

Summary of Significant Accounting Policies - New Accounting Pronouncements (Details)	12 Months Ended
	Dec. 31, 2019
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	true
Accounting Standards Update 2014-09
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	true
Change in Accounting Principle, Accounting Standards Update, Adoption Date	Jan. 1, 2018
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Change in Accounting Principle, Accounting Standards Update, Transition Option Elected	Modified Retrospective
New Accounting Pronouncement or Change in Accounting Principle, Prior Period Not Restated	true
Accounting Standards Update 2016-02
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adoption Date	Jan. 1, 2019
Change in Accounting Principle, Accounting Standards Update, Early Adoption	true
Accounting Standards Update 2016-13
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2017-04
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-07
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	true
Change in Accounting Principle, Accounting Standards Update, Adoption Date	Mar. 31, 2019
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-09
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	true
Change in Accounting Principle, Accounting Standards Update, Adoption Date	Mar. 31, 2019
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-13
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-15
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-17
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false

Summary of Significant Accou_19

Summary of Significant Accounting Policies - New Accounting Pronouncements - Recognition of Assets and Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Jan. 01, 2019
Leases
Operating lease right-of-use assets	$ 17,743	$ 88,300
Lease liabilities	$ 23,228	$ 94,900
Lease liabilities	us-gaap:OperatingLeaseLiability	us-gaap:OperatingLeaseLiability

Cyclerion Separation - Separati

Cyclerion Separation - Separation Agreement (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Apr. 01, 2019	Dec. 31, 2018
Assets:
Prepaid expenses and other current assets	$ 10,685		$ 10,216
Property and equipment, net	12,429		7,652
Other assets	5		89
Total assets	402,748		332,050
Liabilities:
Accrued research and development costs	2,956		2,963
Accrued expenses and other current liabilities	$ 30,465		$ 38,001
Cyclerion Therapeutics, Inc.
Assets:
Prepaid expenses and other current assets		$ 1,169
Property and equipment, net		10,241
Other assets		21
Total assets		11,431
Liabilities:
Accrued research and development costs		5,673
Accrued expenses and other current liabilities		3,149
Total liabilities		8,822
Net Assets Transferred to Cyclerion		$ 2,609

Cyclerion Separation - General

Cyclerion Separation - General Information (Details) $ in Millions	12 Months Ended
	Dec. 31, 2019USD ($)agreement	Sep. 30, 2019USD ($)
Cyclerion Separation
Initial term of service, low end of range	1 year
Initial term of service, high end of range	2 years
Incremental stock-based compensation expense	$ 0
Transition services agreements | agreement	2
Transition Service Agreement [Member]
Cyclerion Separation
Other Income	$ 0.3
Affiliated Entity
Cyclerion Separation
Tenant improvement reimbursement provisions		$ 1.3
Affiliated Entity | Research and development | Development Agreement [Member]
Cyclerion Separation
Expense for service provided by related party	$ 4.5

Cyclerion Separation - Summary

Cyclerion Separation - Summary of Expenses of Cyclerion (Details) - USD ($) $ in Thousands	3 Months Ended					12 Months Ended
	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Net Loss from Discontinued Operations
Net loss from discontinued operations	$ 37,438	$ 23,866	$ 22,528	$ 25,243	$ 16,585	$ 37,438	$ 88,222	$ 62,022
sGC Business | Discontinued Operations, Disposed of by Means Other than Sale, Spinoff
Net Loss from Discontinued Operations
Net loss from discontinued operations						37,438	88,222	62,022
Research and development | sGC Business | Discontinued Operations, Disposed of by Means Other than Sale, Spinoff
Net Loss from Discontinued Operations
Net loss from discontinued operations						21,792	65,443	60,083
Selling, general and administrative | sGC Business | Discontinued Operations, Disposed of by Means Other than Sale, Spinoff
Net Loss from Discontinued Operations
Net loss from discontinued operations						$ 15,646	21,615	$ 1,939
Restructuring expenses | sGC Business | Discontinued Operations, Disposed of by Means Other than Sale, Spinoff
Net Loss from Discontinued Operations
Net loss from discontinued operations							$ 1,164

Cyclerion Separation - Summar_2

Cyclerion Separation - Summary of Assets and Liabilities Held for Disposition (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Liabilities:
Liabilities	$ 0
Discontinued Operations, Disposed of by Means Other than Sale, Spinoff | sGC Business
Assets:
Prepaid expenses and other current assets		$ 847
Property and equipment, net		9,618
Other assets		25
Assets	$ 0	10,490
Liabilities:
Accounts payable		3,232
Accrued research and development costs		5,256
Accrued expenses and other current liabilities		7,251
Liabilities		$ 15,739

Net Income (Loss) Per Share - C

Net Income (Loss) Per Share - Computation of EPS (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Numerator:
Net income (loss)	$ 47,858	$ 20,648	$ 12,283	$ (59,284)	$ (15,493)	$ (174,351)	$ (49,380)	$ (43,144)	$ 21,505	$ (282,368)	$ (116,937)
Denominator:
Weighted average number of common shares outstanding used in net income (loss) per share - basic and diluted									156,023	152,634	148,993
Net income (loss) per share - basic and diluted					$ (0.10)	$ (1.14)	$ (0.32)	$ (0.29)	$ 0.14	$ (1.85)	$ (0.78)

Net Income (Loss) Per Share - N

Net Income (Loss) Per Share - Notes Payable (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018	Jun. 30, 2015
Convertible Senior Notes | 2.25% Convertible Senior Notes due 2022
Notes Payable
Aggregate principal amount of notes issued	$ 120,699	$ 335,699	$ 335,700

Net Income (Loss) Per Share - P

Net Income (Loss) Per Share - Potentially Dilutive Securities (Details) - shares shares in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	67,087	64,080	63,925
Employee stock options
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	17,194	20,457	21,086
Shares subject to repurchase
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	182	65	62
Restricted stock units
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	3,207	3,058	2,277
Note Hedge Warrants
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	8,318	20,250	20,250
2.25% Convertible Senior Notes due 2022
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	8,318	20,250	20,250
0.75% Convertible Senior Notes due 2024
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	14,934
1.50% Convertible Senior Notes due 2026
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	14,934

Goodwill and Intangible Assets

Goodwill and Intangible Assets - Intangible Assets - General Information (Details) - Developed Technology - USD ($) $ in Millions	Jul. 31, 2018	Jun. 02, 2016
DUZALLO
Goodwill and Intangible Assets
Intangible assets, net		$ 145.1
Accumulated amortization	$ 11.7
ZURAMPIC
Goodwill and Intangible Assets
Intangible assets, net		$ 22
Accumulated amortization	$ 3.6

Goodwill and Intangible Asset_2

Goodwill and Intangible Assets - Intangible Assets - Impairment (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2018USD ($)
Goodwill and Intangible Assets
Impairment of intangible assets	$ 151,794
Developed Technology
Goodwill and Intangible Assets
Impairment of intangible assets	$ 151,800

Goodwill and Intangible Asset_3

Goodwill and Intangible Assets - Goodwill Impairment (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Goodwill
Impairment of goodwill	$ 0	$ 0	$ 0

Collaboration, License, Co-Pr_3

Collaboration, License, Co-Promotion and Other Commercial Agreements - Summary (Details) - USD ($) $ in Thousands	Aug. 01, 2019	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Revenues:
Revenue		$ 126,301	$ 131,167	$ 102,215	$ 68,730	$ 130,692	$ 65,686	$ 81,106	$ 69,155	$ 428,413	$ 346,639	$ 298,276
Collaborative arrangements revenue
Revenues:
Revenue										379,652	272,839	265,533
Collaborative arrangement, other agreements
Revenues:
Revenue										1,845	1,226	419
Sale of active pharmaceutical ingredient
Revenues:
Revenue										48,761	70,355	29,682
Allergan | Collaborative arrangement, co-promotion agreements
Revenues:
Revenue										3,723	4,290	1,535
Allergan | Sale of active pharmaceutical ingredient
Revenues:
Revenue											800
Allergan | North America | Collaborative arrangements revenue
Revenues:
Revenue										327,591	266,177	260,210
Allergan | North America | Collaborative arrangement, collaboration and license agreements
Revenues:
Revenue										327,591	266,177	260,210
Allergan | Europe and Other | Collaborative arrangement, collaboration and license agreements
Revenues:
Revenue										1,718	1,146	617
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangement, collaboration and license agreements
Revenues:
Revenue										32,628		208
AstraZeneca | China, Hong Kong, and Macau | Sale of active pharmaceutical ingredient
Revenues:
Revenue										2,973
Exact Sciences | Collaborative arrangement, co-promotion agreements
Revenues:
Revenue												2,544
Astellas Pharma Inc. | Sale of active pharmaceutical ingredient
Revenues:
Revenue											756
Astellas Pharma Inc. | Japan | Collaborative arrangement, collaboration and license agreements
Revenues:
Revenue	$ 20,400									10,147
Astellas Pharma Inc. | Japan | Sale of active pharmaceutical ingredient
Revenues:
Revenue										45,788	$ 69,599	$ 29,682
Alnylam | Collaborative arrangement, co-promotion agreements
Revenues:
Revenue										$ 2,000

Collaboration, License, Co-Pr_4

Collaboration, License, Co-Promotion and Other Commercial Agreements - Accounts Receivable (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Accounts receivable, net
Accounts receivable, net	$ 32,597
Accounts payable from related party	1,509
Collaborative arrangements and active pharmaceutical ingredient
Accounts receivable, net
Accounts receivable, net	43,900	$ 21,000
Accounts receivable, net and related party accounts receivable, net, net of related party accounts payable	110,100	63,000
Accounts payable from related party	4,100	$ 3,100
Deferred revenue	$ 900

Collaboration, License, Co-Pr_5

Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - General Information (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2019USD ($)paymentitem	Dec. 31, 2018USD ($)	Dec. 31, 2017USD ($)
Collaboration, License and Co-Promotion Agreements
Research and development expense	$ 115,044	$ 101,060	$ 88,145
Sales milestones
Collaboration, License and Co-Promotion Agreements
Sales-related milestone if certain conditions are met	100,000
Allergan
Collaboration, License and Co-Promotion Agreements
Equity investment in the entity's capital stock	$ 25,000
Net cost sharing offset or incremental expense related to research and development expense			600
Remaining commercial-period performance obligations | item	3
Cost sharing amount, reduction to research and development	$ 7,200	9,000
Allergan | Development and sales milestones
Collaboration, License and Co-Promotion Agreements
Cumulative license fees and development milestone payments received	$ 205,000
Allergan | Development milestones
Collaboration, License and Co-Promotion Agreements
Number of milestone payments received | payment	6
Allergan | Sales milestones
Collaboration, License and Co-Promotion Agreements
Percentage of net profit from commercialization (as a percent)	50.00%
Percentage of net loss from commercialization (as a percent)	50.00%
North America
Collaboration, License and Co-Promotion Agreements
Research and development expense	$ 37,600	$ 39,200	$ 28,500

