Ironwood Pharmaceuticals (IRWD) 10-Q 30 Jul 19 2019 Q2 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - $ / shares	6 Months Ended
	Jun. 30, 2019	Jul. 26, 2019
Document and Entity Information [Abstract]
Entity Central Index Key	0001446847
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Jun. 30, 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	301 Binney Street
Entity Address, City or Town	Cambridge
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	02142
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 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 Common Stock, Shares Outstanding		156,495,574
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	Q2
Amendment Flag	false

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 98,908	$ 173,172
Accounts receivable, net	22,604	20,991
Related party accounts receivable, net	81,182	59,959
Inventory, net	1,735
Prepaid expenses and other current assets	8,880	10,216
Restricted cash	7,676	1,250
Current assets of discontinued operations		847
Total current assets	220,985	266,435
Restricted cash, net of current portion	971	6,426
Property and equipment, net	6,665	7,652
Operating lease right-of-use assets	25,569
Convertible note hedges	60,720	41,020
Goodwill	785	785
Other assets	26	89
Non-current assets of discontinued operations		9,643
Total assets	315,721	332,050
Current liabilities:
Accounts payable	7,872	14,891
Related party accounts payable, net	2,036
Accrued research and development costs	6,270	2,963
Accrued expenses and other current liabilities	33,982	38,001
Capital lease obligations		73
Current portion of deferred rent		252
Current portion of 2026 Notes	48,797	47,554
Current portion of operating lease liabilities	11,904
Current portion of contingent consideration		51
Current liabilities of discontinued operations		15,739
Total current liabilities	110,861	119,524
Capital lease obligations, net of current portion		158
Deferred rent, net of current portion		6,308
Note hedge warrants	50,191	33,763
Convertible senior notes	274,395	265,601
Operating lease liabilities, net of current portion	22,508
Operating lease liabilities, net of current portion	18,685
2026 Notes, net of current portion	78,330	100,537
Other liabilities	2,626	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 XXX issued and outstanding at June 30, 2019 and 500,000,000 shares authorized and 154,414,691 shares issued and outstanding at December 31, 2018	156	154
Additional paid-in capital	1,421,215	1,394,603
Accumulated deficit	(1,640,738)	(1,591,128)
Total stockholders' deficit	(219,367)	(196,371)
Total liabilities and stockholders' deficit	$ 315,721	$ 332,050

Condensed Consolidated Balanc_2

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 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	156,442,332	154,414,691
Common stock, shares outstanding	156,442,332	154,414,691

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Revenues:
Total revenues	$ 102,215	$ 81,106	$ 170,945	$ 150,261
Cost and expenses:
Cost of revenues, excluding amortization of acquired intangible assets	11,313	4,065	12,356	6,672
Write-down of commercial supply and inventory to net realizable value and loss on non-cancellable purchase commitments		1,836		1,836
Research and development	28,758	23,187	60,956	43,663
Selling, general and administrative	43,246	59,771	92,341	118,716
Amortization of acquired intangible assets		3,476		6,952
Loss on fair value remeasurement of contingent consideration		1,962		2,474
Gain on lease modification	(3,169)		(3,169)
Restructuring expenses	490	1,486	3,818	3,908
Total cost and expenses	80,638	95,783	166,302	184,221
Income (loss) from operations	21,577	(14,677)	4,643	(33,960)
Other (expense) income:
Interest expense	(9,430)	(9,383)	(19,022)	(18,656)
Interest and investment income	668	732	1,404	1,413
(Loss) gain on derivatives	(672)	(809)	3,272	507
Other income	140		140
Other expense, net	(9,294)	(9,460)	(14,206)	(16,736)
Net income (loss) from continuing operations	12,283	(24,137)	(9,563)	(50,696)
Net loss from discontinued operations		(25,243)	(37,438)	(41,828)
Net income (loss)	$ 12,283	$ (49,380)	$ (47,001)	$ (92,524)
Net income (loss) per share from continuing operations-basic and diluted (in dollars per share)	$ 0.08	$ (0.16)	$ (0.06)	$ (0.33)
Net loss per share from discontinued operations-basic and diluted (in dollars per share)		(0.17)	(0.24)	(0.28)
Net income (loss) per share-basic and diluted (in dollars per share)	$ 0.08	$ (0.32)	$ (0.30)	$ (0.61)
Weighted average number of common shares-basic and diluted (in shares)	155,849	152,163	155,405	151,591
Collaborative arrangements revenue
Revenues:
Total revenues	$ 77,322	$ 71,207	$ 143,474	$ 134,293
Product revenue, net
Revenues:
Total revenues		1,096		1,731
Sale of active pharmaceutical ingredient
Revenues:
Total revenues	$ 24,893	$ 8,803	$ 27,471	$ 14,237

Condensed Consolidated Statem_2

Condensed Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Condensed Consolidated Statements of Comprehensive Loss
Net income (loss)	$ 12,283	$ (49,380)	$ (47,001)	$ (92,524)
Other comprehensive income:
Unrealized gains on available-for-sale securities		47		35
Total other comprehensive income		47		35
Comprehensive income (loss)	$ 12,283	$ (49,333)	$ (47,001)	$ (92,489)

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, 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 related to share-based awards and employee stock purchase plan	$ 1		6,193			6,194
Issuance of common stock related to share-based awards and employee stock purchase plan (in shares)	882,448	272,146
Issuance of common stock awards, net of cancellations (in shares)	162
Conversion of Class B common stock to Class A common stock (in shares)	258,551	(258,551)
Share-based compensation expense related to share-based awards and employee stock purchase plan			9,062			9,062
Unrealized gains (losses) on available-for-sale securities					(12)	(12)
Net income (loss)				(43,144)		(43,144)
Balance at Mar. 31, 2018	$ 138	$ 14	1,333,791	(1,351,904)	(91)	(18,052)
Balance (in shares) at Mar. 31, 2018	137,606,687	13,997,357
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
Unrealized gains (losses) on available-for-sale securities						35
Net income (loss)						(92,524)
Balance at Jun. 30, 2018	$ 139	$ 14	1,357,224	(1,401,284)	(44)	(43,951)
Balance (in shares) at Jun. 30, 2018	138,860,929	13,992,491
Balance at Mar. 31, 2018	$ 138	$ 14	1,333,791	(1,351,904)	(91)	(18,052)
Balance (in shares) at Mar. 31, 2018	137,606,687	13,997,357
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to share-based awards and employee stock purchase plan	$ 1		12,865			12,866
Issuance of common stock related to share-based awards and employee stock purchase plan (in shares)	989,830	129,501
Issuance of common stock awards, net of cancellations (in shares)	130,045
Conversion of Class B common stock to Class A common stock (in shares)	134,367	(134,367)
Share-based compensation expense related to share-based awards and employee stock purchase plan			10,568			10,568
Unrealized gains (losses) on available-for-sale securities					47	47
Net income (loss)				(49,380)		(49,380)
Balance at Jun. 30, 2018	$ 139	$ 14	1,357,224	(1,401,284)	$ (44)	(43,951)
Balance (in shares) at Jun. 30, 2018	138,860,929	13,992,491
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 related to share-based awards and employee stock purchase plan	$ 2		3,486			3,488
Issuance of common stock related to share-based awards and employee stock purchase plan (in shares)	1,210,858
Share-based compensation expense related to share-based awards and employee stock purchase plan			14,988			14,988
Net income (loss)				(59,284)		(59,284)
Balance at Mar. 31, 2019	$ 156		1,413,077	(1,650,412)		(237,179)
Balance (in shares) at Mar. 31, 2019	155,625,549
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
Net income (loss)						(47,001)
Balance at Jun. 30, 2019	$ 156		1,421,215	(1,640,738)		(219,367)
Balance (in shares) at Jun. 30, 2019	156,442,332
Balance at Mar. 31, 2019	$ 156		1,413,077	(1,650,412)		(237,179)
Balance (in shares) at Mar. 31, 2019	155,625,549
Increase (Decrease) in Stockholders' Equity
Issuance of common stock upon exercise of stock options and employee stock purchase plan, net of cancellations			1,801			1,801
Issuance of common stock upon exercise of stock options and employee stock purchase plan, net of cancellations (in shares)	621,588
Share-based compensation expense related to share-based awards and employee stock purchase plan			6,337			6,337
Share-based compensation expense related to share-based awards and employee stock purchase plan (in shares)	195,195
Dividend of sGC business				(2,609)		(2,609)
Net income (loss)				12,283		12,283
Balance at Jun. 30, 2019	$ 156		$ 1,421,215	$ (1,640,738)		$ (219,367)
Balance (in shares) at Jun. 30, 2019	156,442,332

Condensed Consolidated Statem_4

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018
Cash flows from operating activities:
Net loss	$ (47,001)	$ (92,524)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	1,539	2,189
Amortization of acquired intangible assets		6,952
Loss (gain) on disposal of property and equipment	109	(275)
Gain on lease modification	(3,169)
Share-based compensation expense	20,271	18,054
Change in fair value of note hedge warrants	16,428	50,831
Change in fair value of convertible note hedges	(19,700)	(51,338)
Write-down of commercial supply and inventory to net realizable value and loss on non-cancellable purchase commitments		1,836
Write-down of excess non-cancellable ZURAMPIC and DUZALLO sample purchase commitments		390
Accretion of discount/premium on investment securities		(138)
Non-cash interest expense	9,300	8,591
Non-cash change in fair value of contingent consideration		2,474
Changes in assets and liabilities:
Accounts receivable and related party accounts receivable, net	(21,529)	1,638
Prepaid expenses and other current assets	2,647	(9,591)
Inventory, net	(635)	(992)
Other assets	(6)	68
Accounts payable, related party accounts payable and accrued expenses	(25,205)	2,096
Accrued research and development costs	2,335	202
Operating lease right-of-use assets	6,315
Operating lease liabilities	(4,685)
Deferred rent		655
Net cash used in continuing operating activities	(62,986)	(58,882)
Net cash provided by discontinued operating activities	11,364	5,305
Net cashed used in operating activities	(51,622)	(53,577)
Cash flows from investing activities:
Purchases of available-for-sale securities		(2,491)
Sales and maturities of available-for-sale securities		62,512
Purchases of property and equipment	(1,444)	(1,447)
Proceeds from sale of property and equipment	261	273
Net cash (used in) provided by continuing investing activities	(1,183)	58,847
Net cash used in discontinued investing activities	(4,223)	(1,754)
Net cash (used in) provided by investing activities	(5,406)	57,093
Cash flows from financing activities:
Proceeds from exercise of stock options and employee stock purchase plan	5,204	19,044
Payments on capital lease obligations		(1,510)
Principal payments on 2026 notes	(21,469)
Payments on contingent purchase price consideration		(121)
Net cash (used in) provided by continuing financing activities	(16,265)	17,413
Net cash (used in) provided by financing activities	(16,265)	17,413
Net (decrease) increase in cash, cash equivalents and restricted cash	(73,293)	20,929
Cash, cash equivalents and restricted cash, beginning of period	180,848	132,792
Cash, cash equivalents and restricted cash, end of period	$ 107,555	$ 153,721

Condensed Consolidated Statem_5

Condensed Consolidated Statements of Cash Flows (Parenthetical) - USD ($) $ in Thousands	Jun. 30, 2019	Jun. 30, 2018
Reconciliation of cash, cash equivalents, and restricted cash to the condensed consolidated balance sheets
Cash and cash equivalents	$ 98,908	$ 145,415
Restricted cash	8,647	8,306
Total cash, cash equivalents, and restricted cash	$ 107,555	$ 153,721

