Ligand Pharmaceuticals (LGND) 10-Q 7 Aug 20 2020 Q2 Quarterly report Financial data

Cover Page

Cover Page - shares	6 Months Ended
	Jun. 30, 2020	Aug. 04, 2020
Cover [Abstract]
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Jun. 30, 2020
Document Transition Report	false
Entity File Number	001-33093
Entity Registrant Name	LIGAND PHARMACEUTICALS INCORPORATED
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	77-0160744
Entity Address, Address Line One	3911 Sorrento Valley Boulevard, Suite 110
Entity Address, City or Town	San Diego
Entity Address, State or Province	CA
Entity Address, Postal Zip Code	92121
City Area Code	858
Local Phone Number	550-7500
Title of 12(b) Security	Common Stock , par value $0.001 per share
Trading Symbol	LGND
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		16,078,143
Amendment Flag	false
Document Fiscal Year Focus	2020
Document Fiscal Period Focus	Q2
Entity Central Index Key	0000886163
Current Fiscal Year End Date	--12-31

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Current assets:
Cash and cash equivalents	$ 115,156	$ 71,543
Short-term investments	694,724	998,324
Accounts receivable, net	41,874	30,387
Inventory	3,702	7,296
Income taxes receivable	2,679	11,361
Other current assets	5,489	4,734
Total current assets	863,624	1,123,645
Deferred income taxes, net	26,411	25,608
Intangible assets, net	215,295	210,448
Goodwill	103,369	95,229
Commercial license and other economic rights, net	10,606	20,090
Property and equipment, net	7,883	7,185
Operating lease right-of-use assets	9,689	10,353
Other assets	6,059	2,357
Total assets	1,242,936	1,494,915
Current liabilities:
Accounts payable	6,103	2,420
Accrued liabilities	12,828	9,836
Current contingent liabilities	1,416	2,607
Deferred revenue	8,917	2,139
Total current liabilities	29,264	17,002
2023 convertible senior notes, net	449,672	638,959
Long-term contingent liabilities	10,005	6,335
Deferred income taxes, net	23,340	32,937
Long-term operating lease liabilities	9,181	9,970
Other long-term liabilities	26,471	22,480
Total liabilities	547,933	727,683
Commitments and contingencies
Stockholders' equity:
Preferred stock, $0.001 par value; 5,000 shares authorized; zero issued and outstanding at June 30, 2020 and December 31, 2019	0	0
Common stock, $0.001 par value; 60,000 shares authorized; 16,071 and 16,823 shares issued and outstanding at June 30, 2020 and December 31, 2019, respectively	16	17
Additional paid-in capital	304,404	367,326
Accumulated other comprehensive loss	(2,310)	(216)
Retained earnings	392,893	400,105
Total stockholders' equity	695,003	767,232
Total liabilities and stockholders' equity	$ 1,242,936	$ 1,494,915

Condensed Consolidated Balanc_2

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2020	Dec. 31, 2019
Statement of Financial Position [Abstract]
Preferred stock, par value (USD per share)	$ 0.001	$ 0.001
Preferred stock authorized (shares)	5,000,000	5,000,000
Preferred stock issued (shares)	0	0
Preferred stock outstanding (shares)	0	0
Common stock, par value (USD per share)	$ 0.001	$ 0.001
Common stock authorized (shares)	60,000,000	60,000,000
Common stock issued (shares)	16,071,000	16,823,000
Common stock outstanding (shares)	16,071,000	16,823,000