Collaboration, License, Co-Pr_6

Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Change in Accounting Estimate (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Change in accounting estimate
Revenue	$ 126,301	$ 131,167	$ 102,215	$ 68,730	$ 130,692	$ 65,686	$ 81,106	$ 69,155	$ 428,413	$ 346,639	$ 298,276
Collaborative arrangements revenue
Change in accounting estimate
Revenue									379,652	272,839	265,533
Collaborative arrangements revenue | Allergan | North America
Change in accounting estimate
Revenue									327,591	266,177	260,210
Collaborative arrangements, LINZESS | Allergan | North America
Change in accounting estimate
Revenue									$ 325,429	$ 264,243	$ 256,238
Sales Returns and Allowances | Collaborative arrangements, LINZESS | Allergan | North America | Collaborative arrangement, collaboration and license agreements
Change in accounting estimate
Revenue						(29,700)
Sales Returns and Allowances | Allergan
Change in accounting estimate
Revenue					$ 200	$ 59,300

Collaboration, License, Co-Pr_7

Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Collaborative Arrangements Revenue (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Revenues:
Revenue	$ 126,301	$ 131,167	$ 102,215	$ 68,730	$ 130,692	$ 65,686	$ 81,106	$ 69,155	$ 428,413	$ 346,639	$ 298,276
Collaborative arrangements revenue
Revenues:
Revenue									379,652	272,839	265,533
Allergan | North America | Collaborative arrangements revenue
Revenues:
Revenue									327,591	266,177	260,210
Allergan | North America | Collaborative arrangements, LINZESS
Revenues:
Revenue									325,429	264,243	256,238
Allergan | North America | Royalty
Revenues:
Revenue									$ 2,162	$ 1,934	2,295
Allergan | North America | Other
Revenues:
Revenue											$ 1,677

Collaboration, License, Co-Pr_8

Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Additional Information (Details) $ in Millions	12 Months Ended
	Dec. 31, 2017USD ($)
North America | Collaborative arrangement, collaboration agreements
Collaboration, License and Co-Promotion Agreements
Net profit share adjustments	$ 1.7

Collaboration, License, Co-Pr_9

Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Commercial Efforts (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Collaboration, License and Co-Promotion Agreements
Revenue	$ 126,301	$ 131,167	$ 102,215	$ 68,730	$ 130,692	$ 65,686	$ 81,106	$ 69,155	$ 428,413	$ 346,639	$ 298,276
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue									379,652	272,839	265,533
Collaborative arrangements, LINZESS | Allergan | U.S.
Collaboration, License and Co-Promotion Agreements
Revenue									325,429	264,243	256,238
Selling, general and administrative costs incurred by the Company									(38,123)	(42,435)	(41,252)
The Company's share of net profit									287,306	221,808	214,986
Patent and litigation costs									$ 2,400	$ 2,200	$ 900

Collaboration, License, Co-P_10

Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Royalty Revenue (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Revenues:
Revenue	$ 126,301	$ 131,167	$ 102,215	$ 68,730	$ 130,692	$ 65,686	$ 81,106	$ 69,155	$ 428,413	$ 346,639	$ 298,276
Collaborative arrangements revenue
Revenues:
Revenue									379,652	272,839	265,533
Collaborative arrangements revenue | North America | Allergan
Revenues:
Revenue									327,591	266,177	260,210
Royalty | North America | Allergan
Revenues:
Revenue									2,162	1,934	2,295
Royalty | Canada and Mexico | Allergan
Revenues:
Revenue									$ 2,200	$ 1,900	$ 2,300

Collaboration, License, Co-P_11

Collaboration, License, Co-Promotion and Other Commercial Agreements - European and Other Territories (Details) - USD ($) $ in Thousands

3 Months Ended

12 Months Ended

Dec. 31, 2019

Sep. 30, 2019

Jun. 30, 2019

Mar. 31, 2019

Dec. 31, 2018

Sep. 30, 2018

Jun. 30, 2018

Mar. 31, 2018

Dec. 31, 2019

Dec. 31, 2018

Dec. 31, 2017

Oct. 31, 2015

Sep. 30, 2012

Collaboration, License and Co-Promotion Agreements

Revenue

$ 126,301

$ 131,167

$ 102,215

$ 68,730

$ 130,692

$ 65,686

$ 81,106

$ 69,155

$ 428,413

$ 346,639

$ 298,276

Collaborative arrangements revenue

Collaboration, License and Co-Promotion Agreements

Revenue

$ 379,652

272,839

265,533

License | Allergan

Collaboration, License and Co-Promotion Agreements

Royalty percentage, five years following the first commercial sale

upper-single digits

Annual royalty

5 years

Royalty percentage, thereafter

low-double digits

Royalty percentage, expanded territory

lower-single digits

License | Allergan | Europe

Collaboration, License and Co-Promotion Agreements

Remaining milestone payment due upon the amendment to the license agreement

$ 42,500

Revenue remaining performance obligation

$ 0

Royalty | Allergan | Europe

Collaboration, License and Co-Promotion Agreements

Revenue

$ 1,700

$ 1,100

$ 600

Collaboration, License, Co-P_12

Collaboration, License, Co-Promotion and Other Commercial Agreements - Japan (Details) $ in Thousands

Aug. 01, 2019USD ($)

Nov. 30, 2009USD ($)

Dec. 31, 2019USD ($)

Sep. 30, 2019USD ($)

Jun. 30, 2019USD ($)

Mar. 31, 2019USD ($)

Dec. 31, 2018USD ($)

Sep. 30, 2018USD ($)

Jun. 30, 2018USD ($)

Mar. 31, 2018USD ($)

Dec. 31, 2019USD ($)

Dec. 31, 2018USD ($)

Dec. 31, 2017USD ($)

Dec. 31, 2016USD ($)item

Collaboration, License and Co-Promotion Agreements

Revenue

$ 126,301

$ 131,167

$ 102,215

$ 68,730

$ 130,692

$ 65,686

$ 81,106

$ 69,155

$ 428,413

$ 346,639

$ 298,276

Astellas Pharma Inc. | Japan

Collaboration, License and Co-Promotion Agreements

Up-front fee received

$ 30,000

Astellas Pharma Inc. | Japan | Additional development milestones

Collaboration, License and Co-Promotion Agreements

Number of milestone payments | item

3

Total milestone payments to be received

$ 45,000

Collaborative arrangements revenue

Collaboration, License and Co-Promotion Agreements

Revenue

379,652

272,839

265,533

Collaborative arrangement, collaboration and license agreements | Astellas Pharma Inc. | Japan

Collaboration, License and Co-Promotion Agreements

Revenue

$ 20,400

10,147

Non-refundable upfront payment

$ 10,000

Collaborative arrangement, collaboration and license agreements, upfront fee | Astellas Pharma Inc. | Japan

Collaboration, License and Co-Promotion Agreements

Revenue

10,000

Sale of active pharmaceutical ingredient

Collaboration, License and Co-Promotion Agreements

Revenue

48,761

70,355

29,682

Sale of active pharmaceutical ingredient | Astellas Pharma Inc.

Collaboration, License and Co-Promotion Agreements

Revenue

756

Sale of active pharmaceutical ingredient | Astellas Pharma Inc. | Japan

Collaboration, License and Co-Promotion Agreements

Revenue

45,788

$ 69,599

$ 29,682

Revenue remaining performance obligation

$ 0

Sale of active pharmaceutical ingredient | Astellas Pharma Inc., 2009 License Agreement | Japan

Collaboration, License and Co-Promotion Agreements

Revenue

27,500

Sale of active pharmaceutical ingredient | Astellas Pharma Inc., 2009 License Agreement, Amended 2019 | Japan

Collaboration, License and Co-Promotion Agreements

Revenue

$ 18,300

Collaboration, License, Co-P_13

Collaboration, License, Co-Promotion and Other Commercial Agreements - China, Hong Kong and Macau (Details) $ in Thousands	1 Months Ended		3 Months Ended								12 Months Ended
	Aug. 31, 2014USD ($)	Oct. 31, 2012USD ($)	Dec. 31, 2019USD ($)	Sep. 30, 2019USD ($)	Jun. 30, 2019USD ($)	Mar. 31, 2019USD ($)	Dec. 31, 2018USD ($)	Sep. 30, 2018USD ($)	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Dec. 31, 2019USD ($)installment	Dec. 31, 2018USD ($)	Dec. 31, 2017USD ($)
Collaboration, License and Co-Promotion Agreements
Revenue			$ 126,301	$ 131,167	$ 102,215	$ 68,730	$ 130,692	$ 65,686	$ 81,106	$ 69,155	$ 428,413	$ 346,639	$ 298,276
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue											379,652	272,839	265,533
Sale of active pharmaceutical ingredient
Collaboration, License and Co-Promotion Agreements
Revenue											48,761	70,355	29,682
AstraZeneca | Collaborative arrangement, collaboration agreements
Collaboration, License and Co-Promotion Agreements
Pre-launch commercial services											1,200	900
Collaborative Arrangements Revenue												200
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Collaborative arrangement, significant financing component, transaction price			2,600								2,600
Collaborative arrangement, expected interest income			$ 2,600								2,600
Allocable to the performance obligations on a relative standalone selling price basis	$ 34,000
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangement, collaboration and license agreements
Collaboration, License and Co-Promotion Agreements
Revenue											32,628		208
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangement, collaboration agreements
Collaboration, License and Co-Promotion Agreements
Up-front fee received		$ 25,000
Milestone payment to be received by company upon milestone achievement											90,000
Additional budget for activities supporting the development of linaclotide	$ 14,000
Amount of non-contingent arrangement consideration		34,000									$ 35,000
Non-contingent consideration installments | installment											3
Percentage of tiered royalties											20.00%
Amount of arrangement consideration for clinical trial material supply services and research, development and regulatory activities		$ 9,000
Percentage of costs of clinical trial material supply services and research, development and regulatory activities allocated		55.00%
Arrangement Consideration allocated to the License Deliverable		$ 29,700
Arrangement Consideration allocated to the R&D Services		1,800
Arrangement Consideration allocated to the JDC services		100
Arrangement Consideration allocated to the clinical trial material supply services		300
Arrangement Consideration allocated to Co-Promotion Deliverable		2,100
Net cost sharing offset or incremental expense related to research and development expense											$ 0	$ 1,200	$ 300
Revenue											$ 32,600
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangement, transition services agreement
Collaboration, License and Co-Promotion Agreements
Regulatory and administrative services initial term											2 years
AstraZeneca | China, Hong Kong, and Macau | Sale of active pharmaceutical ingredient
Collaboration, License and Co-Promotion Agreements
Revenue											$ 2,973
AstraZeneca | China, Hong Kong, and Macau | Commercialization milestone | Collaborative arrangement, collaboration agreements
Collaboration, License and Co-Promotion Agreements
Milestone payment to be received by company upon milestone achievement		$ 125,000
Percentage of net profit from commercialization (as a percent)		55.00%
Percentage of net loss from commercialization (as a percent)		55.00%
AstraZeneca License Agreement | China, Hong Kong, and Macau | Collaborative arrangement, collaboration agreements
Collaboration, License and Co-Promotion Agreements
Revenue											32,400
AstraZeneca Service Agreement | China, Hong Kong, and Macau | Collaborative arrangement, collaboration agreements
Collaboration, License and Co-Promotion Agreements
Revenue											$ 200