Nature of Business

Nature of Business	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Nature of Business	1. Nature of Business ​ Overview ​ Ironwood Pharmaceuticals, Inc. (“Ironwood” or the “Company”) is a gastrointestinal (“GI”) healthcare company dedicated to creating medicines that make a difference for people living with GI diseases. The Company is advancing innovative product opportunities in areas of large unmet need, capitalizing on its proven development and commercial capabilities and its deep expertise 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 called Cyclerion Therapeutics, Inc. (“Cyclerion”). ​ The Company’s commercial product, linaclotide, is available to adult men and women suffering from irritable bowel syndrome with constipation (“IBS-C”), or chronic idiopathic constipation (“CIC”), in certain countries around the world. As many as 13 million adults suffer from IBS-C and as many as 35 million adults suffer from CIC in the U.S. alone, according to our analysis of studies including P Pare, et al. (published in 2001 in the American Journal of Gastroenterology) and J.F. Johanson, et al. (published in 2007 in Alimentary Pharmacology and Therapeutics) and American College of Gastroenterology Chronic Constipation Task Force (2005), American Journal of Gastroenterology Vol. 100, No. S1, 2005. Symptoms of IBS-C include abdominal pain, discomfort or bloating and constipation symptoms (for example, incomplete evacuation, infrequent bowel movements, hard/lumpy stools), while CIC is primarily characterized by constipation symptoms. ​ Linaclotide is available under the trademarked name LINZESS ® ® to adult men and women suffering from IBS-C or CIC in Canada, and to adult men and women suffering from IBS-C in certain European countries. ​ The Company has formed 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, Hong Kong, 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. The Company has a collaboration agreement with AstraZeneca AB (together with its affiliates, “AstraZeneca”), to co-develop and co-commercialize linaclotide in China, Hong Kong and Macau, with AstraZeneca having primary responsibility for the local operational execution. In January 2019, the National Medical Products Administration approved the marketing application for LINZESS for adults with IBS-C in China. ​ 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 also advancing MD-7246, a delayed release form of linaclotide, as an oral, intestinal, non-opioid pain relieving agent for patients suffering from abdominal pain associated with certain GI diseases. There are an estimated 16 million Americans who suffer from symptoms of IBS-D, according to Grundmann and Yoon in Irritable Bowel Syndrome: epidemiology, diagnosis and treatment: an update for health-care practitioners (published in the Journal of Gastroenterology and Hepatology in 2010) and the United States Census Bureau. In May 2019, the Company and Allergan initiated a Phase II clinical trial evaluating 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 persistent gastroesophageal reflux disease (“GERD”). There are an estimated 10 million Americans who suffer regularly from symptoms of GERD, such as heartburn and regurgitation, despite receiving treatment with the current standard of care, a proton pump inhibitor, to suppress stomach acid, according to a study published in 2014 by HB El-Sarag, Sweet S, Winchester CC et al Gut ​ 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 2). Cyclerion is a clinical-stage biopharmaceutical company harnessing the power of sGC pharmacology to discover, develop, and commercialize breakthrough treatments for serious and orphan diseases. ​ 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 ​ Additionally, the Company has periodically entered into co-promotion agreements to maximize its salesforce productivity, such as its co-promotion agreement with Allergan to perform sales detailing activities for VIBERZI for treatment for adults suffering from IBS-D (Note 4). ​ Basis of Presentation ​ The accompanying condensed consolidated financial statements and the related disclosures are unaudited and have been prepared in accordance with accounting principles generally accepted in the U.S. Additionally, certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. Accordingly, these interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2018, which was filed with the Securities and Exchange Commission on February 25, 2019 (the “2018 Annual Report on Form 10-K”). ​ The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all normal recurring adjustments considered necessary for a fair presentation of the Company’s financial position as of June 30, 2019, and the results of its operations for the three and six months ended June 30, 2019 and 2018, its statements of stockholders’ deficit for the three and six months ended June 30, 2019 and 2018, and its cash flows for the six months ended June 30, 2019 and 2018. The results of operations for the three and six months ended June 30, 2019 and 2018 are not necessarily indicative of the results that may be expected for the full year or any other subsequent interim period. ​ ​ Principles of Consolidation ​ The accompanying condensed consolidated financial statements include the accounts of Ironwood and its wholly-owned subsidiaries as of June 30, 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. ​ Use of Estimates ​ The preparation of condensed 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 condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. On an on-going basis, the Company’s management evaluates its estimates, judgments and methodologies. Significant estimates and assumptions in the condensed consolidated financial statements include those related to revenue recognition; available-for-sale securities; accounts receivable; inventory valuation, and related reserves; impairment of long-lived assets, including goodwill; valuation procedures for right-of-use assets and operating lease liabilities; initial valuation procedures for the issuance 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. ​ Reclassifications of Prior Period Financial Statements ​ Certain prior period financial statement items, such as discontinued operations, have been reclassified to conform to current period presentation. ​ Summary of Significant Accounting Policies ​ The Company’s significant accounting policies are described in Note 2, Summary of Significant Accounting Policies ​ 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 ​ Leases Effective January 1, 2019, the Company adopted ASC Topic 842, Leases Leases ​ The recognition of right-of-use assets and lease liabilities related to our operating leases under ASC 842 has had a material impact on the Company’s condensed 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; ● 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 includes: leases for its current and future 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 condensed consolidated balance sheets. As of June 30, 2019, the Company did not have 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. ​ 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 three and six months ended June 30, 2019 that had a material effect on its condensed consolidated financial statements. ​ In February 2016, the FASB issued ASU No. 2016-02, Leases Leases (Topic 842), Codification Improvements Leases (Topic 842), Targeted Improvements , Leases (Topic 842), Codification Improvements . . ​ In June 2016, the FASB issued ASU No. 2016-13, Measurement of Credit Losses on Financial Instruments Codification Improvements to Topic 326, Financial Instruments—Credit Losses, Topic 815, Derivatives and Hedging, and Topic 825, Financial Instruments Financial Instruments—Credit Losses (Topic 326): Targeted Transition Relief is permitted. The Company is currently evaluating the potential impact that the adoption of these ASUs will have 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) ​ In June 2018, the FASB issued ASU No. 2018-07, Compensation—Stock Compensation (Topic 718) Improvements to Nonemployee Share-Based Payment Accounting . ​ In July 2018, the FASB issued ASU 2018-09, Codification Improvements Compensation—Stock Compensation—Income Taxes Compensation—Stock Compensation—Income Taxes ​ 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 ​ 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) ​ In October 2018, the FASB issued ASU No. 2018-17, Consolidation (Topic 810): Targeted Improvements to Related Party Guidance for Variable Interest Entities ​

Cyclerion Separation

Cyclerion Separation	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Cyclerion Separation	2. Cyclerion Separation ​ On April 1, 2019, Ironwood completed the Separation of 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 distribution, 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 it provides for when and how these transfers, assumptions and assignments occur. The purpose of the separation agreement is to provide Cyclerion and Ironwood with assets to operate their respective businesses and retain or assume liabilities related to those assets. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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 is due approximately $1.3 million as of June 30, 2019 associated with tenant improvement reimbursement provisions related to the Cyclerion lease in accordance with the separation agreement, which has been included in related party accounts receivable. ​ 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 was recognized during the three months ended June 30, 2019 (Note 10). ​ 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 for services provided to Cyclerion are recorded as other income and amounts for services provided by Cyclerion are recorded as selling, general and administrative expense and research and development expense, as applicable. During each of the three and six months ended June 30, 2019, the Company recorded an insignificant amount as other income for services provided to Cyclerion. During each of the three and six months ended June 30, 2019, the Company recorded an insignificant amount in both selling, general and administrative expense and research and development expense for services provided by Cyclerion. ​ 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 $1.7 million in research and development expenses under the development agreement during the three months ended June 30, 2019. ​ Discontinued Operations ​ Discontinued Operations ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ ​ 2019 2018 ​ 2019 2018 Costs and expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Research and development ​ ​ — ​ 15,745 ​ ​ 21,792 ​ 31,774 ​ Selling, general and administrative ​ ​ — ​ 8,592 ​ ​ 15,646 ​ 9,148 ​ Restructuring expenses ​ ​ — ​ ​ 906 ​ ​ — ​ ​ 906 ​ Net loss from discontinued operations ​ ​ — ​ ​ 25,243 ​ ​ 37,438 ​ ​ 41,828 ​ ​ ​ ​ ​ ​ ​ 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	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Net Income (Loss) Per Share	3. Net Income (Loss) Per Share ​ Basic and diluted net income (loss) per common share is computed by dividing net (income) loss by the weighted average number of common shares outstanding during the period. ​ In June 2015, in connection with the issuance of approximately $335.7 million in aggregate principal amount of 2.25% Convertible Senior Notes due 2022 (the “2022 Notes”) (Note 9), the Company entered into convertible note hedge transactions (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 Notes and/or offset any cash payments the Company is required to make in excess of the principal amount of converted 2022 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 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 anti-dilutive. ​ 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 9). 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 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): ​ ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended ​ ​ ​ June 30, ​ ​ 2019 2018 Options to purchase Class A common stock ​ 19,324 22,056 Shares subject to repurchase 182 130 Restricted stock units ​ 2,799 ​ 3,207 ​ Note Hedge Warrants ​ 23,135 ​ 20,250 ​ 2022 Notes ​ 23,135 ​ 20,250 ​ Total 68,575 65,893 ​ ​ During the three and six months ended June 30, 2019, the Company recorded net income of approximately $12.3 million and net loss of approximately $47.0 million, respectively. The inclusion of applicable securities in the calculation of diluted earnings per share was anti-dilutive for the three months ended June 30, 2019. As a result, diluted earnings per share is equivalent to basic earnings per share for the three and six months ended June 30, 2019. ​ ​