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Revenues:
Total revenues	$ 41,420	$ 24,987	$ 74,581	$ 68,471
Operating costs and expenses:
Cost of Captisol	7,644	2,405	12,327	6,263
Amortization of intangibles	3,875	3,505	7,410	7,008
Research and development	12,732	12,213	24,623	23,502
General and administrative	10,069	10,994	19,333	22,082
Total operating costs and expenses	34,320	29,117	63,693	58,855
Gain from sale of Promacta license	0	0	0	812,797
Income from operations	7,100	(4,130)	10,888	822,413
Other income (expense):
Gain (loss) from short-term investments	23,460	(15,061)	(7,281)	4,488
Interest income	1,969	9,285	6,699	15,194
Interest expense	(6,213)	(9,012)	(14,761)	(17,918)
Other income, net	1,803	890	2,159	508
Total other income (loss), net	21,019	(13,898)	(13,184)	2,272
Income (loss) before income taxes	28,119	(18,028)	(2,296)	824,685
Income tax benefit (expense)	(6,033)	3,609	251	(172,767)
Net income (loss)	$ 22,086	$ (14,419)	$ (2,045)	$ 651,918
Earnings Per Share, Basic and Diluted:
Basic net income (loss) per share (USD per share)	$ 1.38	$ (0.74)	$ (0.13)	$ 32.60
Shares used in basic per share calculations (shares)	16,055,000	19,558,000	16,292,000	20,000,000
Diluted net income (loss) per share (USD per share)	$ 1.32	$ (0.74)	$ (0.13)	$ 31.34
Shares used in diluted per share calculations (shares)	16,694,000	19,558,000	16,292,000	20,799,000
Royalties
Revenues:
Total revenues	$ 7,181	$ 6,626	$ 13,746	$ 26,164
Captisol
Revenues:
Total revenues	24,468	8,549	45,577	17,508
Service Revenue
Revenues:
Total revenues	4,582	4,559	7,939	8,442
Contract Revenue
Revenues:
Total revenues	$ 5,189	$ 5,253	$ 7,319	$ 16,357

Condensed Consolidated Statem_2

Condensed Consolidated Statements of Comprehensive Income (Loss) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Statement of Comprehensive Income [Abstract]
Net income (loss):	$ 22,086	$ (14,419)	$ (2,045)	$ 651,918
Unrealized net gain (loss) on available-for-sale securities, net of tax	2,742	503	(30)	733
Foreign currency translation	(185)	(542)	(2,064)	(251)
Comprehensive income (loss)	$ 24,643	$ (14,458)	$ (4,139)	$ 652,400