Collaboration, License, Co-P_14

Collaboration, License, Co-Promotion and Other Commercial Agreements - Co-Promotion Agreements (Details) - USD ($) $ in Thousands

Aug. 09, 2019

Dec. 31, 2019

Sep. 30, 2019

Jun. 30, 2019

Mar. 31, 2019

Dec. 31, 2018

Sep. 30, 2018

Jun. 30, 2018

Mar. 31, 2018

Dec. 31, 2019

Dec. 31, 2018

Dec. 31, 2017

Collaboration, License and Co-Promotion Agreements

Revenue

$ 126,301

$ 131,167

$ 102,215

$ 68,730

$ 130,692

$ 65,686

$ 81,106

$ 69,155

$ 428,413

$ 346,639

$ 298,276

Collaborative arrangements and active pharmaceutical ingredient

Collaboration, License and Co-Promotion Agreements

Deferred revenue

900

900

Collaborative arrangements revenue

Collaboration, License and Co-Promotion Agreements

Revenue

379,652

272,839

265,533

Collaborative arrangement, promotion agreements

Collaboration, License and Co-Promotion Agreements

Revenue

3,700

Exact Sciences | Collaborative arrangement, co-promotion agreements

Collaboration, License and Co-Promotion Agreements

Revenue

2,544

Allergan | Collaborative arrangement, co-promotion agreements

Collaboration, License and Co-Promotion Agreements

Revenue

3,723

4,290

1,535

Allergan | Collaborative arrangement, promotion agreements

Collaboration, License and Co-Promotion Agreements

Milestone payment to be received by company upon milestone achievement

4,200

Collaborative arrangement compensated amount

4,100

Alnylam | Collaborative arrangement, co-promotion agreements

Collaboration, License and Co-Promotion Agreements

Revenue

2,000

Alnylam | Collaborative arrangement, promotion agreements

Collaboration, License and Co-Promotion Agreements

Deferred revenue

$ 900

900

Revenue

$ 2,000

Total annual service fees due

$ 9,500

Term of agreement

3 years

Collaborative Arrangement Copromotions [Member] | Exact Sciences | Collaborative arrangements revenue

Collaboration, License and Co-Promotion Agreements

Revenue

2,500

Collaborative Arrangement Copromotions [Member] | Allergan | Collaborative arrangements revenue

Collaboration, License and Co-Promotion Agreements

Revenue

$ 1,300

Collaborative arrangement compensated amount

$ 1,500

Collaborative Arrangement Copromotions [Member] | Sales milestones | Allergan

Collaboration, License and Co-Promotion Agreements

Milestone payment to be received by company upon milestone achievement

$ 3,000

Collaboration, License, Co-P_15

Collaboration, License, Co-Promotion and Other Commercial Agreements - Other Collaborations and License Agreements (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Collaboration, License and Co-Promotion Agreements
Research and development	$ 115,044	$ 101,060	$ 88,145
Regulatory milestones
Collaboration, License and Co-Promotion Agreements
Milestone payment made	0
Collaborative arrangement, co-promotion and other agreements | Development and sales milestones
Collaboration, License and Co-Promotion Agreements
Maximum payment receivable under the milestone	63,500
Collaborative arrangement, other agreements
Collaboration, License and Co-Promotion Agreements
Research and development	0	$ 5,000	$ 0
Revenue related to nonrefundable upfront payments	500
Collaborative arrangement, other agreements | Regulatory milestones
Collaboration, License and Co-Promotion Agreements
Contingent milestone payable	$ 18,000

Fair Value of Financial Instr_3

Fair Value of Financial Instruments - General Information (Details)	Dec. 31, 2019
Fair Value of Financial Instruments
Threshold percentage of collateralized value (as a percent)	102.00%

Fair Value of Financial Instr_4

Fair Value of Financial Instruments - Measured on Recurring Basis (Details) - Recurring basis - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Assets:
Convertible note hedges	$ 31,366	$ 41,020
Total assets measured at fair value	210,577	214,113
Liabilities:
Note hedge warrants	24,260	33,763
Contingent consideration		51
Total liabilities measured at fair value	24,260	33,814
Money market funds
Assets:
Cash and cash equivalents	139,190	142,218
Restricted cash	2,221
Repurchase agreements
Assets:
Cash and cash equivalents	37,800	30,875
Quoted Prices in Active Markets for Identical Assets (Level 1)
Assets:
Total assets measured at fair value	179,211	173,093
Quoted Prices in Active Markets for Identical Assets (Level 1) | Money market funds
Assets:
Cash and cash equivalents	139,190	142,218
Restricted cash	2,221
Quoted Prices in Active Markets for Identical Assets (Level 1) | Repurchase agreements
Assets:
Cash and cash equivalents	37,800	30,875
Significant Unobservable Inputs (Level 3)
Assets:
Convertible note hedges	31,366	41,020
Total assets measured at fair value	31,366	41,020
Liabilities:
Note hedge warrants	24,260	33,763
Contingent consideration		51
Total liabilities measured at fair value	$ 24,260	$ 33,814

Fair Value of Financial Instr_5

Fair Value of Financial Instruments - Transfers Between Fair Value Measurement Levels (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Fair value transfers
Fair value transfer between measurement levels	$ 0	$ 0

Fair Value of Financial Instr_6

Fair Value of Financial Instruments - Assumptions - Convertible Note Hedges (Details)	Dec. 31, 2019$ / sharesY	Dec. 31, 2018$ / sharesY
Fair Value of Financial Instruments
Derivative asset, valuation technique	us-gaap:ValuationTechniqueOptionPricingModelMember	us-gaap:ValuationTechniqueOptionPricingModelMember
Measurement Input, Risk Free Interest Rate
Fair Value of Financial Instruments
Derivative asset, measurement input	0.016	0.025
Measurement Input, Expected Term
Fair Value of Financial Instruments
Derivative asset, measurement input | Y	2.5	3.5
Measurement Input, Share Price
Fair Value of Financial Instruments
Derivative asset, measurement input	13.31	10.36
Measurement Input, Exercise Price
Fair Value of Financial Instruments
Derivative asset, measurement input	14.51	16.58
Measurement Input, Price Volatility
Fair Value of Financial Instruments
Derivative asset, measurement input	0.491	0.438
Measurement Input, Expected Dividend Rate
Fair Value of Financial Instruments
Derivative asset, measurement input	0	0

Fair Value of Financial Instr_7

Fair Value of Financial Instruments - Assumptions - Note Hedge Warrants (Details) $ in Millions	12 Months Ended
	Dec. 31, 2019USD ($)$ / sharesY	Sep. 16, 2019USD ($)	Aug. 31, 2019USD ($)	Dec. 31, 2018Y$ / shares
Fair Value of Financial Instruments
(Loss) gain on derivatives	$ 3
Derivative liability, valuation technique	us-gaap:ValuationTechniqueOptionPricingModelMember			us-gaap:ValuationTechniqueOptionPricingModelMember
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Fair Value of Financial Instruments
Debt redeemed/repurchased		$ 215	$ 215
Debt redemption/repurchase price			$ 227.3
Warrants
Fair Value of Financial Instruments
(Loss) gain on derivatives	$ 3
Measurement Input, Risk Free Interest Rate
Fair Value of Financial Instruments
Derivative liability, measurement input	0.016			0.025
Measurement Input, Expected Term
Fair Value of Financial Instruments
Derivative liability, measurement input | Y	3			4.1
Measurement Input, Share Price
Fair Value of Financial Instruments
Derivative liability, measurement input | $ / shares	13.31			10.36
Measurement Input, Exercise Price
Fair Value of Financial Instruments
Derivative liability, measurement input | $ / shares	18.82			21.50
Measurement Input, Price Volatility
Fair Value of Financial Instruments
Derivative liability, measurement input	0.465			0.436
Measurement Input, Expected Dividend Rate
Fair Value of Financial Instruments
Derivative liability, measurement input	0			0

Fair Value of Financial Instr_8

Fair Value of Financial Instruments - Change in Level 3 - Convertible Note Hedges (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Change in Level 3 Assets
Balance at beginning of period	$ 41,020	$ 108,188
Cash settlement (received) paid upon early termination of derivatives		(28,909)
Change in fair value, recorded as a component of gain (loss) on derivatives	19,255	(67,168)
Balance at end of period	$ 31,366	$ 41,020

Fair Value of Financial Instr_9

Fair Value of Financial Instruments - Change in Level 3 - Note Hedge Warrants (Details) - Warrants - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Change in Level 3 Liabilities
Balance at beginning of period	$ (33,763)	$ (92,188)
Cash settlement (received) paid upon early termination of derivatives		25,735
Change in fair value, recorded as a component of gain (loss) on derivatives	(16,232)	58,425
Balance at end of period	$ (24,260)	$ (33,763)

Fair Value of Financial Inst_10

Fair Value of Financial Instruments - Contingent Consideration - Liability Recorded (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Jun. 02, 2016
Contingent Consideration
Non-cash change in fair value of contingent consideration	$ (31,045)	$ (31,310)
Lesinurad transaction
Contingent Consideration
Estimated fair value of contingent acquisition consideration payable			$ 67,900
Non-cash change in fair value of contingent consideration	$ (31,000)

Fair Value of Financial Inst_11

Fair Value of Financial Instruments - Change in Level 3 - Contingent consideration (Details) - Business Combination Contingent Consideration Liability [Member] - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Change in Level 3 Liabilities
Balance at beginning of period	$ (51)	$ (31,258)
Cash settlement (received) paid upon early termination of derivatives		(162)
Change in fair value, recorded as a component of gain (loss) on derivatives	(51)	(31,045)
Balance at end of period	$ 0	$ (51)