Collaboration, License, Co-Prom

Collaboration, License, Co-Promotion and Other Commercial Agreements	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Collaboration, License, Co-Promotion and Other Commercial Agreements	4. Collaboration, License, Co-Promotion and Other Commercial Agreements ​ For the three and six months ended June 30, 2019, the Company had linaclotide collaboration agreements with Allergan for North America and AstraZeneca for China, 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. The following table provides amounts included in the Company’s condensed consolidated statements of operations as collaborative arrangements revenue and sale of active pharmaceutical ingredient (“API”) attributable to transactions from these arrangements (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ Collaborative Arrangements Revenue ​ 2019 2018 ​ 2019 2018 Linaclotide Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Allergan (North America) ​ $ 75,498 ​ $ 69,810 ​ $ 140,283 ​ $ 131,408 ​ Allergan (Europe and other) ​ ​ 262 ​ ​ 304 ​ ​ 682 ​ ​ 576 ​ Co-Promotion and Other Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Allergan (VIBERZI) ​ ​ 1,239 ​ ​ 750 ​ ​ 1,239 ​ ​ 1,500 ​ Other ​ ​ 323 ​ ​ 343 ​ ​ 1,270 ​ ​ 809 ​ Total collaborative arrangements revenue ​ $ 77,322 ​ $ 71,207 ​ $ 143,474 ​ $ 134,293 ​ Sale of API (1) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Linaclotide Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Astellas (Japan) ​ $ 24,893 ​ $ 8,803 ​ $ 27,468 ​ $ 14,237 ​ Other (1) ​ ​ — ​ ​ — ​ ​ 3 ​ ​ — ​ Total sale of API ​ $ 24,893 ​ $ 8,803 ​ $ 27,471 ​ $ 14,237 ​ (1) Sale of API includes an insignificant amount of revenue from the sale of drug product to AstraZeneca in China during the six months ended June 30, 2019. ​ Accounts receivable, net and related party accounts receivable, net included approximately $103.8 million related to collaborative arrangements revenue and sale of API as of June 30, 2019, net of approximately $4.3 million related to related party accounts payable. ​ As of June 30, 2019, there were no impairment indicators for the accounts receivable recorded. During the three and six months ended June 30, 2019, there was no significant unusual activity in accounts receivable. ​ 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 June 30, 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 (Note 11). 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. ​ As a result of the research and development cost-sharing provisions of the linaclotide collaboration for North America, the Company offset approximately $2.4 million and approximately $5.6 million in incremental research and development costs during the three and six months ended June 30, 2019, respectively, and offset approximately $1.9 million and approximately $3.3 million in incremental research and development costs during the three and six months ended June 30, 2018, respectively, to reflect the obligations of each party under the collaboration to bear half of the development costs incurred. ​ The Company and Allergan began commercializing LINZESS in the U.S. in December 2012. The Company receives 50% of the net profits and bears 50% of the net losses from the commercial sale of LINZESS in the U.S. Net profits or net losses consist of net sales of LINZESS to third-party customers and sublicense income in the U.S. less the cost of goods sold as well as selling, general and administrative expenses. LINZESS net sales are calculated and recorded by Allergan and may include gross sales net of discounts, rebates, allowances, sales taxes, freight and insurance charges, and other applicable deductions. If either party provided fewer calls on physicians in a particular year than it was contractually required to provide, such party’s share of the net profits would be adjusted as set forth in the collaboration agreement for North America. The Company has completed its obligations under the terms of the commercial agreement with Allergan, pursuant to which it promoted CANASA, and these adjustments to the share of the net profits have been eliminated, in full, in 2018 and all subsequent years. ​ The Company evaluated this collaboration arrangement under ASC 606, Revenue from Contracts with Customers with the right-to-invoice exemption, 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. ​ The Company recognized collaborative arrangements revenue from the Allergan collaboration agreement for North America during the three and six months ended June 30, 2019 and 2018 as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ 2019 2018 2019 2018 Collaborative arrangements revenue related to sales of LINZESS in the U.S. ​ $ 74,973 ​ $ 69,264 ​ $ 139,267 ​ $ 130,413 ​ Royalty revenue ​ 525 ​ 546 ​ 1,016 ​ 995 ​ Total collaborative arrangements revenue ​ $ 75,498 ​ $ 69,810 ​ $ 140,283 ​ $ 131,408 ​ ​ The collaborative arrangements revenue recognized in the three and six months ended June 30, 2019 and 2018 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 three and six months ended June 30, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ 2019 2018 2019 2018 Collaborative arrangements revenue related to sales of LINZESS in the U.S. (1)(2) ​ $ 74,973 ​ $ 69,264 ​ $ 139,267 ​ $ 130,413 ​ Selling, general and administrative costs incurred by the Company (1) ​ (10,359) ​ (11,713) ​ (20,636) ​ (22,641) ​ The Company’s share of net profit ​ $ 64,614 ​ $ 57,551 ​ $ 118,631 ​ $ 107,772 ​ (1) Includes only collaborative arrangement revenue or selling, general and administrative costs attributable to the cost-sharing arrangement with Allergan for the three and six months ended June 30, 2019 and 2018. ​ In May 2014, CONSTELLA became commercially available in Canada and in June 2014, LINZESS became commercially available in Mexico. The Company records royalties on sales of CONSTELLA in Canada and LINZESS in Mexico in the period earned. The Company recognized approximately $0.5 million and approximately $1.0 million of combined royalty revenues from Canada and Mexico during the three and six months ended June 30, 2019, respectively. The Company recognized approximately $0.6 million and approximately $1.0 million of combined royalty revenues from Canada and Mexico during the three and six months ended June 30, 2018, respectively. ​ License Agreement with Allergan (All countries other than the countries and territories of North America, China, Hong Kong, 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 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 condensed consolidated financial statements as there was no deferred revenue associated with the 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. In evaluating the terms of the 2009 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 $0.3 million and approximately $0.7 million of royalty revenue from the European License Agreement during the three and six months ended June 30, 2019, respectively, and recognized approximately $0.3 million and approximately $0.6 million during the three and six months ended June 30, 2018, 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 is required to participate on a joint development committee over linaclotide’s development period. During the year ended December 31, 2017, the Company and Astellas entered into a commercial API supply agreement (the “Astellas Commercial Supply Agreement”). Pursuant to the Astellas Commercial Supply Agreement, the Company sells linaclotide API supply to Astellas at a contractually defined rate and recognizes related revenue as sale of API. Under the license agreement, the Company receives royalties which escalate based on sales volume, beginning in the low-twenties percent, less the transfer price paid for the API included in the product actually sold and other contractual deductions. Under the 2009 License Agreement with Astellas, the Company received an up-front licensing fee of $30.0 million and three development milestone payments that totaled up to $45.0 million, which were recognized as revenue prior to the adoption of ASC 606 on January 1, 2018. ​ 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 the adoption of ASC 606. However, there continues 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 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. ​ Additionally, under the terms of the Astellas Commercial Supply Agreement, the Company continues to have 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 results in earlier revenue recognition than the Company’s historical accounting. ​ The Company recognized approximately $24.9 million and approximately $27.5 million from the sale of API to Astellas under the license agreement and the Astellas Commercial Supply Agreement during the three and six months ended June 30, 2019, respectively, and recognized approximately $8.8 million and approximately $14.2 million during the three and six months ended June 30, 2018, respectively. The royalties on sales of LINZESS in Japan did not exceed the transfer price of API sold and other contractual deductions during each of the periods presented. ​ Collaboration Agreement for China, Hong Kong and Macau with AstraZeneca ​ In October 2012, the Company entered into a collaboration agreement with AstraZeneca (the “AstraZeneca Collaboration Agreement”) to co-develop and co-commercialize linaclotide in China, Hong Kong and Macau (the “License Territory”). The collaboration provides AstraZeneca with an exclusive nontransferable license to exploit the underlying technology in the License Territory. The parties share 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 includes the planned development of linaclotide in China, including the lead responsibility for each activity and the related internal and external costs. The IDP indicates that AstraZeneca is responsible for a multinational Phase III clinical trial (the “Phase III Trial”). The Company is responsible for nonclinical development and supplying clinical trial material and both parties are responsible for the regulatory submission process. The IDP indicates that the party specifically designated as being responsible for a particular development activity under the IDP shall implement and conduct such activities. The activities are governed by a Joint Development Committee (“JDC”), with equal representation from each party. The JDC is 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. The AstraZeneca Collaboration Agreement will continue until there is no longer a development plan or commercialization plan in place, however, it can be terminated by AstraZeneca at any time upon 180 days’ prior written notice. Under certain circumstances, either party may terminate the AstraZeneca Collaboration Agreement in the event of bankruptcy or an uncured material breach of the other party. Upon certain change in control scenarios of AstraZeneca, the Company may elect to terminate the AstraZeneca Collaboration Agreement and may re-acquire its product rights in a lump sum payment equal to the fair market value of such product rights. ​ There are 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 is also eligible for $125.0 million in additional commercial milestone payments contingent on the achievement of certain sales targets. The parties will also share in the net profits and losses associated with the development and commercialization of linaclotide in the License Territory, with AstraZeneca receiving 55% of the net profits or incurring 55% of the net losses until a certain specified commercial milestone is achieved, at which time profits and losses will be shared equally thereafter. 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. These additional activities serve to support the continued development of linaclotide in the License Territory, including the Phase III Trial. Pursuant to the terms of the modified IDP and development budget, certain of the Company’s deliverables were modified, specifically the research, development and regulatory services pursuant to the IDP, as modified from time to time (the “R&D Services”) and the obligation to supply clinical trial material. The modification did not have a material impact on the Company’s condensed consolidated financial statements. The total amount of the non-contingent consideration allocable to the AstraZeneca Collaboration Agreement and a co-promotion agreement was approximately $34.0 million (“Arrangement Consideration”), which includes 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. Prior to adoption of ASC 606, 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 a co-promotion deliverable in the relative selling price model. Because the Company shares 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 License Territory are recorded as a reduction in expense, in accordance with the Company’s policy, which is 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, are recorded as research and development expense as incurred. Payments to AstraZeneca are recorded as incremental research and development expense. The following remaining performance obligations are ongoing as of June 30, 2019: ● R&D Services, ● JDC services, ● obligation to supply clinical trial material, and ● Joint Commercialization Committee (“JCC”) services. The Company determined that the supply of linaclotide drug product for commercial requirements was an optional service at inception of the arrangement and did not provide a material right to AstraZeneca. 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 (“SSP”) basis. Under ASC 606, consideration allocated to the R&D Services will be recognized as such services are provided over the performance period using an output method based on full-time employee hours incurred. Consideration allocated to the JDC Services are recognized ratably over the development period using a time-based, straight-line attribution model. Revenue from the supply of clinical trial material is recognized as the clinical trial material is delivered to the customer. ​ Upon commercialization, the Company’s only remaining performance obligation will be JCC Services. During commercialization, the Company will be entitled to receive sales-based milestone payments from AstraZeneca. Additionally, the parties will share in the net profits and losses associated with the development and commercialization of linaclotide in the License Territory, with AstraZeneca receiving 55% of the net profits or incurring 55% of the net losses until a certain specified commercial milestone is achieved; from that point, profits and losses will be shared equally thereafter. 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 related predominately to the license granted to AstraZeneca. Any cost reimbursements received from AstraZeneca during the commercialization period will be recognized as incurred in accordance with the right-to-invoice exemption, as the Company’s right to consideration corresponds directly with the value of the services transferred during the commercialization period. ​ During the three and six months ended June 30, 2019, the Company incurred no costs and offset an insignificant amount of costs related to R&D Services and JDC Services, respectively. During each of the three and six months ended June 30, 2018, the Company offset costs of approximately $0.7 million related to R&D Services and JDC Services. During the three and six months ended June 30, 2019, the Company recognized no revenue and an insignificant amount of revenue related to linaclotide drug product as sale of API, respectively. The Company recorded no revenue related to linaclotide drug product and sale of API during each of the three and six months ended June 30, 2018. Additionally, the Company incurred approximately $0.3 million and approximately $0.5 million in costs related to pre-launch commercial services and supply chain services during the three and six months ended June 30, 2019, respectively. ​ Co-Promotion and Other Agreements ​ In January 2017, concurrently with entering into the amendment to the European License Agreement, the Company and Allergan entered into an agreement under which the adjustments to the Company’s or Allergan’s share of the net profits under the share adjustment provision of the collaboration agreement for linaclotide in North America relating to the contractually required calls on physicians in each year were eliminated, in full, in 2018 and all subsequent years (the “Commercial Agreement”). Pursuant to the Commercial Agreement, Allergan appointed the Company, on a non-exclusive basis, to promote CANASA, approved for the treatment of ulcerative proctitis in the U.S. for approximately two years through February 2019. Under the terms of the Commercial Agreement, the Company was obligated to perform third position sales details and offer samples of such products to gastroenterology prescribers who were on the then-current call panel for LINZESS to which the Company was providing first or second position details. On a product-by-product basis, Allergan paid the Company a royalty in the mid-teens on incremental sales of CANASA above a mutually agreed upon sales baseline. The Company discontinued its promotion of CANASA on December 31, 2018. ​ Upon adoption of ASC 606, the Company evaluated the commercial agreement and the amendment to the European License Agreement under the contract combination and contract modification guidance in ASC 606. The Company determined that the agreements should be accounted for as separate contracts because each agreement adds distinct goods or services at an amount that reflects standalone selling price. The Company concluded that the CANASA sales detailing deliverable under ASC 605 was also considered a performance obligation in accordance with ASC 606. Accordingly, the Company recorded royalties on sales of CANASA and any estimated detailing shortfall penalty over the period of performance for the sales details; collaborative arrangements revenue was recognized when it was probable that a significant reversal of revenue would not occur and the associated constraint has been lifted. The Company estimated sales detailing royalties based on royalty reports from its partner, if available, or the projected sales and historical trends. At the inception of the arrangement, the consideration associated with the agreement comprised of royalties and a sales detailing shortfall penalty are fully constrained. During each of the three and six months ended June 30, 2018, the Company did not recognize royalty revenue related to the Commercial Agreement with Allergan for sales of CANASA. ​ In December 2017, the Company and Allergan entered into an amendment to the commercial agreement with Allergan (the “VIBERZI Amendment”), as described below, to include the VIBERZI promotional activities through December 31, 2018. Under the terms of the VIBERZI Amendment, the Company’s clinical sales specialists detailed VIBERZI in the second position to the same health care practitioners to whom they detailed LINZESS in the first position and provided certain medical education services. The Company had the potential to achieve a milestone payment of up to $7.5 million based on the net sales of VIBERZI during 2018, and was compensated approximately $3.0 million over the term of the agreement for its medical education initiatives. The Company evaluated the VIBERZI Amendment in accordance with ASC 606 and determined that it would be treated as a separate contract because it adds a distinct good or service at an amount that reflects standalone selling price. The following performance obligations under the VIBERZI Amendment were identified: ● sales detailing of VIBERZI in either first or second position, and ● medical education services. ​ The sales-based milestone payment was recognized as collaborative arrangements revenue when it was probable that a significant reversal of revenue would not occur and the associated constraint had been lifted. During the three months ended December 31, 2018, the Company determined the sales-based milestone payment was no longer constrained and recognized approximately $1.3 million in collaborative arrangements revenue. The consideration related to medical education events of approximately $3.0 million was recognized over the period of performance that medical education services are provided. During the three and six months ended June 30, 2018, the Company recognized approximately $0.8 million and approximately $1.5 million of collaborative arrangements revenue, respectively, related to VIBERZI medical education services. In December 2018 and in March 2019, the Company extended the VIBERZI Amendment through April 2019. ​ In April 2019, the Company entered into a new agreement with Allergan to perform sales detailing activities for VIBERZI, effective April 1, 2019 through December 31, 2019 (the “VIBERZI Promotion Agreement”). Under the terms of the VIBERZI Promotion Agreement, the Company’s clinical sales specialists will continue detailing VIBERZI in the second position to the same health care practitioners to whom they detail LINZESS in the first position. The Company has the potential to achieve a milestone payment of up to approximately $4.2 million based on the number of VIBERZI prescription extended units filled over the term of the agreement. The Company will be compensated based on the number of VIBERZI sales details performed, up to a maximum amount of approximately $4.1 million over the term of the agreement. In accordance with ASC 606, the VIBERZI Promotion Agreement will be accounted for as a separate contract as it contains distinct services at an amount that reflects standalone selling price, incremental t

Fair Value of Financial Instrum

Fair Value of Financial Instruments	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Fair Value of Financial Instruments	5. 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 June 30, 2019 and December 31, 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 includes 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 deposits in the form of 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 ​ ​ ​ ​ ​ Identical Assets ​ Inputs ​ Inputs ​ ​ June 30, 2019 ​ ​ (Level 1) ​ (Level 2) ​ (Level 3) ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 82,918 ​ ​ $ 82,918 ​ $ — ​ $ — ​ Repurchase agreements ​ ​ 15,875 ​ ​ ​ 15,875 ​ ​ — ​ ​ — ​ Convertible Note Hedges ​ ​ 60,720 ​ ​ ​ — ​ ​ — ​ ​ 60,720 ​ Total assets measured at fair value ​ $ 159,513 ​ ​ $ 98,793 ​ $ — ​ $ 60,720 ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Note Hedge Warrants ​ $ 50,191 ​ ​ $ — ​ $ — ​ $ 50,191 ​ Total liabilities measured at fair value ​ $ 50,191 ​ ​ $ — ​ $ — ​ $ 50,191 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements at Reporting Date Using ​ ​ ​ Quoted Prices in Significant Other Significant ​ ​ ​ ​ ​ ​ Active Markets for ​ Observable ​ Unobservable ​ ​ ​ ​ ​ Identical Assets ​ Inputs ​ Inputs ​ ​ December 31, 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 three and six months ended June 30, 2019 or 2018. ​ Cash equivalents, accounts receivable, related party accounts receivable, prepaid expenses and other current assets, accounts payable, related party accounts payable, accrued expenses and other current liabilities, the current portion of capital lease obligations, deferred rent, and operating lease obligations at June 30, 2019 and December 31, 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, and are classified as Level 3 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 June 30, 2019 included the price per share of the Company’s Class A common stock, time to maturity of the derivative instruments, strike prices of the derivative instruments, risk-free interest rate, expected volatility of the Company’s Class A common stock, and expected dividend yield. Changes to these inputs could materially affect the valuation of the Convertible Note Hedges and Note Hedge Warrants. ​ In April 2019, the Company announced an adjustment to the conversion rate applicable to the 2022 Notes, effective April 15, 2019 (Note 9). ​ The following inputs were used in the fair market valuation of the Convertible Note Hedges and Note Hedge Warrants as of June 30, 2019 and December 31, 2018: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended ​ Year Ended ​ ​ ​ June 30, ​ December 31, ​ ​ 2019 ​ 2018 ​ ​ ​ Convertible Note Hedge ​ Convertible Note Hedge ​ ​ Note Hedges ​ Warrants Note Hedges ​ Warrants Risk-free interest rate (1) ​ ​ 1.7 % ​ 1.7 % ​ 2.5 % ​ 2.5 % Time to maturity ​ 3.0 ​ 3.5 ​ ​ 3.5 ​ 4.1 ​ Stock price (2) ​ $ 10.94 ​ $ 10.94 ​ $ 10.36 ​ $ 10.36 ​ Strike price (3) ​ $ 14.51 ​ $ 18.82 ​ $ 16.58 ​ $ 21.50 ​ Common stock volatility (4) ​ ​ 47.2 % ​ 47.1 % ​ 43.8 % ​ 43.6 % Dividend yield ​ — % — % — % — % (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 day of the quarter ended June 30, 2019 and December 31, 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 9). (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 period and changes in fair value are recorded in other expense, net within the Company’s condensed consolidated statements of operations. Gains and losses for these derivative financial instruments are presented separately in the Company’s condensed consolidated statements of cash flows. ​ The following table reflects the change in the Company’s Level 3 convertible note derivatives from December 31, 2018 through June 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Convertible ​ Note Hedge ​ ​ Note Hedges Warrants Balance at December 31, 2018 ​ $ 41,020 ​ $ (33,763) ​ Change in fair value, recorded as a component of gain (loss) on derivatives ​ ​ 19,700 ​ ​ (16,428) ​ Balance at June 30, 2019 ​ $ 60,720 ​ $ (50,191) ​ ​ 2.25% Convertible Senior Notes ​ In June 2015, the Company issued approximately $335.7 million of its 2022 Notes. The Company separately accounted for the liability and equity components of the 2022 Notes by allocating the proceeds between the liability component and equity component (Note 9). The fair value of the 2022 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 2022 Notes observed in market trading, which are Level 2 inputs. The estimated fair value of the 2022 Notes was approximately $359.1 million and approximately $315.0 million as of June 30, 2019 and December 31, 2018, respectively. ​ 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 estimated fair value of the 2026 Notes was approximately $133.0 million and approximately $148.2 million as of June 30, 2019 and December 31, 2018, respectively. 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.

Inventory

Inventory	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Inventory	6. Inventory ​ Inventory consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, 2019 December 31, 2018 ​ Raw Materials ​ $ 1,475 ​ $ — ​ ​ Work in Progress ​ ​ 260 ​ ​ — ​ ​ ​ ​ $ 1,735 ​ $ — ​ ​ ​ The Company’s inventory represents linaclotide API and drug product. 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. ​ No impairment of inventory was recorded during the three and six months ended June 30, 2019. The Company wrote down approximately $1.8 million related to lesinurad inventory and commercial supply purchase commitments during the three months ended June 30, 2018 as a result of revised demand forecasts. The adjustment was recorded as write-down of lesinurad commercial supply to net realizable value and loss on non-cancelable purchase commitments.