Condensed Consolidated Statem_3

Condensed Consolidated Statements of Stockholders' Equity - USD ($)	Total	Adjustment	Common Stock	Additional paid in capital	Accumulated other comprehensive income (loss)	Retained earnings (Accumulated deficit)	Retained earnings (Accumulated deficit)Adjustment
Balance at beginning of period (in shares) at Dec. 31, 2018			20,765,000
Balance at beginning of period at Dec. 31, 2018	$ 560,914,000		$ 21,000	$ 791,114,000	$ (1,024,000)	$ (229,197,000)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock under employee stock compensation plans, net (shares)			135,000
Issuance of common stock under employee stock compensation plans, net	(991,000)			(991,000)
Share-based compensation	5,347,000			5,347,000
Repurchase of common stock (shares)			(1,236,000)
Repurchase of common stock	(151,585,000)		$ (1,000)	(151,584,000)
Unrealized net gain (loss) on available-for-sale securities, net of deferred tax	230,000				230,000
Foreign currency translation adjustment	291,000				291,000
Other tax adjustments	(569,000)			(569,000)
Net loss	666,337,000					666,337,000
Balance at end of period (in shares) at Mar. 31, 2019			19,664,000
Balance at end of period at Mar. 31, 2019	1,079,974,000		$ 20,000	643,317,000	(503,000)	437,140,000
Balance at beginning of period (in shares) at Dec. 31, 2018			20,765,000
Balance at beginning of period at Dec. 31, 2018	560,914,000		$ 21,000	791,114,000	(1,024,000)	(229,197,000)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net loss	651,918,000
Balance at end of period (in shares) at Jun. 30, 2019			19,390,000
Balance at end of period at Jun. 30, 2019	1,041,453,000		$ 19,000	619,255,000	(542,000)	422,721,000
Balance at beginning of period (in shares) at Mar. 31, 2019			19,664,000
Balance at beginning of period at Mar. 31, 2019	1,079,974,000		$ 20,000	643,317,000	(503,000)	437,140,000
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock under employee stock compensation plans, net (shares)			17,000
Issuance of common stock under employee stock compensation plans, net	740,000			740,000
Share-based compensation	6,571,000			6,571,000
Repurchase of common stock (shares)			(291,000)
Repurchase of common stock	(33,717,000)		$ (1,000)	(33,716,000)
Unrealized net gain (loss) on available-for-sale securities, net of deferred tax	503,000				503,000
Foreign currency translation adjustment	(542,000)				(542,000)
Other tax adjustments	2,343,000			2,343,000
Net loss	(14,419,000)					(14,419,000)
Balance at end of period (in shares) at Jun. 30, 2019			19,390,000
Balance at end of period at Jun. 30, 2019	1,041,453,000		$ 19,000	619,255,000	(542,000)	422,721,000
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Cumulative-effect adjustment from adoption of ASU 2016-13, net of tax		$ (5,167,000)					$ (5,167,000)
Balance at beginning of period (in shares) at Dec. 31, 2019			16,823,000
Balance at beginning of period at Dec. 31, 2019	767,232,000		$ 17,000	367,326,000	(216,000)	400,105,000
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock under employee stock compensation plans, net (shares)			105,000
Issuance of common stock under employee stock compensation plans, net	(1,008,000)			(1,008,000)
Share-based compensation	5,653,000			5,653,000
Repurchase of common stock (shares)			(878,000)
Repurchase of common stock	(73,287,000)		$ (1,000)	(73,286,000)
Unrealized net gain (loss) on available-for-sale securities, net of deferred tax	(2,772,000)				(2,772,000)
Foreign currency translation adjustment	(1,879,000)				(1,879,000)
Reacquisition of equity due to 2023 debt extinguishment, net of tax	(2,745,000)			(2,745,000)
Net loss	(24,131,000)					(24,131,000)
Balance at end of period (in shares) at Mar. 31, 2020			16,050,000
Balance at end of period at Mar. 31, 2020	$ 661,896,000		$ 16,000	295,940,000	(4,867,000)	370,807,000
Accounting Standards Update	us-gaap:AccountingStandardsUpdate201613Member
Balance at beginning of period (in shares) at Dec. 31, 2019			16,823,000
Balance at beginning of period at Dec. 31, 2019	$ 767,232,000		$ 17,000	367,326,000	(216,000)	400,105,000
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net loss	(2,045,000)
Balance at end of period (in shares) at Jun. 30, 2020			16,071,000
Balance at end of period at Jun. 30, 2020	695,003,000		$ 16,000	304,404,000	(2,310,000)	392,893,000
Balance at beginning of period (in shares) at Mar. 31, 2020			16,050,000
Balance at beginning of period at Mar. 31, 2020	661,896,000		$ 16,000	295,940,000	(4,867,000)	370,807,000
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock under employee stock compensation plans, net (shares)			21,000
Issuance of common stock under employee stock compensation plans, net	1,128,000			1,128,000
Share-based compensation	7,359,000			7,359,000
Repurchase of common stock	0
Unrealized net gain (loss) on available-for-sale securities, net of deferred tax	2,742,000				2,742,000
Foreign currency translation adjustment	(185,000)				(185,000)
Reacquisition of equity due to 2023 debt extinguishment, net of tax	(23,000)			(23,000)
Net loss	22,086,000					22,086,000
Balance at end of period (in shares) at Jun. 30, 2020			16,071,000
Balance at end of period at Jun. 30, 2020	$ 695,003,000		$ 16,000	$ 304,404,000	$ (2,310,000)	$ 392,893,000