Fair Value of Financial Inst_12

Fair Value of Financial Instruments - Notes Payable (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Sep. 16, 2019	Aug. 31, 2019	Aug. 12, 2019	Dec. 31, 2018	Sep. 23, 2016	Jun. 30, 2015
Notes Payable | 8.375% Notes due 2026
Fair value disclosures
Stated interest rate (as a percent)	8.375%					8.375%
Debt Instrument, Repurchased Face Amount		$ 116,500	$ 116,500
Aggregate principal amount of notes issued	$ 150,000					$ 150,000
Notes Payable | 8.375% Notes due 2026 | Significant Unobservable Inputs (Level 3)
Fair value disclosures
Estimated fair value					$ 148,200
Convertible Senior Notes | 2.25% Convertible Senior Notes due 2022
Fair value disclosures
Stated interest rate (as a percent)		2.25%					2.25%
Debt Instrument, Repurchased Face Amount		$ 215,000	215,000
Aggregate principal amount of notes issued	120,699				335,699		$ 335,700
Convertible Senior Notes | 2.25% Convertible Senior Notes due 2022 | Significant Other Observable Inputs (Level 2)
Fair value disclosures
Estimated fair value	141,300				$ 315,000
Convertible Senior Notes | 0.75% Convertible Senior Notes due 2024
Fair value disclosures
Stated interest rate (as a percent)				0.75%
Aggregate principal amount of notes issued	200,000		200,000	$ 200,000
Convertible Senior Notes | 0.75% Convertible Senior Notes due 2024 | Significant Other Observable Inputs (Level 2)
Fair value disclosures
Estimated fair value	235,700
Convertible Senior Notes | 1.50% Convertible Senior Notes due 2026
Fair value disclosures
Stated interest rate (as a percent)				1.50%
Aggregate principal amount of notes issued	200,000		$ 200,000	$ 200,000
Convertible Senior Notes | 1.50% Convertible Senior Notes due 2026 | Significant Other Observable Inputs (Level 2)
Fair value disclosures
Estimated fair value	$ 240,100

Fair Value of Financial Inst_13

Fair Value of Financial Instruments - Capped Calls in connection with issuance of 2024 Convertible Notes and the 2026 Convertible Notes (Details) - Capped Calls	1 Months Ended
	Aug. 31, 2019$ / shares$ / itemshares
Capped Calls
Number of shares covered by capped calls (in shares) | shares	29,867,480
Strike price (in dollars per share) | $ / shares	$ 13.39
Cap price | $ / item	17.05

Fair Value of Financial Inst_14

Fair Value of Financial Instruments - Nonrecurring Fair Value Measurements - Intangible Assets (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2018USD ($)
Impairment of Intangible Assets (Excluding Goodwill) [Abstract]
Impairment of intangible assets	$ 151,794

Inventory - Tabular Disclosure

Inventory - Tabular Disclosure (Details) $ in Thousands	Dec. 31, 2019USD ($)
Inventory
Raw Materials	$ 65
Work in Progress	392
Finished Goods	191
Total	$ 648

Inventory - General Information

Inventory - General Information (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2019USD ($)agreement	Dec. 31, 2018USD ($)	Dec. 31, 2016USD ($)
Inventory
Number of supply agreements containing minimum purchase commitments | agreement	2
Impairments of Linaclotide	$ 0	$ 0
Write-down of inventory			$ 10,100

Inventory - Purchase Commitment

Inventory - Purchase Commitments (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Purchase commitments
Write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancellable purchase commitments	$ (3,530)	$ 247	$ 309
Lesinurad
Purchase commitments
Write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancellable purchase commitments		2,500	$ 300
Linaclotide
Purchase commitments
Write-down of commercial supply and inventory to net realizable value and settlement on non-cancellable purchase commitments		$ 2,500

Inventory - Commercial Supply A

Inventory - Commercial Supply Agreements - Accrual for Non-cancelable Inventory Purchase Commitments (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Accrual for non-cancellable purchase commitments
Recorded settlement	$ 3.5
Accrued Expenses and Other Current Liabilities
Accrual for non-cancellable purchase commitments
Other Accrued Liabilities Current, Purchase Commitment Write Down	4.1
Linaclotide
Accrual for non-cancellable purchase commitments
Purchase commitment write down gain amount	0.7
Recorded settlement	$ 2.5
Linaclotide | Accrued Expenses and Other Current Liabilities | Commercial and Sample Supply Commitments
Accrual for non-cancellable purchase commitments
Accrual for non-cancellable purchase commitments		$ 2.5
Linaclotide | Other Liabilities | Commercial and Sample Supply Commitments
Accrual for non-cancellable purchase commitments
Accrual for non-cancellable purchase commitments		$ 2.5

Inventory - Commercial Supply_2

Inventory - Commercial Supply Agreements - Write-downs (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017
Inventory
Write-down of excess non-cancellable ZURAMPIC sample purchase commitments	$ 390	$ 309
Commercial and Sample Supply Commitments | Lesinurad
Inventory
Write-down of loss on non-cancellable commercial supply purchase commitments	$ 400
Commercial and Sample Supply Commitments | ZURAMPIC
Inventory
Write-down of prepaid ZURAMPIC sample supply		$ 1,700

Leases - Lease Cost (Details)

Leases - Lease Cost (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2019USD ($)
Lease cost
Operating lease cost during period, net	$ 16,452
Variable lease payments	1,526
Short-term lease cost	1,512
Total lease cost	19,490
Sublease income	$ 300

Leases - Operating Leases - Sup

Leases - Operating Leases - Supplemental Cash Flow Information (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2019USD ($)
Operating leases
Right-of-use assets obtained in exchange for new operating lease upon adoption of ASC 842	$ 88,299
Adjustment to right-of-use assets as a result of the lease modification at the Separation date	(40,427)
Adjustment to right-of-use assets as a result of the termination of the Binney Street Lease	(34,440)
Right-of-use assets obtained in exchange for new operating lease liabilities	18,452
Cash paid for amounts included in the measurement of lease liabilities	$ 18,598
Weighted-average remaining lease term of operating leases (in years)	10 years 2 months 12 days
Weighted-average discount rate of operating leases (as a percent)	5.80%

Leases - Operating Leases - Fut

Leases - Operating Leases - Future Minimum Lease Payments - ASC 842 (Details) $ in Thousands	Dec. 31, 2019USD ($)
Future minimum lease payments
2020	$ 1,146
2021	3,128
2022	3,129
2023	3,065
2024	3,126
2025 and thereafter	18,044
Total future minimum lease payments	$ 31,638

Leases - Operating Leases - Ope

Leases - Operating Leases - Operating Lease Obligations (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Jan. 01, 2019
Operating lease obligations
Total future minimum lease payments	$ 31,638
Less: present value adjustment	8,410
Operating lease liabilities	23,228	$ 94,900
Less: current portion of operating lease obligations	1,146
Operating lease obligations, net of current portion	$ 22,082
Lease liabilities	us-gaap:OperatingLeaseLiability	us-gaap:OperatingLeaseLiability

Leases - Operating Leases - F_2

Leases - Operating Leases - Future Minimum Lease Payments - ASC 840 (Details) $ in Thousands	Dec. 31, 2019USD ($)
Future minimum lease payments
2019	$ 18,736
2020	18,312
2021	18,863
2022	19,365
2023	19,818
2024 and thereafter	22,118
Total future minimum lease payments	$ 117,212

Leases - Operating Leases - Sum

Leases - Operating Leases - Summer Street Lease (Details) - USD ($) $ in Thousands	Jun. 11, 2019	Dec. 31, 2019	Jan. 01, 2019	Dec. 31, 2018
Operating leases
Restricted cash, noncurrent		$ 971		$ 6,426
Operating lease right-of-use assets		$ 17,743	$ 88,300
Weighted-average discount rate of operating leases (as a percent)		5.80%
Asset retirement obligation		$ 486
Operating lease cost		16,452
Summer Street Lease
Operating leases
Option to extend the term of the lease	true
Operating lease, renewal term	5 years
Annual rent escalation (as a percent)	2.00%
Restricted cash, noncurrent		1,000
Operating lease right-of-use assets		17,700
Lease liability, net of tenant improvement allowance reimbursement		$ 22,800
Weighted-average discount rate of operating leases (as a percent)		5.80%
Asset retirement obligation		$ 500
Operating lease cost		$ 1,500

Leases - Operating Leases - Bin

Leases - Operating Leases - Binney Street Lease (Details) $ in Thousands	Jun. 11, 2019USD ($)ft²	Apr. 01, 2019ft²	Jan. 31, 2007USD ($)ft²	Dec. 31, 2019USD ($)	Dec. 31, 2018USD ($)	Dec. 31, 2017USD ($)	Jan. 01, 2019USD ($)
Operating leases
Restricted cash, noncurrent				$ 971	$ 6,426
Operating lease right-of-use assets				17,743			$ 88,300
Lease liability				$ 23,228			94,900
Weighted-average discount rate of operating leases (as a percent)				5.80%
Operating lease cost				$ 16,452
Sublease income				300
Binney Street Lease
Operating leases
Rentable area leased (in square feet) | ft²	108,000	108,000	223,000
Option to extend the term of the lease			true
Operating lease, renewal term			5 years
Annual rent escalation (as a percent)			3.00%
Restricted cash, noncurrent			$ 6,400
Operating lease right-of-use assets				0			87,700
Lease liability							$ 94,300
Surrendered space (in square feet) | ft²		114,000
Weighted-average discount rate of operating leases (as a percent)	4.00%	5.10%
Gain on modification of lease				3,200
Lease termination cost	$ 9,000
Operating lease cost				16,300
Sublease income				$ 300
Rent expense					$ 10,000	$ 7,600

Leases - Operating Leases - Dat

Leases - Operating Leases - Data center colocation lease (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Jan. 01, 2019
Operating leases
Operating lease right-of-use assets	$ 17,743		$ 88,300
Lease liability	$ 23,228		94,900
Asset impairment charge
Weighted-average discount rate of operating leases (as a percent)	5.80%
Lease cost	$ 19,490
Data Center Lease, Boston, Massachusetts
Operating leases
Annual rent escalation (as a percent)	4.00%
Operating lease right-of-use assets			600
Lease liability	$ 400		$ 600
Asset impairment charge
Weighted-average discount rate of operating leases (as a percent)	6.00%
Lease cost	$ 200
Rent expense		$ 200
Data Center Lease, Boston, Massachusetts | Selling, general and administrative
Asset impairment charge
Asset impairment charge	$ 500

Leases - Operating Leases - Veh

Leases - Operating Leases - Vehicle fleet leases (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Apr. 30, 2018
Operating leases
Restricted cash, noncurrent	$ 971	$ 6,426
Operating lease cost	16,452
Vehicles, 2018 Vehicle Leases
Operating leases
Operating lease, term			12 months
Operating lease, renewal term			1 month
Restricted cash, noncurrent			$ 1,300
Operating lease cost	$ 1,500	800
Vehicles
Operating leases
Capital lease obligations		$ 0

Leases - Other Leases (Details)

Leases - Other Leases (Details) - Computer and office equipment, under capital lease $ in Millions	Dec. 31, 2018USD ($)
Capital leases
Capital lease obligations	$ 0.2
Weighted average interest rate on the outstanding capital lease obligations (as a percent)	3.40%

Property and Equipment - Tabula

Property and Equipment - Tabular Disclosure (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Property and Equipment
Property and equipment, gross	$ 22,511	$ 33,490
Less accumulated depreciation and amortization	(10,082)	(25,838)
Property and equipment, net	12,429	7,652
Software
Property and Equipment
Property and equipment, gross	9,568	10,976
Leasehold improvements
Property and Equipment
Property and equipment, gross	7,318	12,472
Laboratory equipment
Property and Equipment
Property and equipment, gross	2,193	1,597
Furniture and fixtures
Property and Equipment
Property and equipment, gross	1,508	1,845
Computer and office equipment
Property and Equipment
Property and equipment, gross	1,293	2,737
Construction in process
Property and Equipment
Property and equipment, gross	$ 631	115
Manufacturing equipment
Property and Equipment
Property and equipment, gross		$ 3,748