Accrued Expenses and Other Curr

Accrued Expenses and Other Current Liabilities	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Accrued Expenses and Other Current Liabilities	7. Accrued Expenses and Other Current Liabilities ​ Accrued expenses and other current liabilities consisted of the following (in thousands): ​ p ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, 2019 December 31, 2018 Salaries ​ $ 2,499 ​ $ 3,054 ​ Accrued vacation ​ ​ 2,887 ​ ​ 3,493 ​ Accrued incentive compensation ​ ​ 5,370 ​ ​ 13,867 ​ Other employee benefits ​ ​ 536 ​ ​ 1,883 ​ Professional fees ​ 5,275 ​ 1,735 ​ Accrued interest ​ 793 ​ 873 ​ Restructuring accruals ​ ​ 1,597 ​ ​ 2,885 ​ Other ​ 15,025 ​ 10,211 ​ ​ ​ $ 33,982 ​ $ 38,001 ​ ​ ​ ​ ​ As of June 30, 2019, other accrued expenses of approximately $15.0 million includes approximately $5.0 million related to goods received but not yet invoiced, approximately $2.5 million related to linaclotide excess purchase commitments, approximately $0.9 million related to a portion of the activities associated with the Separation, and approximately $1.4 million related to excess non-cancelable ZURAMPIC and DUZALLO (the “Lesinurad Products”) commercial supply and sample purchase commitments. ​ 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. ​

Leases

Leases	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Leases	8. Leases ​ Effective January 1, 2019, the Company adopted ASC 842 using the optional transition method. The Company’s lease portfolio includes: leases for its current and future 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 three and six months ended June 30, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ ​ 2019 ​ 2019 ​ Operating lease cost during period, net (1) ​ $ 3,155 ​ ​ 7,680 ​ Variable lease payments ​ ​ 654 ​ ​ 654 ​ Short-term lease cost ​ ​ 379 ​ ​ 768 ​ Total lease cost ​ $ 4,188 ​ ​ 9,102 ​ (1) Operating lease cost is presented net of approximately $0.3 million of sublease income for the three months ended June 30, 2019. Sublease income relates 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: ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended ​ ​ June 30, ​ ​ 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) ​ ​ 6,619 ​ Weighted-average remaining lease term of operating leases (in years) ​ ​ 7.9 ​ Weighted-average discount rate of operating leases ​ ​ 5.3 % ​ (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 June 30, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ Operating ​ Lease ​ ​ Payments 2019 (1) ​ $ 11,979 2020 ​ ​ 1,146 2021 ​ ​ 3,128 2022 ​ ​ 3,129 2023 ​ ​ 3,065 2024 and thereafter ​ 21,170 Total future minimum lease payments ​ ​ 43,617 Less: present value adjustment ​ ​ 9,205 Operating lease liabilities at June 30, 2019 ​ ​ 34,412 Less: current portion of operating lease liabilities ​ ​ 11,904 Operating lease liabilities, net of current portion ​ $ 22,508 (1) Amounts are for the six months ending December 31, 2019. ​ 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 (future 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 is expected to serve as the Company’s new headquarters beginning in the fourth quarter of 2019, replacing its existing 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 condensed consolidated balance sheets as of June 30, 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 June 30, 2019, the balance of the right-of-use asset for the Summer Street Lease was approximately $18.3 million. The balance of the lease liability for the Summer Street Lease was approximately $18.3 million, net of approximately $3.8 million related to the tenant improvement allowance reimbursement expected to be received. ​ Lease cost related to the Summer Street Lease recorded during each of the three and months ended June 30, 2019 was approximately $0.2 million. ​ Binney Street Lease (current headquarters) ​ The Company rents 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”). The Binney Street Property currently serves as the Company’s headquarters, but is expected to be replaced by the Summer Street Property, as discussed above. ​ Prior to the modifications discussed below, the term of the Binney Street Lease was through January 31, 2025 for the approximately 223,000 square feet of laboratory and office space. The Binney Street Lease includes 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, a tenant improvement allowance, and an option to extend the term of the lease for an additional five years at a market base rental rate. The rent expense for the Binney Street Lease, inclusive of the escalating rent payments, lease incentives and free rent periods, is recognized on a straight-line basis over the lease term through January 2025. Additionally, the Binney Street Lease requires a letter of credit to secure the Company’s obligations under the lease agreement of approximately $6.4 million, which is recorded as restricted cash. ​ 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 is now 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% in accordance with ASC 842, and recognized a gain of approximately $3.2 million, recorded as operating expenses on its condensed 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 is expected to go into effect on or before November 1, 2019 (subject to the Company’s one-time right to extend the termination date for up to 30 days ) 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%. ​ At June 30, 2019, the balances of the right-of-use asset and lease liability for the Binney Street Lease were approximately $7.3 million and approximately $11.8 million, respectively. ​ Lease cost related to the Binney Street Lease recorded during the three and six months ended June 30, 2019 was approximately $3.6 million and approximately $8.0 million, respectively, net of sublease income of approximately $0.3 million and approximately $0.3 million, respectively. Under ASC 840, rent expense related to the Binney Street Lease recorded during the three and six months ended June 30, 2018 was approximately $2.5 million and $5.1 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. 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 condensed consolidated statement of operations as a result of the impairment. ​ At June 30, 2019, the lease liability associated with the Data Center Lease was approximately $0.5 million, and the right-of-use asset remained fully impaired. The incremental borrowing rate for the outstanding Data Center Lease obligation upon adoption of ASC 842 was approximately 6.0%. ​ Under ASC 842, the lease costs related to the Data Center Lease were insignificant for each of the three and six months ended June 30, 2019. Under ASC 840, rent expenses related to the Data Center Lease were insignificant for each of the three and six months ended June 30, 2018, 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. ​ Lease cost related to the 2018 Vehicle Leases was approximately $0.4 million and approximately $0.8 million for the three and six months ended June 30, 2019, respectively. There were no rent expenses incurred under ASC 840 during the three and six months ended June 30, 2018 related to the 2018 Vehicle Leases. ​ 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 that 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 3.4%.

Notes Payable

Notes Payable	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Notes Payable	9. 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 8.375% notes due 2026 on January 5, 2017. The Company capitalized approximately $0.5 million of debt issuance costs, which were netted against the carrying value of the 2026 Notes. ​ The 2026 Notes bear 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 on June 15, 2017. Principal of the 2026 Notes are payable on the 8.375% Payment Dates beginning March 15, 2019. From March 15, 2019, the Company makes 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 will be repaid in an amount equal to the 8.375% Synthetic Royalty Amount minus the 8.375% Required Interest Amount, when this is a positive number, until the principal has been paid in full. Given the principal payments on the 2026 Notes are based on the 8.375% Synthetic Royalty Amount, which will vary from quarter to quarter, the 2026 Notes may be repaid prior to September 15, 2026, the final legal maturity date. During the three and six months ended June 30, 2019, the Company made principal payments of approximately $9.2 million and approximately $21.5 million, respectively, and expects to pay approximately $48.8 million of the principal within twelve months following June 30, 2019. ​ The 2026 Notes are secured by a security interest in a segregated bank account established to receive the required quarterly payments as well as certain limited accounts receivables, payment intangibles or other rights to payment or proceeds, in each case, up to the 8.375% Synthetic Royalty Amount or estimated equivalent thereto, as applicable. Up to the amount of the required quarterly payments under the 2026 Notes, Allergan deposits its quarterly profit (loss) sharing payments due to the Company related to net sales of linaclotide in the U.S. pursuant to the collaboration agreement for North America, if any, into the segregated bank account. If the funds deposited by Allergan into the segregated bank account are insufficient to make a required payment of interest or principal on a particular 8.375% Payment Date, the Company is obligated to deposit such shortfall out of the Company’s general funds into the segregated bank account. ​ The 2026 Notes may be redeemed at any time prior to maturity, in whole or in part, at the option of the Company. If applicable, the Company will pay a redemption price equal to the percentage of outstanding principal balance of the 2026 Notes being redeemed specified below for the period in which the redemption occurs (plus the accrued and unpaid interest to the redemption date on the 2026 Notes being redeemed): ​ ​ ​ ​ ​ ​ Redemption Payment Dates ​ Percentage From and including March 15, 2019 to and including March 14, 2020 105.50 % From and including March 15, 2020 to and including March 14, 2021 102.75 % From and including March 15, 2021 and thereafter 100.00 % ​ The 2026 Notes contain certain covenants related to the Company’s obligations with respect to the commercialization of linaclotide and the related collaboration agreement with Allergan for North America, as well as certain customary covenants, including covenants that limit or restrict the Company’s ability to incur certain liens, merge or consolidate or make dispositions of assets. The 2026 Notes also specify a number of events of default (some of which are subject to applicable cure periods), including, among other things, covenant defaults, other non-payment defaults, and bankruptcy and insolvency defaults. Upon the occurrence of an event of default, subject to cure periods in certain circumstances, all amounts outstanding may become immediately due and payable. ​ The accounting for the 2026 Notes requires the Company to make certain estimates and assumptions about the future net sales of linaclotide in the U.S. Linaclotide has been marketed as LINZESS in the U.S. since December 2012 and the estimates of the magnitude and timing of linaclotide net sales are subject to significant variability and uncertainty. These estimates and assumptions are likely to change, which may result in future adjustments to the portion of the 2026 Notes that is classified as a current liability, the amortization of debt issuance costs, the accretion of discounts and recognition of interest expense. Any such adjustments could be material to the Company’s condensed consolidated financial statements. ​ 2.25% Convertible Senior Notes due 2022 ​ In June 2015, the Company issued approximately $335.7 million aggregate principal amount of the 2022 Notes. The Company received net proceeds of approximately $324.0 million from the sale of the 2022 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 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 Notes are governed by an indenture (the “Indenture”) between the Company and U.S. Bank National Association, as the trustee. The 2022 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 Notes will mature on June 15, 2022, unless earlier converted or repurchased. The Company may settle conversions of the 2022 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 Indenture). The initial conversion rate for the 2022 Notes was 60.3209 shares of Class A common stock (subject to adjustment as provided for in the Indenture) per $1,000 principal amount of the 2022 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 in April 2019, the conversion rate under the Indenture was adjusted to equal 68.9172 shares of Ironwood Class A common stock per $1,000 principal amount of the 2022 Notes, which is equal to an adjusted conversion price of approximately $14.51 per share and 23,135,435 shares. ​ Holders of the 2022 Notes may convert their 2022 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 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 Indenture) per $1,000 principal amount of the 2022 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 Notes on each such trading day; or ​ ● upon the occurrence of specified corporate events described in the 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 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 Indenture, occurs and a holder elects to convert its 2022 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 Indenture. The Company may not redeem the 2022 Notes prior to the maturity date and no “sinking fund” is provided for by the 2022 Notes, which means that the Company is not required to periodically redeem or retire the 2022 Notes. Upon the occurrence of certain fundamental changes involving the Company, holders of the 2022 Notes may require the Company to repurchase for cash all or part of their 2022 Notes at a repurchase price equal to 100% of the principal amount of the 2022 Notes to be repurchased, plus accrued and unpaid interest. ​ The 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 Indenture provides for customary events of default. In the case of an event of default with respect to the 2022 Notes arising from specified events of bankruptcy or insolvency, all outstanding 2022 Notes will become due and payable immediately without further action or notice. If any other event of default with respect to the 2022 Notes under the Indenture occurs or is continuing, the trustee or holders of at least 25% in aggregate principal amount of the then outstanding 2022 Notes may declare the principal amount of the 2022 Notes to be immediately due and payable. Notwithstanding the foregoing, the 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 Indenture consists exclusively of the right to receive additional interest on the 2022 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 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 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 Notes was recognized as a debt discount and represents the difference between the gross proceeds from the issuance of the 2022 Notes and the fair value of the liability of the 2022 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 Notes. The equity component is not remeasured as long as it continues to meet the conditions for equity classification. ​ The Company’s outstanding Convertible Note balances as of June 30, 2019 and December 31, 2018 consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, 2019 ​ ​ ​ December 31, 2018 ​ Liability component: ​ ​ ​ ​ ​ ​ ​ ​ ​ Principal ​ $ 335,699 ​ ​ ​ $ 335,699 ​ Less: unamortized debt discount ​ ​ (56,855) ​ ​ ​ ​ (65,094) ​ Less: unamortized debt issuance costs ​ ​ (4,449) ​ ​ ​ ​ (5,004) ​ Net carrying amount ​ $ 274,395 ​ ​ ​ $ 265,601 ​ Equity component ​ $ 114,199 ​ ​ ​ $ 114,199 ​ ​ In connection with the issuance of the 2022 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. 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 balance sheet and are amortized to interest expense using the effective interest method over the expected life of the 2022 Notes. ​ The Company determined the expected life of the 2022 Notes was equal to their seven-year term. The effective interest rate on the liability components of the 2022 Notes for the period from the date of issuance through June 30, 2019 was 9.34%. The following table sets forth total interest expense recognized related to the 2022 Notes during the three and six months ended June 30, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ 2019 2018 2019 2018 Contractual interest expense ​ $ 1,889 ​ $ 1,888 ​ $ 3,777 ​ $ 3,777 ​ Amortization of debt issuance costs ​ ​ 283 ​ ​ 237 ​ ​ 555 ​ ​ 464 ​ Amortization of debt discount ​ ​ 4,164 ​ ​ 3,816 ​ ​ 8,239 ​ ​ 7,550 ​ Total interest expense ​ $ 6,336 ​ $ 5,941 ​ $ 12,571 ​ $ 11,791 ​ ​ Convertible Note Hedge and Note Hedge Warrant Transactions with Respect to 2022 Notes ​ To minimize the impact of potential dilution to the Company’s Class A common stockholders upon conversion of the 2022 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 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 were exercisable if the 2022 Notes were converted. In connection with the adjustment to the conversion rate of the Indenture, the exercise price of the Convertible Note Hedges and the Note Hedge Warrants were adjusted to $14.51 per share and $18.82 per share, respectively (Note 5). If upon conversion of the 2022 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 also 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 ​ 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 Notes. Holders of the 2022 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 the condensed 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. The Convertible Note Hedges and Note Hedge Warrants are accounted for as derivative assets and liabilities, respectively, in accordance with ASC Topic 815, Derivatives and Hedging