Condensed Consolidated Statem_4

Condensed Consolidated Statements of Cash Flows $ in Thousands	6 Months Ended
	Jun. 30, 2020USD ($)	Jun. 30, 2019USD ($)
Cash flows from operating activities:
Net income (loss)	$ (2,045)	$ 651,918
Adjustments to reconcile net income (loss) to net cash provided by operating activities:
Gain from sale of Promacta license	0	(812,797)
Change in estimated fair value of contingent liabilities	(371)	984
Depreciation and amortization of intangible assets	7,869	7,699
Amortization of premium (discount) on investments, net	1,198	(6,023)
Amortization of debt discount and issuance fees	12,442	14,999
Amortization of commercial license and other economic rights	2,733	5,452
Gain on debt extinguishment	(659)	0
Share-based compensation	13,012	11,918
Deferred income taxes	(8,890)	55,661
Loss (gain) from short-term investments	7,281	(4,488)
Other	(1,499)	(4,429)
Changes in operating assets and liabilities, net of acquisition:
Accounts receivable, net	(11,466)	35,591
Inventory	6,977	(4,573)
Accounts payable and accrued liabilities	2,909	(3,764)
Income tax receivable	8,673	47,455
Other economic rights	0	(12,000)
Other	3,140	597
Net cash provided by (used in ) operating activities	41,304	(15,800)
Cash flows from investing activities:
Proceeds from sale of Promacta license	0	812,797
Purchase of short-term investments	(336,726)	(1,281,274)
Proceeds from sale of short-term investments	179,431	43,724
Proceeds from maturity of short-term investments	452,405	791,006
Cash paid for acquisition	(15,140)	0
Other	1,809	(5,673)
Net cash provided by investing activities	281,779	360,580
Cash flows from financing activities:
Repurchase of 2023 Notes	(203,210)	0
Net proceeds from stock option exercises and ESPP	1,550	2,643
Taxes paid related to net share settlement of equity awards	(1,429)	(2,893)
Share repurchase	(73,287)	(189,917)
Payments to CVR Holders	(1,800)	0
Other	(1,134)	0
Net cash used in financing activities	(279,310)	(190,167)
Effect of exchange rate changes on cash	(160)	7
Net increase in cash, cash equivalents and restricted cash	43,613	154,620
Cash, cash equivalents and restricted cash at beginning of period	72,273	119,780
Cash, cash equivalents and restricted cash at end of period	115,886	274,400
Supplemental disclosure of cash flow information:
Interest paid	2,531	2,915
Taxes paid	0	69,703
Restricted cash in other current assets	730	1,353
Supplemental schedule of non-cash activity:
Accrued fixed asset purchases	292	54
Accrued inventory purchases	3,553	0
Unrealized gain (loss) on AFS investments	$ (38)	$ 938