Property and Equipment - Capita

Property and Equipment - Capital Leases (Details) $ in Millions	Dec. 31, 2018USD ($)
Property and Equipment
Assets under capital lease	$ 0.2

Property and Equipment - Expens

Property and Equipment - Expenses (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Property and Equipment
Depreciation and amortization	$ 5.6	$ 3.9	$ 6.4

Accrued Expenses and Other Cu_3

Accrued Expenses and Other Current Liabilities - Tabular Disclosure (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Accrued Expenses
Salaries	$ 2,973	$ 3,054
Accrued vacation	2,540	3,493
Accrued incentive compensation	11,760	13,867
Other employee benefits	1,260	1,883
Professional fees	1,421	1,735
Accrued interest	301	873
Restructuring accruals	179	2,885
Other	10,031	10,211
Total accrued expenses and other current liabilities	$ 30,465	$ 38,001

Accrued Expenses and Other Cu_4

Accrued Expenses and Other Current Liabilities - Additional Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2016
Accrued Expenses
Other accrued expenses	$ 10,031	$ 10,211
Move activities	900
Unbilled inventories	600
Other accrued expenses contracted services	200
Recorded settlement	3,500
Write-down of inventory			$ 10,100
Accrued Expenses and Other Current Liabilities
Accrued Expenses
Accrued non-cancelable purchase	4,100
Linaclotide
Accrued Expenses
Recorded settlement	$ 2,500
Commercial and Sample Supply Commitments
Accrued Expenses
Write-down of excess non-cancellable sample purchase commitments		1,400
Commercial and Sample Supply Commitments | Linaclotide | Accrued Expenses and Other Current Liabilities
Accrued Expenses
Write-down of inventory		$ 2,500

Notes Payable - 8.375% Notes du

Notes Payable - 8.375% Notes due 2026 - General Information (Details) - USD ($) $ in Thousands	Aug. 31, 2019	Sep. 23, 2016	Aug. 31, 2019	Jun. 30, 2015	Dec. 31, 2019	Dec. 31, 2017	Sep. 16, 2019	Dec. 31, 2018
Notes Payable
Net proceed received						$ 146,250
Proceeds from partial termination of convertible note hedges and note hedge warrants			$ 3,200		$ 3,174
Loss on extinguishment of debt					30,977	$ 2,009
Equity component of convertible senior notes					92,502
Convertible Senior Notes
Notes Payable
Debt issuance costs capitalized					8,005			$ 5,004
8.375% Notes due 2026 | Notes Payable
Notes Payable
Aggregate principal amount of notes issued		$ 150,000			$ 150,000
Stated interest rate (as a percent)		8.375%			8.375%
Net proceed received		$ 11,200
Redemption Percentage		11.00%
Debt redeemed/repurchased	$ 116,500		116,500				$ 116,500
Debt redemption/repurchase price							$ 123,000
Loss on extinguishment of debt		$ 7,600			$ 31,000
Debt issuance costs capitalized		$ 500
Percentage of net sales to determine quarterly payments (as a percent)					7.50%
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued				$ 335,700	$ 120,699			$ 335,699
Stated interest rate (as a percent)				2.25%			2.25%
Net proceed received				$ 324,000
Debt redeemed/repurchased	215,000		215,000				$ 215,000
Debt redemption/repurchase price	227,300		227,300
Loss on extinguishment of debt	$ 23,400		23,400
Initial debt issuance costs			2,800
Equity component of convertible senior notes			$ 27,000
Debt issuance costs capitalized					$ 8,005

Notes Payable - 8.375% Notes _2

Notes Payable - 8.375% Notes due 2026 - Redemption Percentage (Details)	Sep. 23, 2016
8.375% Notes due 2026 | Notes Payable
Notes Payable
Redemption Percentage	11.00%

Notes Payable - 2.25% Convertib

Notes Payable - 2.25% Convertible Senior Notes due 2022 - General Information (Details)	Apr. 15, 2019USD ($)$ / sharesshares	Aug. 31, 2019USD ($)	Jun. 30, 2015USD ($)D$ / sharesshares	Dec. 31, 2019USD ($)$ / sharesshares	Dec. 31, 2017USD ($)	Sep. 16, 2019	Dec. 31, 2018USD ($)
Notes Payable
Net proceed received					$ 146,250,000
Payments for convertible note hedges		$ 25,200,000	$ 21,100,000
Net proceeds received				$ 400,000,000
Note Hedge Warrants
Notes Payable
Warrants strike price (in dollars per share) | $ / shares	$ 18.82			$ 21.50
Convertible Note Hedge
Notes Payable
Conversion price (in dollars per share) | $ / shares	$ 14.51			$ 16.58
Shares issuable upon conversion of debt (in shares) | shares				20,249,665
Convertible Senior Notes
Notes Payable
Debt issuance costs capitalized				$ 8,005,000			$ 5,004,000
2.25% Convertible Senior Notes due 2022 | Note Hedge Warrants
Notes Payable
Shares issuable upon conversion of debt (in shares) | shares	23,135,435
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued			335,700,000	120,699,000			$ 335,699,000
Net proceed received			324,000,000
Fees and expenses			$ 11,700,000
Stated interest rate (as a percent)			2.25%			2.25%
Conversion rate, number of shares to be issued per	68.9172		60.3209
Principal amount used for debt instrument conversion ratio	$ 1,000		$ 1,000
Conversion price (in dollars per share) | $ / shares	$ 14.51		$ 16.58
Shares issuable upon conversion of debt (in shares) | shares	23,135,435		20,249,665
Number of trading days | D			20
Consecutive trading days | D			30
Minimum percentage of stock price			130.00%
Number of business days immediately after any five consecutive trading day period during the measurement period | D			5
Number of consecutive trading days before five business days during the measurement period | D			5
Repurchase price, as percentage of principal amount, if company undergoes change of control			100.00%
Debt issuance costs capitalized				$ 8,005,000
Maximum period of the sole remedy for event failures in the Indenture				180 days
Amortization period			7 years
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes | Minimum
Notes Payable
Percentage of aggregate principal amount payable, in case of event of default			25.00%
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes | Maximum
Notes Payable
Percentage of the trading price to the product of the sale price of the entity's common stock and the conversion rate			98.00%

Notes Payable - 2.25% Convert_2

Notes Payable - 2.25% Convertible Senior Notes due 2022 - Balances (Details) - Convertible Senior Notes - USD ($) $ in Thousands	Dec. 31, 2019	Aug. 31, 2019	Aug. 12, 2019	Dec. 31, 2018	Jun. 30, 2015
Liability component:
Less: unamortized debt discount	$ (104,700)			$ (65,094)
Less: unamortized debt issuance costs	(8,005)			(5,004)
Net carrying amount	407,994			265,601
Total equity component	112,309			114,199
2.25% Convertible Senior Notes due 2022
Liability component:
Aggregate principal amount of notes issued	120,699			335,699	$ 335,700
Long-term Debt, Gross	553,738
Less: unamortized debt discount	(104,700)
Less: unamortized debt issuance costs	(8,005)
Net carrying amount	407,994
Total equity component	19,807			$ 114,199
0.75% Convertible Senior Notes due 2024
Liability component:
Aggregate principal amount of notes issued	200,000	$ 200,000	$ 200,000
Total equity component	41,152
1.50% Convertible Senior Notes due 2026
Liability component:
Aggregate principal amount of notes issued	200,000	$ 200,000	$ 200,000
Total equity component	$ 51,350

Notes Payable - 2.25% Convert_3

Notes Payable - 2.25% Convertible Senior Notes due 2022 - Additional Information (Details) - 2.25% Convertible Senior Notes due 2022 - Convertible Senior Notes - USD ($) $ in Millions	1 Months Ended
	Jun. 30, 2015	Dec. 31, 2019	Jun. 30, 2019
Notes Payable
Debt issuance costs incurred	$ 11.7
Debt issuance costs allocated to equity components	4
Debt issuance costs allocated to liability components	$ 7.7
Debt instrument term	7 years
Effective interest rate on liability components		7.50%	9.34%

Notes Payable - 2.25% Convert_4

Notes Payable - 2.25% Convertible Senior Notes due 2022 - Total Interest Expense (Details) - 2.25% Convertible Senior Notes due 2022 - Convertible Senior Notes - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Interest Expense
Contractual interest expense	$ 7,361	$ 7,553	$ 7,553
Amortization of debt issuance costs	1,190	971	806
Amortization of debt discount	17,683	15,437	14,145
Total interest expense	$ 26,234	$ 23,961	$ 22,504

Notes Payable - 2.25% Convert_5

Notes Payable - 2.25% Convertible Senior Notes due 2022 - Future Minimum Payments (Details) - Convertible Senior Notes - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Future minimum payments of Convertible senior notes
Less: unamortized debt discount	$ (104,700)	$ (65,094)
Less: unamortized debt issuance costs	(8,005)	(5,004)
Net carrying amount	407,994	$ 265,601
2.25% Convertible Senior Notes due 2022
Future minimum payments of Convertible senior notes
2020	7,216
2021	7,216
2022	126,556
2023	4,500
2024	203,750
2025 and Thereafter	204,500
Total future minimum payments under the convertible senior notes	553,738
Less: amounts representing interest	(33,039)
Less: unamortized debt discount	(104,700)
Less: unamortized debt issuance costs	(8,005)
Net carrying amount	$ 407,994