Employee Stock Benefit Plans

Employee Stock Benefit Plans	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Employee Stock Benefit Plans	10. Employee Stock Benefit Plans ​ The Company has several share-based compensation plans under which stock options, restricted stock awards, restricted stock units (“RSUs”), and other share-based awards are available for grant to employees, officers, directors and consultants of the Company. ​ In May 2019, the Company’s stockholders approved the 2019 Equity Incentive Plan (the “2019 Equity Plan) under which stock options, restricted stock awards, 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. As of June 30, 2019, 9,923,183 shares are available for future grant under the 2019 Equity Plan. ​ The following table summarizes share-based compensation expense reflected in the condensed consolidated statements of operations for the three and six months ended June 30, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ 2019 2018 2019 2018 Research and development ​ $ 1,179 ​ $ 2,920 ​ $ 4,098 ​ $ 5,472 ​ Selling, general and administrative ​ ​ 5,021 ​ 6,539 ​ 15,519 ​ ​ 12,065 ​ Restructuring expenses ​ ​ 137 ​ ​ 324 ​ 654 ​ 517 ​ ​ ​ $ 6,337 ​ $ 9,783 ​ $ 20,271 ​ $ 18,054 ​ ​ 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 a modification to certain share-based payment awards. As a result of the modification, the Company recorded stock-based compensation expense of approximately $0.2 million to restructuring expenses during the three months ended March 31, 2018. ​ During the three months ended June 30, 2018, the Company initiated a reduction in 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 approximately $0.3 million of restructuring expenses during each of the three and six months ended June 30, 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 ​ 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 the modifications. Additionally, modifications with respect to the Company’s Employee Stock Purchase Plan (“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 share-based compensation expense of approximately ​ In connection with certain other modifications of share-based payment awards during the six months ended June 30, 2019, the Company recognized approximately $2.4 million in share-based compensation expense. ​ ​

Related Party Transactions

Related Party Transactions	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Related Party Transactions	11. Related Party Transactions ​ In September 2009, Allergan became a related party when the Company sold to Allergan 2,083,333 shares of the Company’s convertible preferred stock. Under the collaboration agreement, the Company and Allergan equally support the development and commercialization of linaclotide (Note 4). 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 June 30, 2019 and December 31, 2018, the Company had approximately $79.4 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 $1.6 million and approximately $4.1 million in insurance premiums to this insurance provider during the three and six months ended June 30, 2019, respectively, and paid approximately $3.0 million and approximately $6.3 million during the three and six months ended June 30, 2018, respectively. At June 30, 2019 and December 31, 2018, the Company had no accounts payable due to this related party. ​ The Company has and currently obtains commercial market and prescription data from a vendor whose Senior Vice President of Strategy, Marketing and Communications became a member of the Company’s Board of Directors in April 2019. The Company paid approximately $0.7 million and approximately $1.2 million in fees to this company during the three and six months ended June 30, 2019, respectively, and approximately $1.1 million and approximately ​ 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 2). As of June 30, 2019, the Company had an insignificant amount of accounts receivable, net of accounts payable due from Cyclerion.

Workforce Reduction

Workforce Reduction	6 Months Ended
	Jun. 30, 2019
Disclosure Text Block
Workforce Reduction	12. 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 Topic 420, Exit or Disposal Activities ​ 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. During the three months ended June 30, 2019, the Company did not record any costs in connection with this workforce reduction. During the six months ended June 30, 2019, the Company recorded an insignificant amount of costs in connection with the reduction in workforce in accordance with ASC 420. During each of the three and six months ended June 30, 2018, the Company recorded approximately $1.5 million of costs in connection with the reduction in workforce in accordance with ASC 420. These costs are reflected in the condensed 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 license related to the Lesinurad Products with AstraZeneca to develop, manufacture, and commercialize in the U.S products containing lesinurad as an active ingredient. During the three and six months ended June 30, 2019, the Company did not record any restructuring costs related to this workforce reduction. These costs are reflected in the condensed 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 by 35 employees, primarily based in the home office. During the three and six months ended June 30, 2019, the Company recorded approximately $0.5 million and approximately $3.8 million, respectively, of costs that are reflected in the condensed 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 three and six months ended June 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ ​ Accrued at ​ ​ ​ ​ ​ ​ ​ ​ Accrued at ​ ​ December 31, 2018 ​ Charges Amount Paid ​ Adjustments ​ June 30, 2019 ​ Employee severance, benefits and related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 2018 Reduction ​ ​ 696 ​ ​ 16 ​ ​ (556) ​ ​ (15) ​ ​ 141 ​ August 2018 Reduction ​ ​ 1,756 ​ ​ — ​ ​ (1,708) ​ ​ (44) ​ ​ 4 ​ February 2019 Reduction ​ ​ — ​ ​ 3,182 ​ ​ (1,878) ​ ​ — ​ ​ 1,304 ​ Total $ 2,452 ​ $ 3,198 ​ $ (4,142) ​ $ (59) ​ $ 1,449 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contract related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ August 2018 Reduction ​ $ 433 ​ $ — ​ $ (287) ​ $ (42) ​ $ 104 ​ Total $ 433 ​ $ — ​ $ (287) ​ $ (42) ​ $ 104 ​ ​

Nature of Business (Policies)

Nature of Business (Policies)	6 Months Ended
	Jun. 30, 2019
Policy Text Blocks
Basis of Presentation	Basis of Presentation ​ The accompanying condensed consolidated financial statements and the related disclosures are unaudited and have been prepared in accordance with accounting principles generally accepted in the U.S. Additionally, certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. Accordingly, these interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2018, which was filed with the Securities and Exchange Commission on February 25, 2019 (the “2018 Annual Report on Form 10-K”). ​ The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all normal recurring adjustments considered necessary for a fair presentation of the Company’s financial position as of June 30, 2019, and the results of its operations for the three and six months ended June 30, 2019 and 2018, its statements of stockholders’ deficit for the three and six months ended June 30, 2019 and 2018, and its cash flows for the six months ended June 30, 2019 and 2018. The results of operations for the three and six months ended June 30, 2019 and 2018 are not necessarily indicative of the results that may be expected for the full year or any other subsequent interim period. ​
Principles of Consolidation	Principles of Consolidation ​ The accompanying condensed consolidated financial statements include the accounts of Ironwood and its wholly-owned subsidiaries as of June 30, 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.
Use of Estimates	Use of Estimates ​ The preparation of condensed 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 condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. On an on-going basis, the Company’s management evaluates its estimates, judgments and methodologies. Significant estimates and assumptions in the condensed consolidated financial statements include those related to revenue recognition; available-for-sale securities; accounts receivable; inventory valuation, and related reserves; impairment of long-lived assets, including goodwill; valuation procedures for right-of-use assets and operating lease liabilities; initial valuation procedures for the issuance 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.
Reclassifications of Prior Period Financial Statements	Reclassifications of Prior Period Financial Statements ​ Certain prior period financial statement items, such as discontinued operations, have been reclassified to conform to current period presentation.
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
Leases	Leases Effective January 1, 2019, the Company adopted ASC Topic 842, Leases Leases ​ The recognition of right-of-use assets and lease liabilities related to our operating leases under ASC 842 has had a material impact on the Company’s condensed 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; ● 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 includes: leases for its current and future 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 condensed consolidated balance sheets. As of June 30, 2019, the Company did not have 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.
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 three and six months ended June 30, 2019 that had a material effect on its condensed consolidated financial statements. ​ In February 2016, the FASB issued ASU No. 2016-02, Leases Leases (Topic 842), Codification Improvements Leases (Topic 842), Targeted Improvements , Leases (Topic 842), Codification Improvements . . ​ In June 2016, the FASB issued ASU No. 2016-13, Measurement of Credit Losses on Financial Instruments Codification Improvements to Topic 326, Financial Instruments—Credit Losses, Topic 815, Derivatives and Hedging, and Topic 825, Financial Instruments Financial Instruments—Credit Losses (Topic 326): Targeted Transition Relief is permitted. The Company is currently evaluating the potential impact that the adoption of these ASUs will have 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) ​ In June 2018, the FASB issued ASU No. 2018-07, Compensation—Stock Compensation (Topic 718) Improvements to Nonemployee Share-Based Payment Accounting . ​ In July 2018, the FASB issued ASU 2018-09, Codification Improvements Compensation—Stock Compensation—Income Taxes Compensation—Stock Compensation—Income Taxes ​ 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 ​ 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) ​ In October 2018, the FASB issued ASU No. 2018-17, Consolidation (Topic 810): Targeted Improvements to Related Party Guidance for Variable Interest Entities ​

Cyclerion Separation (Tables)

Cyclerion Separation (Tables)	6 Months Ended
	Jun. 30, 2019
Table Text Blocks
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	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ ​ 2019 2018 ​ 2019 2018 Costs and expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Research and development ​ ​ — ​ 15,745 ​ ​ 21,792 ​ 31,774 ​ Selling, general and administrative ​ ​ — ​ 8,592 ​ ​ 15,646 ​ 9,148 ​ Restructuring expenses ​ ​ — ​ ​ 906 ​ ​ — ​ ​ 906 ​ Net loss from discontinued operations ​ ​ — ​ ​ 25,243 ​ ​ 37,438 ​ ​ 41,828 ​ ​ ​ ​ ​ ​ 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)	6 Months Ended
	Jun. 30, 2019
Table Text Blocks
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): ​ ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended ​ ​ ​ June 30, ​ ​ 2019 2018 Options to purchase Class A common stock ​ 19,324 22,056 Shares subject to repurchase 182 130 Restricted stock units ​ 2,799 ​ 3,207 ​ Note Hedge Warrants ​ 23,135 ​ 20,250 ​ 2022 Notes ​ 23,135 ​ 20,250 ​ Total 68,575 65,893

Collaboration, License, Co-Pr_2

Collaboration, License, Co-Promotion and Other Commercial Agreements (Tables)	6 Months Ended
	Jun. 30, 2019
Table Text Blocks
Schedule of revenue attributable to transactions from collaboration and license arrangements	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ Collaborative Arrangements Revenue ​ 2019 2018 ​ 2019 2018 Linaclotide Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Allergan (North America) ​ $ 75,498 ​ $ 69,810 ​ $ 140,283 ​ $ 131,408 ​ Allergan (Europe and other) ​ ​ 262 ​ ​ 304 ​ ​ 682 ​ ​ 576 ​ Co-Promotion and Other Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Allergan (VIBERZI) ​ ​ 1,239 ​ ​ 750 ​ ​ 1,239 ​ ​ 1,500 ​ Other ​ ​ 323 ​ ​ 343 ​ ​ 1,270 ​ ​ 809 ​ Total collaborative arrangements revenue ​ $ 77,322 ​ $ 71,207 ​ $ 143,474 ​ $ 134,293 ​ Sale of API (1) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Linaclotide Agreements: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Astellas (Japan) ​ $ 24,893 ​ $ 8,803 ​ $ 27,468 ​ $ 14,237 ​ Other (1) ​ ​ — ​ ​ — ​ ​ 3 ​ ​ — ​ Total sale of API ​ $ 24,893 ​ $ 8,803 ​ $ 27,471 ​ $ 14,237 ​ (1) Sale of API includes an insignificant amount of revenue from the sale of drug product to AstraZeneca in China during the six months ended June 30, 2019.
Allergan
Table Text Blocks
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 three and six months ended June 30, 2019 and 2018 as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ 2019 2018 2019 2018 Collaborative arrangements revenue related to sales of LINZESS in the U.S. ​ $ 74,973 ​ $ 69,264 ​ $ 139,267 ​ $ 130,413 ​ Royalty revenue ​ 525 ​ 546 ​ 1,016 ​ 995 ​ Total collaborative arrangements revenue ​ $ 75,498 ​ $ 69,810 ​ $ 140,283 ​ $ 131,408 ​
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 three and six months ended June 30, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ 2019 2018 2019 2018 Collaborative arrangements revenue related to sales of LINZESS in the U.S. (1)(2) ​ $ 74,973 ​ $ 69,264 ​ $ 139,267 ​ $ 130,413 ​ Selling, general and administrative costs incurred by the Company (1) ​ (10,359) ​ (11,713) ​ (20,636) ​ (22,641) ​ The Company’s share of net profit ​ $ 64,614 ​ $ 57,551 ​ $ 118,631 ​ $ 107,772 ​ (1) Includes only collaborative arrangement revenue or selling, general and administrative costs attributable to the cost-sharing arrangement with Allergan for the three and six months ended June 30, 2019 and 2018. ​

Fair Value of Financial Instr_2

Fair Value of Financial Instruments (Tables)	6 Months Ended
	Jun. 30, 2019
Table Text Blocks
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 ​ ​ ​ ​ ​ Identical Assets ​ Inputs ​ Inputs ​ ​ June 30, 2019 ​ ​ (Level 1) ​ (Level 2) ​ (Level 3) ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 82,918 ​ ​ $ 82,918 ​ $ — ​ $ — ​ Repurchase agreements ​ ​ 15,875 ​ ​ ​ 15,875 ​ ​ — ​ ​ — ​ Convertible Note Hedges ​ ​ 60,720 ​ ​ ​ — ​ ​ — ​ ​ 60,720 ​ Total assets measured at fair value ​ $ 159,513 ​ ​ $ 98,793 ​ $ — ​ $ 60,720 ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Note Hedge Warrants ​ $ 50,191 ​ ​ $ — ​ $ — ​ $ 50,191 ​ Total liabilities measured at fair value ​ $ 50,191 ​ ​ $ — ​ $ — ​ $ 50,191 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements at Reporting Date Using ​ ​ ​ Quoted Prices in Significant Other Significant ​ ​ ​ ​ ​ ​ Active Markets for ​ Observable ​ Unobservable ​ ​ ​ ​ ​ Identical Assets ​ Inputs ​ Inputs ​ ​ December 31, 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 June 30, 2019 and December 31, 2018: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended ​ Year Ended ​ ​ ​ June 30, ​ December 31, ​ ​ 2019 ​ 2018 ​ ​ ​ Convertible Note Hedge ​ Convertible Note Hedge ​ ​ Note Hedges ​ Warrants Note Hedges ​ Warrants Risk-free interest rate (1) ​ ​ 1.7 % ​ 1.7 % ​ 2.5 % ​ 2.5 % Time to maturity ​ 3.0 ​ 3.5 ​ ​ 3.5 ​ 4.1 ​ Stock price (2) ​ $ 10.94 ​ $ 10.94 ​ $ 10.36 ​ $ 10.36 ​ Strike price (3) ​ $ 14.51 ​ $ 18.82 ​ $ 16.58 ​ $ 21.50 ​ Common stock volatility (4) ​ ​ 47.2 % ​ 47.1 % ​ 43.8 % ​ 43.6 % Dividend yield ​ — % — % — % — % (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 day of the quarter ended June 30, 2019 and December 31, 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 9). (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 derivatives from December 31, 2018 through June 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Convertible ​ Note Hedge ​ ​ Note Hedges Warrants Balance at December 31, 2018 ​ $ 41,020 ​ $ (33,763) ​ Change in fair value, recorded as a component of gain (loss) on derivatives ​ ​ 19,700 ​ ​ (16,428) ​ Balance at June 30, 2019 ​ $ 60,720 ​ $ (50,191) ​

Inventory (Tables)

Inventory (Tables)	6 Months Ended
	Jun. 30, 2019
Table Text Blocks
Schedule of Inventory	Inventory consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, 2019 December 31, 2018 ​ Raw Materials ​ $ 1,475 ​ $ — ​ ​ Work in Progress ​ ​ 260 ​ ​ — ​ ​ ​ ​ $ 1,735 ​ $ — ​ ​

Accrued Expenses and Other Cu_2

Accrued Expenses and Other Current Liabilities (Tables)	6 Months Ended
	Jun. 30, 2019
Table Text Blocks
Schedule of accrued expenses and other current liabilities	Accrued expenses and other current liabilities consisted of the following (in thousands): ​ p ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, 2019 December 31, 2018 Salaries ​ $ 2,499 ​ $ 3,054 ​ Accrued vacation ​ ​ 2,887 ​ ​ 3,493 ​ Accrued incentive compensation ​ ​ 5,370 ​ ​ 13,867 ​ Other employee benefits ​ ​ 536 ​ ​ 1,883 ​ Professional fees ​ 5,275 ​ 1,735 ​ Accrued interest ​ 793 ​ 873 ​ Restructuring accruals ​ ​ 1,597 ​ ​ 2,885 ​ Other ​ 15,025 ​ 10,211 ​ ​ ​ $ 33,982 ​ $ 38,001 ​

Leases (Tables)

Leases (Tables)	6 Months Ended
	Jun. 30, 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 three and six months ended June 30, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ ​ 2019 ​ 2019 ​ Operating lease cost during period, net (1) ​ $ 3,155 ​ ​ 7,680 ​ Variable lease payments ​ ​ 654 ​ ​ 654 ​ Short-term lease cost ​ ​ 379 ​ ​ 768 ​ Total lease cost ​ $ 4,188 ​ ​ 9,102 ​ (1) Operating lease cost is presented net of approximately $0.3 million of sublease income for the three months ended June 30, 2019. Sublease income relates 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: ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended ​ ​ June 30, ​ ​ 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) ​ ​ 6,619 ​ Weighted-average remaining lease term of operating leases (in years) ​ ​ 7.9 ​ Weighted-average discount rate of operating leases ​ ​ 5.3 % ​ (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 June 30, 2019 are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ Operating ​ Lease ​ ​ Payments 2019 (1) ​ $ 11,979 2020 ​ ​ 1,146 2021 ​ ​ 3,128 2022 ​ ​ 3,129 2023 ​ ​ 3,065 2024 and thereafter ​ 21,170 Total future minimum lease payments ​ ​ 43,617 Less: present value adjustment ​ ​ 9,205 Operating lease liabilities at June 30, 2019 ​ ​ 34,412 Less: current portion of operating lease liabilities ​ ​ 11,904 Operating lease liabilities, net of current portion ​ $ 22,508 (1) Amounts are for the six months ending December 31, 2019.
Schedule of future minimum lease payments under non-cancelable operating leases - ASC 842	​
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

Notes Payable (Tables)

Notes Payable (Tables)	6 Months Ended
	Jun. 30, 2019
Table Text Blocks
Schedule of redemption price as percentage of outstanding principal balance	​ ​ ​ ​ ​ ​ Redemption Payment Dates ​ Percentage From and including March 15, 2019 to and including March 14, 2020 105.50 % From and including March 15, 2020 to and including March 14, 2021 102.75 % From and including March 15, 2021 and thereafter 100.00 %
Schedule of outstanding Convertible Note	The Company’s outstanding Convertible Note balances as of June 30, 2019 and December 31, 2018 consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, 2019 ​ ​ ​ December 31, 2018 ​ Liability component: ​ ​ ​ ​ ​ ​ ​ ​ ​ Principal ​ $ 335,699 ​ ​ ​ $ 335,699 ​ Less: unamortized debt discount ​ ​ (56,855) ​ ​ ​ ​ (65,094) ​ Less: unamortized debt issuance costs ​ ​ (4,449) ​ ​ ​ ​ (5,004) ​ Net carrying amount ​ $ 274,395 ​ ​ ​ $ 265,601 ​ Equity component ​ $ 114,199 ​ ​ ​ $ 114,199 ​ ​
Schedule of interest expense related to Convertible Notes	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ 2019 2018 2019 2018 Contractual interest expense ​ $ 1,889 ​ $ 1,888 ​ $ 3,777 ​ $ 3,777 ​ Amortization of debt issuance costs ​ ​ 283 ​ ​ 237 ​ ​ 555 ​ ​ 464 ​ Amortization of debt discount ​ ​ 4,164 ​ ​ 3,816 ​ ​ 8,239 ​ ​ 7,550 ​ Total interest expense ​ $ 6,336 ​ $ 5,941 ​ $ 12,571 ​ $ 11,791 ​

Employee Stock Benefit Plans (T

Employee Stock Benefit Plans (Tables)	6 Months Ended
	Jun. 30, 2019
Table Text Blocks
Share-based compensation expense reflected in the condensed consolidated statements of operations	The following table summarizes share-based compensation expense reflected in the condensed consolidated statements of operations for the three and six months ended June 30, 2019 and 2018 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ 2019 2018 2019 2018 Research and development ​ $ 1,179 ​ $ 2,920 ​ $ 4,098 ​ $ 5,472 ​ Selling, general and administrative ​ ​ 5,021 ​ 6,539 ​ 15,519 ​ ​ 12,065 ​ Restructuring expenses ​ ​ 137 ​ ​ 324 ​ 654 ​ 517 ​ ​ ​ $ 6,337 ​ $ 9,783 ​ $ 20,271 ​ $ 18,054 ​
Summary of RSU activity	​ ​

Workforce Reduction (Tables)

Workforce Reduction (Tables)	6 Months Ended
	Jun. 30, 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 three and six months ended June 30, 2019 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ ​ ​ ​ ​ ​ ​ ​ Amounts ​ ​ ​ Accrued at ​ ​ ​ ​ ​ ​ ​ ​ Accrued at ​ ​ December 31, 2018 ​ Charges Amount Paid ​ Adjustments ​ June 30, 2019 ​ Employee severance, benefits and related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 2018 Reduction ​ ​ 696 ​ ​ 16 ​ ​ (556) ​ ​ (15) ​ ​ 141 ​ August 2018 Reduction ​ ​ 1,756 ​ ​ — ​ ​ (1,708) ​ ​ (44) ​ ​ 4 ​ February 2019 Reduction ​ ​ — ​ ​ 3,182 ​ ​ (1,878) ​ ​ — ​ ​ 1,304 ​ Total $ 2,452 ​ $ 3,198 ​ $ (4,142) ​ $ (59) ​ $ 1,449 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contract related costs ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ August 2018 Reduction ​ $ 433 ​ $ — ​ $ (287) ​ $ (42) ​ $ 104 ​ Total $ 433 ​ $ — ​ $ (287) ​ $ (42) ​ $ 104 ​

Nature of Business - General In

Nature of Business - General Information (Details) person in Millions	6 Months Ended
	Jun. 30, 2019person
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Number of adults suffering with irritable bowel syndrome with constipation ("IBS-C")	13
Number of adults suffering with chronic idiopathic constipation ("CIC")	35
Number of adults suffering with irritable bowel syndrome with diarrhea ("IBS-D")	16
Number of adults suffering with gastroesophageal reflux disease ("GERD")	10

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 - Segment In

Nature of Business - Segment Information (Details) - segment	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Segment Information
Number of reportable segments	1	1	1	1

Nature of Business - Leases - C

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

Nature of Business - Leases - P

Nature of Business - Leases - Practical Expedients (Details)	6 Months Ended
	Jun. 30, 2019
Leases
Lease, Practical Expedients, Package	true
Lease, Practical Expedient, Lessor Single Lease Component	true

Nature of Business - Leases - R

Nature of Business - Leases - Recognition of Assets and Liabilities (Details) - USD ($) $ in Thousands	Jun. 30, 2019	Jan. 01, 2019
Leases
Operating lease right-of-use assets	$ 25,569
Current portion of operating lease liabilities	$ 34,412
Accounting Standards Update 2016-02 | Restatement
Leases
Operating lease right-of-use assets		$ 88,300
Current portion of operating lease liabilities		$ 94,900

Nature of Business - New Accoun

Nature of Business - New Accounting Pronouncements (Details)	Jun. 30, 2019
Accounting Standards Update 2016-02
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	true
Change in Accounting Principle, Accounting Standards Update, Adoption Date	Jan. 1, 2019
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
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, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false

Cyclerion Separation - Separati

Cyclerion Separation - Separation Agreement (Details) - USD ($) $ in Thousands	Jun. 30, 2019	Apr. 01, 2019	Dec. 31, 2018
Assets:
Prepaid expenses and other current assets	$ 8,880		$ 10,216
Property and equipment, net	6,665		7,652
Other assets	26		89
Total assets	315,721		332,050
Liabilities:
Accrued research and development costs	6,270		2,963
Accrued expenses and other current liabilities	$ 33,982		$ 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
Liabilities		8,822
Net Assets Transferred to Cyclerion		$ 2,609

Cyclerion Separation - General

Cyclerion Separation - General Information (Details) $ in Millions	3 Months Ended	6 Months Ended
	Jun. 30, 2019USD ($)	Jun. 30, 2019USD ($)
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
Affiliated Entity
Cyclerion Separation
Tenant improvement reimbursement provisions	1.3	$ 1.3
Affiliated Entity | Research and development
Cyclerion Separation
Expense for service provided by related party	$ 1.7

Cyclerion Separation - Summary

Cyclerion Separation - Summary of Expenses of Cyclerion (Details) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended
	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Net Loss from Discontinued Operations
Net loss from discontinued operations	$ 25,243	$ 37,438	$ 41,828
Discontinued Operations, Disposed of by Means Other than Sale, Spinoff | sGC Business
Net Loss from Discontinued Operations
Net loss from discontinued operations	25,243	37,438	41,828
Discontinued Operations, Disposed of by Means Other than Sale, Spinoff | sGC Business | Research and development
Net Loss from Discontinued Operations
Net loss from discontinued operations	15,745	21,792	31,774
Discontinued Operations, Disposed of by Means Other than Sale, Spinoff | sGC Business | Selling, general and administrative
Net Loss from Discontinued Operations
Net loss from discontinued operations	8,592	$ 15,646	9,148
Discontinued Operations, Disposed of by Means Other than Sale, Spinoff | sGC Business | Restructuring expenses
Net Loss from Discontinued Operations
Net loss from discontinued operations	$ 906		$ 906

Cyclerion Separation - Summar_2

Cyclerion Separation - Summary of Assets and Liabilities Held for Disposition (Details) - Discontinued Operations, Disposed of by Means Other than Sale, Spinoff - sGC Business - USD ($) $ in Thousands	Jun. 30, 2019	Dec. 31, 2018
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	$ 0	$ 15,739

Net Income (Loss) Per Share - N

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

Net Income (Loss) Per Share - P

Net Income (Loss) Per Share - Potentially Dilutive Securities (Details) - shares shares in Thousands	6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	68,575	65,893
Employee stock options
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	19,324	22,056
Shares subject to repurchase
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	182	130
Restricted stock units
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	2,799	3,207
Note Hedge Warrants
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	23,135	20,250
Convertible debt securities
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	23,135	20,250

Net Income (Loss) Per Share - C

Net Income (Loss) Per Share - Computation of EPS (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended				6 Months Ended
	Jun. 30, 2019	Mar. 31, 2019	Jun. 30, 2018	Mar. 31, 2018	Jun. 30, 2019	Jun. 30, 2018
Numerator:
Net income (loss)	$ 12,283	$ (59,284)	$ (49,380)	$ (43,144)	$ (47,001)	$ (92,524)
Denominator:
Weighted average number of common shares used in net loss per share-basic and diluted	155,849		152,163		155,405	151,591
Net income (loss) per share-basic and diluted (in dollars per share)	$ 0.08		$ (0.32)		$ (0.30)	$ (0.61)

Collaboration, License, Co-Pr_3

Collaboration, License, Co-Promotion and Other Commercial Agreements - Summary (Details) - USD ($) $ in Thousands	3 Months Ended			6 Months Ended
	Jun. 30, 2019	Dec. 31, 2018	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Revenues:
Revenue	$ 102,215		$ 81,106	$ 170,945	$ 150,261
Collaborative arrangements revenue
Revenues:
Revenue	77,322		71,207	143,474	134,293
Collaborative arrangement, other agreements
Revenues:
Revenue	323		343	1,270	809
Sale of active pharmaceutical ingredient
Revenues:
Revenue	24,893		8,803	27,471	14,237
Allergan | Collaborative arrangement, co-promotion agreements
Revenues:
Revenue	1,239	$ 1,300	750	1,239	1,500
Allergan | Sale of active pharmaceutical ingredient
Revenues:
Revenue				3
Allergan | North America | Collaborative arrangements revenue
Revenues:
Revenue	75,498		69,810	140,283	131,408
Allergan | North America | Collaborative arrangement, collaboration and license agreements
Revenues:
Revenue	75,498		69,810	140,283	131,408
Allergan | Europe and Other | Collaborative arrangement, collaboration and license agreements
Revenues:
Revenue	262		304	682	576
Astellas Pharma Inc. | Japan | Sale of active pharmaceutical ingredient
Revenues:
Revenue	$ 24,893		$ 8,803	$ 27,468	$ 14,237