Notes Payable - 0.75% Convertib

Notes Payable - 0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 (Details)	Aug. 12, 2019USD ($)	Aug. 07, 2019USD ($)$ / shares	Apr. 15, 2019USD ($)$ / sharesshares	Aug. 31, 2019USD ($)D	Jun. 30, 2015USD ($)D$ / sharesshares	Dec. 31, 2017USD ($)	Dec. 31, 2019USD ($)	Sep. 16, 2019	Dec. 31, 2018USD ($)
Notes Payable
Net proceed received						$ 146,250,000
Payments for convertible note hedges				$ 25,200,000	$ 21,100,000
Repurchase price				100.00%
The percentage of aggregate principal amount of notes outstanding and payable in case of event of default under the agreement.				25.00%
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued					335,700,000		$ 120,699,000		$ 335,699,000
Net proceed received					324,000,000
Fees and expenses					$ 11,700,000
Stated interest rate (as a percent)					2.25%			2.25%
Conversion rate, number of shares to be issued per			68.9172		60.3209
Principal amount used for debt instrument conversion ratio			$ 1,000		$ 1,000
Initial conversion price (in dollars per share) | $ / shares			$ 14.51		$ 16.58
Shares issuable upon conversion of debt (in shares) | shares			23,135,435		20,249,665
Number of trading days | D					20
Consecutive trading days | D					30
Minimum percentage of stock price					130.00%
Number of business days immediately after any five consecutive trading day period during the measurement period | D					5
Number of consecutive trading days before five business days during the measurement period | D					5
Repurchase price, as percentage of principal amount, if company undergoes change of control					100.00%
Amortization period					7 years
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes | Minimum
Notes Payable
Percentage of aggregate principal amount payable, in case of event of default					25.00%
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes | Maximum
Notes Payable
Percentage of the trading price to the product of the sale price of the entity's common stock and the conversion rate					98.00%
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes
Notes Payable
Net proceed received				$ 391,000,000
Fees and expenses				9,000,000
Conversion rate, number of shares to be issued per	74.6687
Principal amount used for debt instrument conversion ratio		$ 1,000		$ 1,000
Initial conversion price (in dollars per share) | $ / shares		$ 13.39
Conversion premium percentage on sale price of common stock		37.50%
Share Price | $ / shares		$ 9.74
Number of consecutive trading days before five business days during the measurement period | D				5
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes | Calendar quarter commencing after December 31, 2019
Notes Payable
Number of trading days | D				20
Consecutive trading days | D				30
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes | Measurement period
Notes Payable
Number of business days immediately after any five consecutive trading day period during the measurement period | D				5
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes | Minimum | Calendar quarter commencing after December 31, 2019
Notes Payable
Minimum percentage of stock price				130.00%
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes | Maximum | Measurement period
Notes Payable
Conversion premium percentage on sale price of common stock				98.00%
0.75% Convertible Senior Notes due 2024 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued	$ 200,000,000			$ 200,000,000			200,000,000
Stated interest rate (as a percent)	0.75%
Amortization period				5 years
1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued	$ 200,000,000			$ 200,000,000			$ 200,000,000
Stated interest rate (as a percent)	1.50%
Amortization period				7 years

Notes Payable - 2.25% Convert_6

Notes Payable - 2.25% Convertible Senior Notes due 2022, 0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 (Details) - Convertible Senior Notes - USD ($) $ in Millions	1 Months Ended
	Aug. 31, 2019	Jun. 30, 2015	Dec. 31, 2019	Jun. 30, 2019
2.25% Convertible Senior Notes due 2022
Debt Instruments [Abstract]
Debt issuance costs incurred		$ 11.7
Debt issuance costs allocated to equity components		4
Debt issuance costs allocated to liability components		$ 7.7
Debt instrument term		7 years
Effective interest rate on liability components			7.50%	9.34%
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026
Debt Instruments [Abstract]
Debt issuance costs incurred	$ 9
Debt issuance costs allocated to equity components	2.1
Debt issuance costs allocated to liability components	$ 6.9
0.75% Convertible Senior Notes due 2024
Debt Instruments [Abstract]
Debt instrument term	5 years
Effective interest rate on liability components			4.73%
1.50% Convertible Senior Notes due 2026
Debt Instruments [Abstract]
Debt instrument term	7 years
Effective interest rate on liability components			4.69%

Notes Payable - Convertible Not

Notes Payable - Convertible Note Hedge and Warrant Transactions (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	12 Months Ended
	Jun. 30, 2015	Dec. 31, 2019	Apr. 15, 2019	Dec. 31, 2018
Notes Payable
Long-term asset		$ 31,366		$ 41,020
Long-term liability		24,260		$ 33,763
Net derivative issuance cost	$ 21,100
(Loss) gain on derivatives		$ 3,000
Convertible Note Hedge
Notes Payable
Shares issuable upon conversion of debt (in shares)		20,249,665
Conversion price (in dollars per share)		$ 16.58	$ 14.51
Long-term asset	91,900
Note Hedge Warrant Derivatives
Notes Payable
Shares into which warrants may be converted (in shares)		20,249,665
Trading day period		150 days
Long-term liability	$ 70,800
Note Hedge Warrants
Notes Payable
Warrants strike price (in dollars per share)		$ 21.50	$ 18.82

Notes Payable - Capped Calls wi

Notes Payable - Capped Calls with Respect to 2024 Convertible Notes and 2026 Convertible Notes (Details) $ / shares in Units, $ in Thousands	1 Months Ended	12 Months Ended
	Aug. 31, 2019USD ($)$ / shares$ / itemshares	Dec. 31, 2019USD ($)
Capped Calls
Purchase of capped calls		$ 25,159
Equity component of issuance costs for convertible senior notes		$ 2,092
Capped Calls
Capped Calls
Payment made to enter into Capped Calls	$ 25,200
Strike price (in dollars per share) | $ / shares	$ 13.39
Cap price | $ / item	17.05
Percentage of cap premium (as a percent)	75.00%
Number of shares covered by capped calls (in shares) | shares	29,867,480
Purchase of capped calls	$ 25,000
Equity component of issuance costs for convertible senior notes	$ 200

Commitments and Contingencies -

Commitments and Contingencies - Commercial Supply Commitments - General Information (Details) $ in Millions	Dec. 31, 2019USD ($)agreement
Purchase obligations
Number of supply agreements | agreement	2
Commercial supply purchase obligations | $	$ 0

Commitments and Contingencies_2

Commitments and Contingencies - Litigation (Details) $ in Millions	12 Months Ended
	Dec. 31, 2019USD ($)
Mylan
Loss Contingencies [Line Items]
Litigation settlement amount	$ 4

Stockholders' Equity (Details)

Stockholders' Equity (Details)	12 Months Ended
	Dec. 31, 2019Voteitemshares	Dec. 31, 2018shares
Stockholders' Equity
Number of series of common stock designated | item	2
Common stock, shares outstanding | shares	157,535,962	154,414,691
Minimum percentage of beneficial ownership in entity's outstanding shares of common stock used to determine number of voting rights allowed per share of common stock	30.00%
Number of shares of Class A common stock to be received for each share of Class B common stock converted	1
Class A common stock
Stockholders' Equity
Number of Class B shares converted | shares		13,972,688
Number of voting rights per share	1
Number of voting rights per share	one
Class B common stock
Stockholders' Equity
Common stock, shares outstanding | shares	0
Number of voting rights per share	1
Number of voting rights per share	one
Number of voting rights per share if the matter is an adoption agreement of merger or consolidation, an adoption of a resolution with respect to sale, lease, or exchange of the Company's assets or an adoption of dissolution or liquidation of the Company	10
Number of voting rights per share if any individual, entity, or group seeks to obtain or has obtained beneficial ownership of 30% or more of the Company's outstanding shares of common stock	10

Employee Stock Benefit Plans -

Employee Stock Benefit Plans - Summary of Expense Recognized by Share-based Compensation Arrangement (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Employee Stock Benefit Plans
Expense recognized for share-based compensation arrangements	$ 31,278	$ 41,082	$ 30,905
Employee stock options
Employee Stock Benefit Plans
Expense recognized for share-based compensation arrangements	12,526	20,478	19,331
Restricted stock units
Employee Stock Benefit Plans
Expense recognized for share-based compensation arrangements	15,488	17,160	7,646
Restricted Stock
Employee Stock Benefit Plans
Expense recognized for share-based compensation arrangements	2,095	2,330	2,441
Non-employee stock options
Employee Stock Benefit Plans
Expense recognized for share-based compensation arrangements			301
Employee Stock Purchase Plan
Employee Stock Benefit Plans
Expense recognized for share-based compensation arrangements	1,115	1,097	1,172
Stock awards
Employee Stock Benefit Plans
Expense recognized for share-based compensation arrangements	$ 54	$ 17	$ 14

Employee Stock Benefit Plans _2

Employee Stock Benefit Plans - Share-based Compensation Reflected in the Consolidated Statement of Operations (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Employee Stock Benefit Plans
Share-based compensation expense	$ 31,278	$ 41,082	$ 30,905
Share-based compensation expense, other modifications	3,000
Research and development
Employee Stock Benefit Plans
Share-based compensation expense	6,343	11,500	9,853
Selling, general and administrative
Employee Stock Benefit Plans
Share-based compensation expense	24,281	27,440	$ 21,052
Restructuring expenses
Employee Stock Benefit Plans
Share-based compensation expense	$ 654	$ 2,142

Employee Stock Benefit Plans _3

Employee Stock Benefit Plans - Workforce Reduction (Details) $ in Thousands	Feb. 07, 2019employee	Aug. 16, 2018employee	Jun. 27, 2018employee	Jan. 30, 2018employee	Sep. 30, 2018employee	Jun. 30, 2018employee	Mar. 31, 2018employee	Dec. 31, 2019USD ($)	Dec. 31, 2018USD ($)	Dec. 31, 2017USD ($)
Employee Stock Benefit Plans
Share-based compensation expense								$ 31,278	$ 41,082	$ 30,905
Employee Stock Purchase Plan
Employee Stock Benefit Plans
Share-based compensation expense								1,115	1,097	1,172
Spin-off | Share-based Payment Awards, Excluding Employee Stock Purchase Plan [Member]
Employee Stock Benefit Plans
Share-based compensation expense								0
Spin-off | Employee Stock Purchase Plan
Employee Stock Benefit Plans
Share-based compensation expense								300
Research and development
Employee Stock Benefit Plans
Share-based compensation expense								6,343	11,500	9,853
Selling, general and administrative
Employee Stock Benefit Plans
Share-based compensation expense								24,281	27,440	$ 21,052
Restructuring expenses
Employee Stock Benefit Plans
Share-based compensation expense								654	2,142
Reduction in Field-based Workforce, January 30, 2018
Workforce Reduction
Number of employees eliminated | employee				60			60
Reduction in Field-based Workforce, January 30, 2018 | Restructuring expenses | Employee severance, benefits and related costs
Employee Stock Benefit Plans
Share-based compensation expense									200
Reduction in Headquarter-based Workforce, June 27, 2018
Workforce Reduction
Number of employees expected to be eliminated | employee			40			40
Reduction in Headquarter-based Workforce, June 27, 2018 | Employee severance, benefits and related costs
Employee Stock Benefit Plans
Share-based compensation expense									1,400
Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018
Workforce Reduction
Number of employees eliminated | employee					100
Number of employees expected to be eliminated | employee		100
Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018 | Restructuring expenses | Employee severance, benefits and related costs
Employee Stock Benefit Plans
Share-based compensation expense									$ 600
Reduction in Workforce, February 7, 2019
Workforce Reduction
Number of employees expected to be eliminated | employee	35
Reduction in Workforce, February 7, 2019 | Restructuring expenses | Employee severance, benefits and related costs
Employee Stock Benefit Plans
Share-based compensation expense								$ 700

Employee Stock Benefit Plans _4

Employee Stock Benefit Plans - Stock Benefit Plans (Details) - shares	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2010
2010 Plan | Employee Stock Purchase Plan
Stock Benefit Plans
Purchase price as a percentage of fair market value of a share of common stock on the first or last day of an offering period (as a percent)		85.00%
Offering period		6 months
Shares reserved for issuance (in shares)		400,000
Threshold number of additional shares available for future grant (in shares)	1,000,000
Shares available for future grant (in shares)	4,913,030
2010 Plan | Employee Stock Purchase Plan | Class A common stock
Stock Benefit Plans
Percentage for the threshold number of additional shares available for future grant, expressed as percentage of common stock outstanding on the last day of the immediately preceding fiscal year (as a percent)	1.00%
2019 Equity plan
Stock Benefit Plans
Shares available for future grant (in shares)	10,954,595
2019 Equity plan | Class A common stock
Stock Benefit Plans
Shares reserved for issuance (in shares)	10,000,000
2005 Equity Plan
Stock Benefit Plans
Shares available for future grant (in shares)	0
2019 Equity Plan and 2010 Purchase Plan
Stock Benefit Plans
Shares available for future grant (in shares)	15,867,625

Employee Stock Benefit Plans _5

Employee Stock Benefit Plans - Restricted Stock Awards - General Information (Details) - shares	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Restricted Stock
Stock Benefit Plans
Granted (in shares)	198,523	129,784	134,793

Employee Stock Benefit Plans _6

Employee Stock Benefit Plans - Restricted Stock Awards - Activity (Details) - Restricted Stock - $ / shares	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Number of Shares
Outstanding at the beginning of the period (in shares)	64,896
Granted (in shares)	198,523	129,784	134,793
Vested (in shares)	(65,547)
Forfeited (in shares)	(16,224)
Outstanding at the end of the period (in shares)	181,648	64,896
Weighted-Average Grant Date Fair Value
Outstanding at the beginning of the period (in dollars per share)	$ 18.58
Granted (in dollars per share)	10.96
Vested (in dollars per share)	17.18
Forfeited (in dollars per share)		$ 18.58
Outstanding at the end of the period (in dollars per share)	$ 10.76	$ 18.58

Employee Stock Benefit Plans _7

Employee Stock Benefit Plans - Restricted Stock Units - General Information (Details) - Restricted stock units - shares	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2015
Stock Benefit Plans
Right to number of shares of common stock per RSU (in shares)	1
Vesting percentage (as a percent)		25.00%

Employee Stock Benefit Plans _8

Employee Stock Benefit Plans - Restricted Stock Units - Activity (Details) - Restricted stock units	12 Months Ended
	Dec. 31, 2019$ / sharesshares
Number of Shares
Outstanding at the beginning of the period (in shares) | shares	3,057,808
Granted (in shares) | shares	3,097,661
Vested (in shares) | shares	(1,298,536)
Forfeited (in shares) | shares	(1,649,844)
Outstanding at the end of the period (in shares) | shares	3,207,089
Weighted-Average Grant Date Fair Value
Outstanding at the beginning of the period (in dollars per share) | $ / shares	$ 15.53
Granted (in dollars per share) | $ / shares	12.11
Vested (in dollars per share) | $ / shares	15.38
Forfeited (in dollars per share) | $ / shares	13.84
Outstanding at the end of the period (in dollars per share) | $ / shares	$ 12.33

Employee Stock Benefit Plans _9

Employee Stock Benefit Plans - Stock Options - General Information (Details) - Employee stock options	12 Months Ended
	Dec. 31, 2019
Stock Benefit Plans
Expiration period	10 years
Vesting period	4 years

Employee Stock Benefit Plans_10

Employee Stock Benefit Plans - Stock Options - Assumptions (Details) - Employee stock options	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Weighted-average assumptions used to estimate the fair value of the stock options using the Black-Scholes option-pricing model
Expected volatility (as a percent)	46.30%	43.70%	45.80%
Expected term	6 years 1 month 6 days	6 years	6 years
Risk-free interest rate (as a percent)	2.50%	2.70%	2.00%
Expected dividend yield (as a percent)	0.00%	0.00%	0.00%

Employee Stock Benefit Plans_11

Employee Stock Benefit Plans - Stock Options - Additional Information (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Stock Benefit Plans
Share-based compensation expense	$ 31,278	$ 41,082	$ 30,905
Employee stock options
Stock Benefit Plans
Weighted average grant date fair value (in dollars per share)	$ 6.10	$ 6.81	$ 7.62
Options outstanding (in shares)	17,194,239	20,457,537
Vesting period	4 years
Number of Shares - Exercisable (in shares)	14,030,936
Shares issuable under outstanding options (in shares)	17,194,239	20,457,537
Share-based compensation expense	$ 12,526	$ 20,478	$ 19,331
Performance-based milestone options
Stock Benefit Plans
Vested (in shares)	0	0
Share-based compensation expense	$ 0	$ 0	$ 0

Employee Stock Benefit Plans_12

Employee Stock Benefit Plans - Stock Options - Activity (Details) - Employee stock options - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Number of Shares
Outstanding at the beginning of the period (in shares)	20,457,537
Granted (in shares)	5,743,167
Exercised (in shares)	(1,369,327)
Cancelled (in shares)	(7,637,138)
Outstanding at the end of the period (in shares)	17,194,239	20,457,537
Weighted-Average Exercise Price
Outstanding at the beginning of the period (in dollars per share)	$ 13.47
Granted (in dollars per share)	11.71
Exercised (in dollars per share)	8.33
Cancelled (in dollars per share)	12.32
Outstanding at the end of the period (in dollars per share)	$ 12.13	$ 13.47
Vested or expected to vest
Number of Shares (in shares)	16,729,428
Weighted-Average Exercise Price (in dollars per share)	$ 12.13
Weighted Average Contractual Life	5 years 3 days
Aggregate Intrinsic Value	$ 24,590
Stock options
Weighted Average Contractual Life - Outstanding	5 years 1 month 9 days	5 years 9 months 18 days
Aggregate Intrinsic Value - Outstanding	$ 25,226	$ 4,147
Number of Shares - Exercisable (in shares)	14,030,936
Weighted-Average Exercise Price - Exercisable (in dollars per share)	$ 12.07
Weighted Average Contractual Life - Exercisable	4 years 3 months 29 days
Aggregate Intrinsic Value - Exercisable	$ 21,423

Employee Stock Benefit Plans_13

Employee Stock Benefit Plans - Stock Options - Total Intrinsic Value (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Employee stock options
Stock options
Total intrinsic value of options exercised	$ 5.1	$ 20.1	$ 16

Employee Stock Benefit Plans_14

Employee Stock Benefit Plans - Unrecognized Share-based Compensation (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2019USD ($)
Employee stock options
Unrecognized share-based compensation
Unrecognized Expense, Net of Estimated Forfeitures	$ 13,849
Weighted-Average Remaining Recognition Period	2 years 7 months 17 days
Restricted Stock
Unrecognized share-based compensation
Unrecognized Expense, Net of Estimated Forfeitures	$ 758
Weighted-Average Remaining Recognition Period	4 months 28 days
Restricted stock units
Unrecognized share-based compensation
Unrecognized Expense, Net of Estimated Forfeitures	$ 24,469
Weighted-Average Remaining Recognition Period	2 years 5 months 12 days
Performance-based milestone options
Unrecognized share-based compensation
Unrecognized Expense, Net of Estimated Forfeitures	$ 147

Income Taxes - General Informat

Income Taxes - General Information (Details) - USD ($) $ in Thousands	Dec. 22, 2017	Dec. 31, 2017
Income Taxes
Effect of tax reform	$ 153,900	$ 153,894

Income Taxes - Reconciliation o

Income Taxes - Reconciliation of Income Taxes (Details) - USD ($) $ in Thousands	Dec. 22, 2017	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Reconciliation of income taxes
Income tax benefit using U.S. federal statutory rate		$ 4,517	$ (59,297)	$ (39,759)
Effect of tax reform	$ 153,900			153,894
Permanent differences		65	218	34
State income taxes, net of federal benefit		(1,902)	(17,121)	(6,117)
Disallowed separation related costs		4,658
Executive compensation - Section 162(m)		662	8
Meals and entertainment		495	995	1,346
Non-deductible share-based compensation		(1,202)	(494)	9
Excess tax benefits		3,324	(1,223)	(2,626)
Fair market valuation of Note Hedge Warrants and Convertible Note Hedges		(290)	2,367	1,289
Tax credits		(4,374)	(7,863)	(12,290)
Expiring net operating losses and tax credits		3,764	250	276
Effect of change in state tax rate on deferred tax assets and deferred tax liabilities		(2,563)	1,476	(232)
Change in the valuation allowance		(7,154)	80,684	(95,824)
Benefit for income taxes from continuing operations		$ 0	$ 0	$ 0

Income Taxes - Deferred Tax Ass

Income Taxes - Deferred Tax Assets and Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Deferred tax assets:
Net operating loss carryforwards	$ 265,494	$ 259,450
Tax credit carryforwards	59,892	60,115
Capitalized research and development	9,952	12,113
Contingent consideration		14
Share-based compensation	24,401	23,242
Basis difference on North America collaboration agreement	48,594	36,423
Accruals and reserves	6,415	10,867
Basis difference on 2022 Notes	4,322	7,220
Interest Expense	22,020	5,104
Intangibles		25,928
Operating lease liability	6,421
Other	5,295	18,867
Total deferred tax assets	452,806	459,343
Deferred tax liabilities:
Basis Difference on 2024 Convertible Notes	(7,381)
Basis Difference on 2026 Convertible Notes	(10,276)
Operating lease right-of-use assets	(4,905)
Total deferred tax liabilities	(22,562)
Net deferred tax assets	430,244	459,343
Valuation allowance	(430,244)	(459,343)
Net deferred tax asset	$ 0	$ 0

Income Taxes - Valuation Allowa

Income Taxes - Valuation Allowance (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Income Taxes
(Decrease) increase in valuation allowance		$ 80.7
Lesinurad transaction
Income Taxes
(Decrease) increase in valuation allowance	$ (29.1)

Income Taxes - Net Operating Lo

Income Taxes - Net Operating Loss Carryforwards (Details) - USD ($) $ in Millions	Dec. 31, 2019	Dec. 31, 2018
Federal
Net operating loss carryforwards
Net operating loss carryforwards	$ 1,200
Federal | Tax Year 2018
Net operating loss carryforwards
Net operating loss carryforwards	32.7	$ 89.1
State
Net operating loss carryforwards
Net operating loss carryforwards	$ 1,000	$ 877,100

Income Taxes - Tax Credit Carry

Income Taxes - Tax Credit Carryforwards (Details) - USD ($) $ in Millions	Dec. 31, 2019	Dec. 31, 2018
Tax credit carryforward
Tax credit carryforward	$ 64.6	$ 63.3

Income Taxes - Unrecognized Inc

Income Taxes - Unrecognized Income Tax Benefits - Tabular Disclosure (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Unrecognized income tax benefits
Unrecognized Tax Benefits, Beginning Balance	$ 38,551	$ 24,078	$ 26,393
Increases based on tax positions related to the current period	51,699	38,551	24,078
Increases for tax positions of prior periods	1,400
Decreases for tax positions in prior periods	(38,551)	(24,078)	(26,393)
Unrecognized Tax Benefits, End Balance	$ 53,099	$ 38,551	$ 24,078