Collaboration, License, Co-Pr_4

Collaboration, License, Co-Promotion and Other Commercial Agreements - Accounts Receivable (Details) $ in Thousands	Jun. 30, 2019USD ($)
Accounts receivable, net
Accounts payable from related party	$ 2,036
Collaborative arrangements and active pharmaceutical ingredient
Accounts receivable, net
Accounts receivable, net and related party accounts receivable, net, net of related party accounts payable	103,800
Accounts payable from related party	$ 4,300

Collaboration, License, Co-Pr_5

Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - General Information (Details) $ in Millions	3 Months Ended		6 Months Ended
	Jun. 30, 2019USD ($)	Jun. 30, 2018USD ($)	Jun. 30, 2019USD ($)itempayment	Jun. 30, 2018USD ($)
Sales milestones
Collaboration, License and Co-Promotion Agreements
Sales-related milestone if certain conditions are met	$ 100		$ 100
Allergan
Collaboration, License and Co-Promotion Agreements
Equity investment in the entity's capital stock			25
Net cost sharing offset or incremental expense related to research and development expense	2.4		$ 5.6
Cost sharing amount, reduction to research and development		$ 1.9		$ 3.3
Remaining commercial-period performance obligations | item			3
Allergan | Development and sales milestones
Collaboration, License and Co-Promotion Agreements
Cumulative license fees and development milestone payments received	$ 205		$ 205
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%

Collaboration, License, Co-Pr_6

Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Collaborative Arrangements Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Revenues:
Revenue	$ 102,215	$ 81,106	$ 170,945	$ 150,261
Collaborative arrangements revenue
Revenues:
Revenue	77,322	71,207	143,474	134,293
Allergan | North America | Collaborative arrangements revenue
Revenues:
Revenue	75,498	69,810	140,283	131,408
Allergan | North America | Collaborative arrangements, LINZESS
Revenues:
Revenue	74,973	69,264	139,267	130,413
Allergan | North America | Royalty
Revenues:
Revenue	$ 525	$ 546	$ 1,016	$ 995

Collaboration, License, Co-Pr_7

Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Commercial Efforts (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Collaboration, License and Co-Promotion Agreements
Revenue	$ 102,215	$ 81,106	$ 170,945	$ 150,261
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue	77,322	71,207	143,474	134,293
Collaborative arrangements, LINZESS | Allergan | U.S.
Collaboration, License and Co-Promotion Agreements
Revenue	74,973	69,264	139,267	130,413
Selling, general and administrative costs incurred by the Company	(10,359)	(11,713)	(20,636)	(22,641)
The Company's share of net profit	$ 64,614	$ 57,551	$ 118,631	$ 107,772

Collaboration, License, Co-Pr_8

Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Royalty Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Revenues:
Revenue	$ 102,215	$ 81,106	$ 170,945	$ 150,261
Collaborative arrangements revenue
Revenues:
Revenue	77,322	71,207	143,474	134,293
Collaborative arrangements revenue | North America | Allergan
Revenues:
Revenue	75,498	69,810	140,283	131,408
Royalty | North America | Allergan
Revenues:
Revenue	525	546	$ 1,016	995
Royalty | Canada and Mexico | Allergan
Revenues:
Revenue	$ 500	$ 600		$ 1,000

Collaboration, License, Co-Pr_9

Collaboration, License, Co-Promotion and Other Commercial Agreements - European and Other Territories (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018	Oct. 31, 2015	Sep. 30, 2012
Collaboration, License and Co-Promotion Agreements
Revenue	$ 102,215	$ 81,106	$ 170,945	$ 150,261
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue	77,322	71,207	$ 143,474	134,293
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	$ 300	$ 300	$ 700	$ 600

Collaboration, License, Co-P_10

Collaboration, License, Co-Promotion and Other Commercial Agreements - Japan (Details) $ in Thousands	1 Months Ended	3 Months Ended		6 Months Ended		12 Months Ended
	Nov. 30, 2009USD ($)	Jun. 30, 2019USD ($)	Jun. 30, 2018USD ($)	Jun. 30, 2019USD ($)	Jun. 30, 2018USD ($)	Dec. 31, 2017USD ($)payment	Dec. 31, 2016USD ($)
Collaboration, License and Co-Promotion Agreements
Revenue		$ 102,215	$ 81,106	$ 170,945	$ 150,261
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 | payment						3
Total milestone payments to be received						$ 45,000
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue		77,322	71,207	143,474	134,293
Sale of active pharmaceutical ingredient
Collaboration, License and Co-Promotion Agreements
Revenue		24,893	8,803	27,471	14,237
Sale of active pharmaceutical ingredient | Astellas Pharma Inc. | Japan
Collaboration, License and Co-Promotion Agreements
Revenue		$ 24,893	$ 8,803	$ 27,468	$ 14,237
Revenue remaining performance obligation							$ 0

Collaboration, License, Co-P_11

Collaboration, License, Co-Promotion and Other Commercial Agreements - China, Hong Kong and Macau (Details) - USD ($) $ in Thousands	1 Months Ended		3 Months Ended		6 Months Ended
	Aug. 31, 2014	Oct. 31, 2012	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Collaboration, License and Co-Promotion Agreements
Revenue			$ 102,215	$ 81,106	$ 170,945	$ 150,261
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue			77,322	71,207	143,474	134,293
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Net cost sharing offset or incremental expense related to research and development expense				700		700
Allocable to the performance obligations on a relative standalone selling price basis	$ 34,000
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangement, collaboration agreements
Collaboration, License and Co-Promotion Agreements
Prior notice period to terminate the agreement		180 days
Up-front fee received		$ 25,000
Additional budget for activities supporting the development of linaclotide	$ 14,000
Total amount of non-contingent arrangement consideration		34,000
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
AstraZeneca | China, Hong Kong, and Macau | Commercialization milestone | Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue			0	$ 0		$ 0
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%
Pre-launch commercial services and supply chain services			$ 300		$ 500

Collaboration, License, Co-P_12

Collaboration, License, Co-Promotion and Other Commercial Agreements - Co-Promotion Agreements (Details) - USD ($) $ in Thousands	3 Months Ended			6 Months Ended		9 Months Ended	12 Months Ended
	Jun. 30, 2019	Dec. 31, 2018	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018	Dec. 31, 2019	Dec. 31, 2018
Collaboration, License and Co-Promotion Agreements
Revenue	$ 102,215		$ 81,106	$ 170,945	$ 150,261
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue	77,322		71,207	143,474	134,293
Collaborative arrangement, promotion agreements
Collaboration, License and Co-Promotion Agreements
Revenue	1,200			1,200
Allergan | Collaborative arrangement, co-promotion agreements
Collaboration, License and Co-Promotion Agreements
Revenue	$ 1,239	$ 1,300	$ 750	1,239	$ 1,500
Milestone payment to be received by company upon milestone achievement							$ 7,500
Collaborative arrangement compensated amount							$ 3,000
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
Sales milestones | Allergan | Collaborative arrangement, co-promotion agreements
Collaboration, License and Co-Promotion Agreements
Milestone payment to be received by company upon milestone achievement				$ 3,000

Collaboration, License, Co-P_13

Collaboration, License, Co-Promotion and Other Commercial Agreements - Other Collaborations and License Agreements (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Collaboration, License and Co-Promotion Agreements
Research and development	$ 28,758	$ 23,187	$ 60,956	$ 43,663
Collaborative arrangement, co-promotion and other agreements
Collaboration, License and Co-Promotion Agreements
Revenue related to nonrefundable upfront payments			500
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		63,500
Collaborative arrangement, other agreements
Collaboration, License and Co-Promotion Agreements
Research and development	$ 0	$ 0	0	$ 0
Collaborative arrangement, other agreements | Development milestones
Collaboration, License and Co-Promotion Agreements
Contingent milestone payable			7,500
Collaborative arrangement, other agreements | Regulatory milestones
Collaboration, License and Co-Promotion Agreements
Contingent milestone payable			18,000
Milestone payment made			$ 0

Fair Value of Financial Instr_3

Fair Value of Financial Instruments - General Information (Details)	Jun. 30, 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	Jun. 30, 2019	Dec. 31, 2018
Assets:
Convertible note hedges	$ 60,720	$ 41,020
Total assets measured at fair value	159,513	214,113
Liabilities:
Note hedge warrants	50,191	33,763
Contingent consideration		51
Total liabilities measured at fair value	50,191	33,814
Money market funds
Assets:
Cash and cash equivalents	82,918	142,218
Repurchase agreements
Assets:
Cash and cash equivalents	15,875	30,875
Quoted Prices in Active Markets for Identical Assets (Level 1)
Assets:
Total assets measured at fair value	98,793	173,093
Quoted Prices in Active Markets for Identical Assets (Level 1) | Money market funds
Assets:
Cash and cash equivalents	82,918	142,218
Quoted Prices in Active Markets for Identical Assets (Level 1) | Repurchase agreements
Assets:
Cash and cash equivalents	15,875	30,875
Significant Unobservable Inputs (Level 3)
Assets:
Convertible note hedges	60,720	41,020
Total assets measured at fair value	60,720	41,020
Liabilities:
Note hedge warrants	50,191	33,763
Contingent consideration		51
Total liabilities measured at fair value	$ 50,191	$ 33,814

Fair Value of Financial Instr_5

Fair Value of Financial Instruments - Transfers Between Fair Value Measurement Levels (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Fair value transfers
Fair value transfer between measurement levels	$ 0	$ 0	$ 0	$ 0

Fair Value of Financial Instr_6

Fair Value of Financial Instruments - Assumptions - Convertible Note Hedges (Details)	Jun. 30, 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	0.017	0.025
Measurement Input, Expected Term
Fair Value of Financial Instruments
Derivative asset, measurement input | Y	3	3.5
Measurement Input, Share Price
Fair Value of Financial Instruments
Derivative asset, measurement input	10.94	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	0.472	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)	Jun. 30, 2019$ / sharesY	Dec. 31, 2018$ / sharesY
Fair Value of Financial Instruments
Derivative liability, valuation technique	us-gaap:ValuationTechniqueOptionPricingModelMember	us-gaap:ValuationTechniqueOptionPricingModelMember
Measurement Input, Risk Free Interest Rate
Fair Value of Financial Instruments
Derivative liability, measurement input	0.017	0.025
Measurement Input, Expected Term
Fair Value of Financial Instruments
Derivative liability, measurement input | Y	3.5	4.1
Measurement Input, Share Price
Fair Value of Financial Instruments
Derivative liability, measurement input	10.94	10.36
Measurement Input, Exercise Price
Fair Value of Financial Instruments
Derivative liability, measurement input	18.82	21.50
Measurement Input, Price Volatility
Fair Value of Financial Instruments
Derivative liability, measurement input	0.471	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) $ in Thousands	6 Months Ended
	Jun. 30, 2019USD ($)
Change in Level 3 Assets
Balance at beginning of period	$ 41,020
Change in fair value, recorded as a component of gain (loss) on derivatives	19,700
Balance at end of period	$ 60,720

Fair Value of Financial Instr_9

Fair Value of Financial Instruments - Change in Level 3 - Note Hedge Warrants (Details) - Warrants $ in Thousands	6 Months Ended
	Jun. 30, 2019USD ($)
Change in Level 3 Liabilities
Balance at beginning of period	$ (33,763)
Change in fair value, recorded as a component of gain (loss) on derivatives	(16,428)
Balance at end of period	$ (50,191)

Fair Value of Financial Inst_10

Fair Value of Financial Instruments - Notes Payable (Details) - USD ($) $ in Thousands	Jun. 30, 2019	Dec. 31, 2018	Sep. 23, 2016	Jun. 30, 2015
Notes Payable | 8.375% Notes due 2026
Fair value disclosures
Annual interest rate of notes (as a percent)	8.375%		8.375%
Aggregate principal amount of notes issued in private placement			$ 150,000
Notes Payable | 8.375% Notes due 2026 | Significant Unobservable Inputs (Level 3)
Fair value disclosures
Estimated fair value	$ 133,000	$ 148,200
Convertible Senior Notes
Fair value disclosures
Aggregate principal amount of notes issued in private placement	335,699	335,699
Convertible Senior Notes | 2.25% Convertible Senior Notes due in 2022
Fair value disclosures
Annual interest rate of notes (as a percent)				2.25%
Aggregate principal amount of notes issued in private placement				$ 335,700
Convertible Senior Notes | 2.25% Convertible Senior Notes due in 2022 | Significant Other Observable Inputs (Level 2)
Fair value disclosures
Estimated fair value	$ 359,100	$ 315,000

Inventory - Tabular Disclosure

Inventory - Tabular Disclosure (Details) $ in Thousands	Jun. 30, 2019USD ($)
Inventory
Raw Materials	$ 1,475
Work in Progress	260
Total	$ 1,735

Inventory - General Information

Inventory - General Information (Details) - USD ($) $ in Millions	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019
Inventory
Write-down of inventory	$ 0	$ 1.8	$ 0

Accrued Expenses and Other Cu_3

Accrued Expenses and Other Current Liabilities - Tabular Disclosure (Details) - USD ($) $ in Thousands	Jun. 30, 2019	Dec. 31, 2018
Accrued Expenses
Salaries	$ 2,499	$ 3,054
Accrued vacation	2,887	3,493
Accrued incentive compensation	5,370	13,867
Other employee benefits	536	1,883
Professional fees	5,275	1,735
Accrued interest	793	873
Restructuring accruals	1,597	2,885
Other	15,025	10,211
Total accrued expenses and other current liabilities	$ 33,982	$ 38,001

Accrued Expenses and Other Cu_4

Accrued Expenses and Other Current Liabilities - Additional Information (Details) - USD ($) $ in Thousands	Jun. 30, 2019	Dec. 31, 2018
Accrued Expenses
Other accrued expenses	$ 15,025	$ 10,211
Goods received but not yet invoiced	5,000
Activities associated with the Company's intent to separate into two independent publicly traded companies	900
Commercial and Sample Supply Commitments
Accrued Expenses
Write-down of excess non-cancellable sample purchase commitments	1,400	1,400
Commercial and Sample Supply Commitments | Linaclotide | Accrued Expenses and Other Current Liabilities
Accrued Expenses
Accrual for non-cancellable purchase commitments	$ 2,500	$ 2,500

Leases - Lease Cost (Details)

Leases - Lease Cost (Details) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended
	Jun. 30, 2019	Jun. 30, 2019
Lease cost
Operating lease cost during period	$ 3,155	$ 7,680
Variable lease payments	654	654
Short-term lease cost	379	768
Total lease cost	4,188	9,102
Sublease income	$ 300	$ 300