Income Taxes - Unrecognized I_2

Income Taxes - Unrecognized Income Tax Benefits - Additional Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Unrecognized tax benefits
Unrecognized tax benefits	$ 53,099	$ 38,551	$ 24,078	$ 26,393
Amount of unrecognized tax benefits that, if recognized, would affect effective tax rate	0
Interest and tax penalties expense	$ 0	$ 0	$ 0

Defined Contribution Plan (Deta

Defined Contribution Plan (Details) - USD ($)	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Defined Contribution Plan
Employer match of first $6,000 of employee contributions (as a percent)	75.00%
Amount of employee contributions matched 75% by employer	$ 6,000
Compensation cost	$ 2,200,000	$ 3,200,000	$ 3,500,000
Minimum
Defined Contribution Plan
Employee contribution per calendar year (as a percent of compensation)	1.00%
Maximum
Defined Contribution Plan
Employee contribution per calendar year (as a percent of compensation)	100.00%

Related Party Transactions (Det

Related Party Transactions (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Related Party Transactions
Accounts payable from related party	$ 1,509
Investor | Allergan
Related Party Transactions
Accounts receivable	106,000	$ 60,000
Board of Directors member
Related Party Transactions
Amount of insurance premium paid to the insurance provider	7,400	11,900	$ 12,100
Accounts payable from related party	0	$ 0
Cyclerion Therapeutics, Inc.
Related Party Transactions
Accounts payable from related party	$ 1,500

Workforce Reduction - General I

Workforce Reduction - General Information (Details) $ in Thousands	Feb. 07, 2019employee	Aug. 16, 2018USD ($)employee	Jun. 27, 2018employeeitem	Jan. 30, 2018employee	Sep. 30, 2018employee	Jun. 30, 2018employee	Mar. 31, 2018USD ($)employee	Dec. 31, 2019USD ($)	Dec. 31, 2018USD ($)
Restructuring expenses
Restructuring expenses								$ 3,620	$ 14,715
Employee severance, benefits and related costs
Restructuring expenses
Restructuring expenses								3,198	10,492
Contract related costs
Restructuring expenses
Restructuring expenses								0	1,265
Reduction in Field-based Workforce, January 30, 2018
Workforce Reduction
Number of employees eliminated | employee				60			60
Restructuring expenses
Employee severance, benefits and related costs							$ 2,400
Reduction in Field-based Workforce, January 30, 2018 | Employee severance, benefits and related costs
Restructuring expenses
Restructuring expenses									2,228
Reduction in Headquarter-based Workforce, June 27, 2018
Workforce Reduction
Number of new business | item			2
Number of employees expected to be eliminated | employee			40			40
Restructuring expenses
Employee severance, benefits and related costs								4,000	4,000
Reduction in Headquarter-based Workforce, June 27, 2018 | Employee severance, benefits and related costs
Restructuring expenses
Restructuring expenses								16	2,881
Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018
Workforce Reduction
Number of employees eliminated | employee					100
Number of employees expected to be eliminated | employee		100
Restructuring expenses
Restructuring expenses		$ 8,300
Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018 | Employee severance, benefits and related costs
Restructuring expenses
Restructuring expenses		5,400						0	5,383
Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018 | Contract related costs
Restructuring expenses
Restructuring expenses		$ 2,900						0	$ 1,265
Reduction in Workforce, February 7, 2019
Workforce Reduction
Number of employees expected to be eliminated | employee	35
Restructuring expenses
Employee severance, benefits and related costs								3,700
Reduction in Workforce, February 7, 2019 | Employee severance, benefits and related costs
Restructuring expenses
Restructuring expenses								$ 3,182

Workforce Reduction - Tabular D

Workforce Reduction - Tabular Disclosure (Details) - USD ($) $ in Thousands	Aug. 16, 2018	Dec. 31, 2019	Dec. 31, 2018
Workforce Reduction
Charges		$ 3,620	$ 14,715
Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018
Workforce Reduction
Charges	$ 8,300
Employee severance, benefits and related costs
Workforce Reduction
Balance at beginning of period		2,452	0
Charges		3,198	10,492
Amounts paid		(5,365)	(7,811)
Adjustments		(210)	(229)
Balance at end of period		75	2,452
Employee severance, benefits and related costs | Reduction in Field-based Workforce, January 30, 2018
Workforce Reduction
Balance at beginning of period		0	0
Charges			2,228
Amounts paid			(2,215)
Adjustments			(13)
Balance at end of period			0
Employee severance, benefits and related costs | Reduction in Headquarter-based Workforce, June 27, 2018
Workforce Reduction
Balance at beginning of period		696	0
Charges		16	2,881
Amounts paid		(689)	(2,074)
Adjustments		(23)	(111)
Balance at end of period		0	696
Employee severance, benefits and related costs | Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018
Workforce Reduction
Balance at beginning of period		1,756	0
Charges	5,400	0	5,383
Amounts paid		(1,708)	(3,522)
Adjustments		(48)	(105)
Balance at end of period		0	1,756
Employee severance, benefits and related costs | Reduction in Workforce, February 7, 2019
Workforce Reduction
Balance at beginning of period		0
Charges		3,182
Amounts paid		(2,968)
Adjustments		(139)
Balance at end of period		75	0
Contract related costs
Workforce Reduction
Balance at beginning of period		433	0
Charges		0	1,265
Amounts paid		(287)	(614)
Adjustments		(42)	(218)
Balance at end of period		104	433
Contract related costs | Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018
Workforce Reduction
Balance at beginning of period		433	0
Charges	$ 2,900	0	1,265
Amounts paid		(287)	(614)
Adjustments		(42)	(218)
Balance at end of period		$ 104	$ 433

Workforce Reduction - Restructu

Workforce Reduction - Restructuring Expenses (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018
Restructuring expenses
Restructuring expenses	$ 3,620	$ 14,715

Selected Quarterly Financial _3

Selected Quarterly Financial Data (Unaudited) - Tabular Disclosure (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Selected Quarterly Financial Data
Total revenues	$ 126,301	$ 131,167	$ 102,215	$ 68,730	$ 130,692	$ 65,686	$ 81,106	$ 69,155	$ 428,413	$ 346,639	$ 298,276
Total cost and expenses	76,709	65,280	80,638	85,663	100,831	212,257	95,783	88,438	308,290	497,309	313,639
Other expense, net	(1,735)	(45,239)	(9,294)	(4,912)	(21,488)	(5,252)	(9,460)	(7,276)	(61,180)	(43,476)	(39,552)
Net (loss) income from continuing operations	47,858	20,648	12,283	(21,846)	8,373	(151,823)	(24,137)	(26,559)	58,943	(194,146)	(54,915)
Net loss from discontinued operations				(37,438)	(23,866)	(22,528)	(25,243)	(16,585)	(37,438)	(88,222)	(62,022)
Net income (loss)	$ 47,858	$ 20,648	$ 12,283	$ (59,284)	$ (15,493)	$ (174,351)	$ (49,380)	$ (43,144)	$ 21,505	$ (282,368)	$ (116,937)
Net (loss) income per share from continuing operations - basic	$ 0.31	$ 0.13	$ 0.08	$ (0.14)					$ 0.38
Net (loss) income per share from continuing operations - diluted	0.30	0.13	0.08	(0.14)					0.38
Net (loss) income per share from continuing operations - basic and diluted					$ 0.05	$ (0.99)	$ (0.16)	$ (0.18)	0.38	$ (1.27)	$ (0.37)
Net loss per share from discontinued operations - basic and diluted				(0.24)	(0.15)	(0.15)	(0.17)	(0.11)	(0.24)	(0.58)	(0.42)
Net (loss) income per share - basic	0.31	0.13	0.08	(0.38)					0.14
Net (loss) income per share - diluted	$ 0.30	$ 0.13	$ 0.08	$ (0.38)					0.14
Net (loss) income per share - basic and diluted					$ (0.10)	$ (1.14)	$ (0.32)	$ (0.29)	$ 0.14	$ (1.85)	$ (0.78)

Selected Quarterly Financial _4

Selected Quarterly Financial Data (Unaudited) - Collaborative Arrangements (Details) - USD ($) $ in Thousands

Aug. 01, 2019

Dec. 31, 2019

Sep. 30, 2019

Jun. 30, 2019

Mar. 31, 2019

Dec. 31, 2018

Sep. 30, 2018

Jun. 30, 2018

Mar. 31, 2018

Dec. 31, 2019

Dec. 31, 2018

Dec. 31, 2017

Collaboration agreements

Revenue

$ 126,301

$ 131,167

$ 102,215

$ 68,730

$ 130,692

$ 65,686

$ 81,106

$ 69,155

$ 428,413

$ 346,639

$ 298,276

Linaclotide Partners | Japan

Collaboration agreements

Revenue

70,400

AstraZeneca

Collaboration agreements

Revenue From Non Contingent Payments

32,400

Astellas Pharma Inc.

Collaboration agreements

Upfront Fee Received

10,000

Collaborative arrangements revenue

Collaboration agreements

Revenue

379,652

272,839

$ 265,533

Collaborative arrangement, collaboration and license agreements | Astellas Pharma Inc. | Japan

Collaboration agreements

Revenue

$ 20,400

$ 10,147

Collaborative arrangement, collaboration agreements | Linaclotide Partners

Collaboration agreements

Revenue

$ 48,800

Selected Quarterly Financial _5

Selected Quarterly Financial Data (Unaudited) - Restructuring Expenses (Details) - USD ($) $ in Thousands	1 Months Ended	12 Months Ended
	Apr. 30, 2019	Dec. 31, 2019	Dec. 31, 2018
Restructuring expenses
Restructuring expenses		$ 3,620	$ 14,715
Gain on lease modification	$ 3,200	$ 3,169

Selected Quarterly Financial _6

Selected Quarterly Financial Data (Unaudited) - Intangible Assets Impairment (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2018USD ($)
Impairment of intangible assets
Impairment of intangible assets	$ 151,794

Selected Quarterly Financial _7

Selected Quarterly Financial Data (Unaudited) - Contingent Consideration (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017
Contingent Consideration
Gain on fair value remeasurement of contingent consideration	$ (31,045)	$ (31,310)
Lesinurad transaction
Contingent Consideration
Gain on fair value remeasurement of contingent consideration	$ (31,000)

Selected Quarterly Financial _8

Selected Quarterly Financial Data (Unaudited) - Gain (Loss) on Derivatives (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Gain (Loss) on Derivatives
Loss on fair value measurement of derivatives	$ (3,023)	$ 8,743	$ 3,284

Selected Quarterly Financial _9

Selected Quarterly Financial Data (Unaudited) - Loss on Extinguishment of Debt (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2017
Notes Payable
Loss on extinguishment of debt	$ 30,977	$ 2,009