Leases - Operating Leases - Sup

Leases - Operating Leases - Supplemental Cash Flow Information (Details) $ in Thousands	6 Months Ended
	Jun. 30, 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	$ 6,619
Weighted-average remaining lease term of operating leases (in years)	7 years 10 months 24 days
Weighted-average discount rate of operating leases (as a percent)	5.30%

Leases - Operating Leases - Fut

Leases - Operating Leases - Future Minimum Lease Payments - ASC 842 (Details) $ in Thousands	Jun. 30, 2019USD ($)
Future minimum lease payments
2019 (remaining six months)	$ 11,979
2020	1,146
2021	3,128
2022	3,129
2023	3,065
2024 and thereafter	21,170
Total future minimum lease payments	$ 43,617

Leases - Operating Leases - Ope

Leases - Operating Leases - Operating Lease Obligations (Details) $ in Thousands	Jun. 30, 2019USD ($)
Operating lease obligations
Total future minimum lease payments	$ 43,617
Less: present value adjustment	9,205
Operating lease obligations	34,412
Less: current portion of operating lease obligations	11,904
Operating lease liabilities, net of current portion	$ 22,508

Leases - Operating Leases - F_2

Leases - Operating Leases - Future Minimum Lease Payments - ASC 840 (Details) $ in Thousands	Dec. 31, 2018USD ($)
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	Jun. 30, 2019	Jun. 30, 2019	Dec. 31, 2018
Operating leases
Restricted cash, noncurrent		$ 971	$ 971	$ 6,426
Operating lease right-of-use assets		$ 25,569	$ 25,569
Weighted-average discount rate of operating leases (as a percent)		5.30%	5.30%
Operating lease cost		$ 3,155	$ 7,680
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	1,000
Operating lease right-of-use assets		18,300	18,300
Lease liability, net of tenant improvement allowance reimbursement		18,300	18,300
Tenant improvement allowance reimbursement		$ 3,800	$ 3,800
Weighted-average discount rate of operating leases (as a percent)		5.80%	5.80%
Operating lease cost		$ 200

Leases - Operating Leases - Bin

Leases - Operating Leases - Binney Street Lease (Details) $ in Thousands	Jun. 11, 2019USD ($)ft²	Apr. 01, 2019ft²	Jan. 31, 2007USD ($)ft²	Jun. 30, 2019USD ($)	Jun. 30, 2018USD ($)	Jun. 30, 2019USD ($)	Jun. 30, 2018USD ($)	Jan. 01, 2019USD ($)	Dec. 31, 2018USD ($)
Operating leases
Restricted cash, noncurrent				$ 971		$ 971			$ 6,426
Operating lease right-of-use assets				25,569		25,569
Lease liability				$ 34,412		$ 34,412
Weighted-average discount rate of operating leases (as a percent)				5.30%		5.30%
Operating lease cost				$ 3,155		$ 7,680
Sublease income				300		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				7,300		7,300		$ 87,700
Lease liability				11,800		11,800		$ 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
Right to extend the termination of lease (in days)	30 days
Lease termination cost	$ 9,000
Operating lease cost				3,600		8,000
Sublease income				$ 300		$ 300
Rent expense					$ 2,500		$ 5,100

Leases - Operating Leases - Dat

Leases - Operating Leases - Data center colocation lease (Details) - USD ($) $ in Thousands	3 Months Ended
	Jun. 30, 2019	Jan. 01, 2019
Operating leases
Operating lease right-of-use assets	$ 25,569
Lease liability	$ 34,412
Asset impairment charge
Weighted-average discount rate of operating leases (as a percent)	5.30%
Data Center Lease, Boston, Massachusetts
Operating leases
Annual rent escalation (as a percent)	4.00%
Operating lease right-of-use assets	$ 500	$ 600
Lease liability	$ 500	$ 600
Asset impairment charge
Weighted-average discount rate of operating leases (as a percent)	6.00%
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	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018	Dec. 31, 2018	Apr. 30, 2018
Operating leases
Restricted cash, noncurrent	$ 971		$ 971		$ 6,426
Operating lease cost	3,155		7,680
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	$ 400		$ 800
Rent expenses		$ 0		$ 0
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%

Notes Payable - 8.375% Notes du

Notes Payable - 8.375% Notes due 2026 - General Information (Details) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended
	Jun. 30, 2019	Jun. 30, 2019	Dec. 31, 2018	Sep. 23, 2016	Jun. 30, 2015
Notes Payable
Principal payments on 2026 notes		$ 21,469
Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued	$ 335,699	335,699	$ 335,699
Debt issuance costs capitalized	$ 4,449	$ 4,449	$ 5,004
8.375% Notes due 2026 | Notes Payable
Notes Payable
Aggregate principal amount of notes issued				$ 150,000
Annual interest rate of notes (as a percent)	8.375%	8.375%		8.375%
Debt issuance costs capitalized				$ 500
Percentage of net sales to determine quarterly payments (as a percent)		7.50%
Amount of principal expected to be paid within twelve months	$ 48,800	$ 48,800
Principal payments on 2026 notes	$ 9,200	$ 21,500
2.25% Convertible Senior Notes due in 2022 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued					$ 335,700
Annual interest rate of notes (as a percent)					2.25%

Notes Payable - 8.375% Notes _2

Notes Payable - 8.375% Notes due 2026 - Redemption Percentage (Details) - 8.375% Notes due 2026 - Notes Payable	6 Months Ended
	Jun. 30, 2019
From and including January 1, 2015 to and including December 31, 2015
Notes Payable
Payment start date	Mar. 15, 2019
Payment end date	Mar. 14, 2020
Redemption Percentage	105.50%
From and including January 1, 2016 to and including December 31, 2016
Notes Payable
Payment start date	Mar. 15, 2020
Payment end date	Mar. 14, 2021
Redemption Percentage	102.75%
From and including January 1, 2017 and thereafter
Notes Payable
Payment start date	Mar. 15, 2021
Redemption Percentage	100.00%

Notes Payable - 2.25% Convertib

Notes Payable - 2.25% Convertible Senior Notes due 2022 - General Information (Details)	Apr. 15, 2019USD ($)$ / sharesshares	Jun. 30, 2015USD ($)D$ / sharesshares	Jun. 30, 2019USD ($)$ / sharesshares	Dec. 31, 2018USD ($)
Notes Payable
Payments for convertible note hedges		$ 21,100,000
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
Aggregate principal amount of notes issued			$ 335,699,000	$ 335,699,000
Debt issuance costs capitalized			$ 4,449,000	$ 5,004,000
2.25% Convertible Senior Notes due in 2022 | Note Hedge Warrants
Notes Payable
Shares issuable upon conversion of debt (in shares) | shares	23,135,435
2.25% Convertible Senior Notes due in 2022 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued		335,700,000
Net proceed received		324,000,000
Fees and expenses		$ 11,700,000
Annual interest rate of notes (as a percent)		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%
Maximum period of the sole remedy for event failures in the Indenture			180 days
Amortization period		7 years
2.25% Convertible Senior Notes due in 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 in 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	Jun. 30, 2019	Dec. 31, 2018	Jun. 30, 2015
Liability component:
Aggregate principal amount of notes issued	$ 335,699	$ 335,699
Less: unamortized debt discount	(56,855)	(65,094)
Less: unamortized debt issuance costs	(4,449)	(5,004)
Net carrying amount	274,395	265,601
Equity component	$ 114,199	$ 114,199
2.25% Convertible Senior Notes due in 2022
Liability component:
Aggregate principal amount of notes issued			$ 335,700

Notes Payable - 2.25% Convert_3

Notes Payable - 2.25% Convertible Senior Notes due 2022 - Additional Information (Details) - 2.25% Convertible Senior Notes due in 2022 - Convertible Senior Notes - USD ($) $ in Millions	1 Months Ended
	Jun. 30, 2015	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		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 in 2022 - Convertible Senior Notes - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Interest Expense
Contractual interest expense	$ 1,889	$ 1,888	$ 3,777	$ 3,777
Amortization of debt issuance costs	283	237	555	464
Amortization of debt discount	4,164	3,816	8,239	7,550
Total interest expense	$ 6,336	$ 5,941	$ 12,571	$ 11,791

Notes Payable - Convertible Not

Notes Payable - Convertible Note Hedge and Warrant Transactions (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	6 Months Ended
	Jun. 30, 2015	Jun. 30, 2019	Apr. 15, 2019	Dec. 31, 2018
Notes Payable
Long-term asset		$ 60,720		$ 41,020
Long-term liability		$ 50,191		$ 33,763
Net derivative issuance cost	$ 21,100
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

Employee Stock Benefit Plans -

Employee Stock Benefit Plans - Equity Plan (Details) - 2019 Equity Plan	May 31, 2019shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares reserved for issuance (in shares)	10,000,000
Shares available for future grant (in shares)	9,923,183

Employee Stock Benefit Plans _2

Employee Stock Benefit Plans - Share-based Compensation Reflected in the Consolidated Statement of Operations (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Employee Stock Benefit Plans
Share-based compensation expense	$ 6,337	$ 9,783	$ 20,271	$ 18,054
Research and development
Employee Stock Benefit Plans
Share-based compensation expense	1,179	2,920	4,098	5,472
Selling, general and administrative
Employee Stock Benefit Plans
Share-based compensation expense	5,021	6,539	15,519	12,065
Restructuring expenses
Employee Stock Benefit Plans
Share-based compensation expense	$ 137	$ 324	$ 654	$ 517

Employee Stock Benefit Plans _3

Employee Stock Benefit Plans - Workforce Reduction (Details) $ in Thousands	Feb. 07, 2019employee	Jun. 27, 2018employee	Jan. 30, 2018employee	Jun. 30, 2019USD ($)	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Jun. 30, 2019USD ($)	Jun. 30, 2018USD ($)
Employee Stock Benefit Plans
Share-based compensation expense				$ 6,337	$ 9,783		$ 20,271	$ 18,054
Spin-off | Share-based Payment Awards, Excluding Employee Stock Purchase Plan [Member]
Employee Stock Benefit Plans
Share-based compensation expense				0			0
Spin-off | 2010 Purchase Plan
Employee Stock Benefit Plans
Share-based compensation expense				300			300
Research and development
Employee Stock Benefit Plans
Share-based compensation expense				1,179	2,920		4,098	5,472
Selling, general and administrative
Employee Stock Benefit Plans
Share-based compensation expense				5,021	6,539		15,519	12,065
Restructuring expenses
Employee Stock Benefit Plans
Share-based compensation expense				$ 137	324		654	517
Reduction in Field-based Workforce, January 30, 2018
Workforce Reduction
Number of employees eliminated | employee			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
Reduction in Headquarter-based Workforce, June 27, 2018 | Restructuring expenses | Employee severance, benefits and related costs
Employee Stock Benefit Plans
Share-based compensation expense					$ 300			$ 300
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 - Share-based Compensation Expense (Details) - USD ($) $ in Millions	3 Months Ended	6 Months Ended
	Jun. 30, 2019	Jun. 30, 2019
Employee Stock Benefit Plans
Share-based compensation expense, other modifications	$ 2.4	$ 2.4

Related Party Transactions (Det

Related Party Transactions (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended		6 Months Ended
	Sep. 30, 2009	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018	Dec. 31, 2018
Related Party Transactions
Accounts payable from related party		$ 2,036		$ 2,036
Investor | Allergan
Related Party Transactions
Accounts receivable		79,400		79,400		$ 60,000
Investor | Allergan | Convertible preferred stock
Related Party Transactions
Shares sold (in shares)	2,083,333
Board of Directors member
Related Party Transactions
Fees paid to related party		700	$ 1,100	1,200	$ 1,800
Amount of insurance premium paid to the insurance provider		1,600	$ 3,000	4,100	$ 6,300
Accounts payable from related party						$ 0
Accounts payable due to related party		$ 300		$ 300

Workforce Reduction - General I

Workforce Reduction - General Information (Details) $ in Thousands	Feb. 07, 2019employee	Aug. 16, 2018employee	Jun. 27, 2018employee	Jan. 30, 2018employee	Jun. 30, 2019USD ($)	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Jun. 30, 2019USD ($)	Jun. 30, 2018USD ($)
Restructuring expenses
Restructuring expenses					$ 490	$ 1,486		$ 3,818	$ 3,908
Employee severance, benefits and related costs
Restructuring expenses
Restructuring expenses								3,198
Reduction in Field-based Workforce, January 30, 2018
Workforce Reduction
Number of employees eliminated | employee				60
Restructuring expenses
Employee severance, benefits and related costs							$ 2,400
Reduction in Headquarter-based Workforce, June 27, 2018
Workforce Reduction
Number of employees expected to be eliminated | employee			40
Restructuring expenses
Employee severance, benefits and related costs						$ 1,500			$ 1,500
Reduction in Headquarter-based Workforce, June 27, 2018 | Employee severance, benefits and related costs
Restructuring expenses
Restructuring expenses								16
Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018
Workforce Reduction
Number of employees expected to be eliminated | employee		100
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					$ 500			3,800
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	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Workforce Reduction
Charges	$ 490	$ 1,486	$ 3,818	$ 3,908
Employee severance, benefits and related costs
Workforce Reduction
Balance at beginning of period			2,452
Charges			3,198
Amounts paid			(4,142)
Adjustments			(59)
Balance at end of period	1,449		1,449
Employee severance, benefits and related costs | Reduction in Headquarter-based Workforce, June 27, 2018
Workforce Reduction
Balance at beginning of period			696
Charges			16
Amounts paid			(556)
Adjustments			(15)
Balance at end of period	141		141
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
Amounts paid			(1,708)
Adjustments			(44)
Balance at end of period	4		4
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			(1,878)
Balance at end of period	1,304		1,304
Contract related costs
Workforce Reduction
Balance at beginning of period			433
Amounts paid			(287)
Adjustments			(42)
Balance at end of period	104		104
Contract related costs | Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018
Workforce Reduction
Balance at beginning of period			433
Amounts paid			(287)
Adjustments			(42)
Balance at end of period	$ 104		$ 104

Workforce Reduction - Restructu

Workforce Reduction - Restructuring Expenses (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2019	Jun. 30, 2018	Jun. 30, 2019	Jun. 30, 2018
Restructuring expenses
Restructuring expenses	$ 490	$ 1,486	$ 3,818	$ 3,908