Basis of Presentation and Summa

Basis of Presentation and Summary of Significant Accounting Policies	6 Months Ended
	Jun. 30, 2020
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Basis of Presentation and Summary of Significant Accounting Policies	Basis of Presentation and Summary of Significant Accounting Policies Basis of Presentation Our condensed consolidated financial statements include the financial statements of Ligand and its wholly-owned subsidiaries. All significant intercompany accounts and transactions have been eliminated in consolidation. We have included all adjustments, consisting only of normal recurring adjustments, which we considered necessary for a fair presentation of our financial results. These unaudited condensed consolidated financial statements and accompanying notes should be read together with the audited consolidated financial statements included in our 2019 Annual Report. Interim financial results are not necessarily indicative of the results that may be expected for the full year. Reclassifications Certain amounts in the prior period condensed consolidated financial statements have been reclassified to conform with the current period presentation. Specifically, effective the first quarter of 2020, we began to present service revenue and contract revenue separately, which were combined in license fees, milestones and other revenues in prior years. As a result, service revenue and contract revenue in the condensed consolidated statements of operations for the three and six months ended June 30, 2019 have been reclassified to conform to the current period presentation. In addition, effective the second quarter of 2020, we began to include our investment in Viking in “short-term investments” in the condensed consolidated balance sheet as of June 30, 2020, and present “gain (loss) from short-term investments” in the condensed consolidated statements of operations for the three and six months ended June 30, 2020 to include both the gain (loss) from investment in Viking and other short-term investments, which was previously included in “other income, net”. As a result, the audited consolidated balance sheet as of December 31, 2019 and the condensed consolidated statements of operations for the three and six months ended June 30, 2019 have been reclassified to conform to the current period presentation. Significant Accounting Policies We have described our significant accounting policies in Note 1, Basis of Presentation and Summary of Significant Accounting Policies , of Notes to Consolidated Financial Statements in our 2019 Annual Report. Use of Estimates The preparation of condensed consolidated financial statements in conformity with GAAP requires the use of estimates and assumptions that affect the amounts reported in the condensed consolidated financial statements and the accompanying notes. Actual results may differ from those estimates. Impact of COVID-19 Pandemic The current COVID-19 worldwide pandemic has presented substantial public health and economic challenges and is affecting our employees and partners, patients, communities and business operations, as well as the U.S. and global economy and financial markets. International and U.S. governmental authorities in impacted regions are taking actions in an effort to slow the spread of COVID-19, including issuing varying forms of “stay-at-home” orders, and restricting business functions outside of one’s home. In response, we have restricted in-person access to our executive offices, our administrative employees are mostly working remotely, and we have limited the number of staff in our research and development laboratories and other facilities. The continued spread of the COVID-19 pandemic and the measures taken by the governments of countries have affected, and could continue to affect, our business and the business of our partners, including future disruptions to our supply chain and the manufacture or shipment of drug substance and finished drug product for Captisol, delays by us or our partners in the initiation or enrollment of patients in clinical trials, discontinuations by patients enrolled in clinical trials, difficulties launching or commercializing products and other related activities, which could delay ongoing clinical trials, increase development costs, reduce royalty revenues and have a material adverse effect on our business, financial condition and results of operations. Several of our partners have reported that their operations have been impacted including delays in research and development programs and deprioritizing clinical trials in favor of treating patients who have contracted the virus or to prevent the spread of the virus. This may lead to clinical trial protocol deviations or to discontinuation of treatment for patients who are currently enrolled in the clinical trials being conducted by us or our partners. In addition, certain of our partners have reported negative impacts on product sales which will impact our royalty revenues. Some of our partners are working to develop drugs to treat COVID-19. For example, we are supplying Captisol to partners, including Gilead for Veklury ® (remdesivir), the first new treatment for COVID-19 available under an EUA and is also being evaluated in multiple ongoing clinical trials and, as a result, we have worked to increase our manufacturing of Captisol to meet this increased demand. We believe our existing production capacity, together with our planned expansion, will provide adequate supply of Captisol and do not expect any significant risk or disruption to our supply chain for the foreseeable future. In addition, certain of our OmniAb and Vernalis partners have initiated antibody discovery programs for the potential treatment of COVID-19. The full extent to which the COVID-19 pandemic will directly or indirectly impact our business, the businesses of our partners, our results of operations and our financial condition will depend on future developments that are highly uncertain and cannot be accurately predicted, including new information that may emerge concerning COVID-19, the actions taken to contain it or treat its impact, including the timing and extent of governments reopening activities, and the economic impact on local, regional, national and international markets. Accounting Standards Recently Adopted Credit Losses - In June 2016, the FASB issued ASU 2016-13, Financial Instruments - Credit Losses: Measurement of Credit Losses on Financial Instruments (Topic 326) , which amends the impairment model by requiring entities to use a forward-looking approach based on expected losses to estimate credit losses on certain types of financial instruments, including trade receivables and available for sale debt securities. This standard includes our financial instruments, such as accounts receivable, investments that are generally of high credit quality, and commercial license rights. Previously, when credit losses were measured under GAAP, an entity generally only considered past events and current conditions in measuring the incurred loss. The new guidance requires us to identify, analyze, document and support new methodologies for quantifying expected credit loss estimates for our financial instruments, using information such as historical experience and current economic conditions, plus the use of reasonable supportable forecast information. We adopted ASU 2016-13 “Short-term Investments” , “Accounts Receivable and Allowance for Credit Losses” and “Commercial License and Other Economic Rights” discussed below. Goodwill Impairment Testing - In January 2017, the FASB issued ASU 2017-04, Simplifying the Test for Goodwill Impairment, which eliminates the requirement to perform a hypothetical purchase price allocation to measure goodwill impairment. Under the new standard the goodwill impairment test is performed by comparing the fair value of a reporting unit with its carrying amount, and recognizing an impairment charge for the amount by which the carrying amount of the reporting unit exceeds its fair value, although it cannot exceed the total amount of goodwill allocated to that reporting unit. We adopted this standard on January 1, 2020, and the adoption did not have a material impact on our condensed consolidated financial statements. Fair Value Measurement - In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement: Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement (Topic 820) , which modifies the disclosure requirements on fair value measurements. We adopted this standard on January 1, 2020, and the adoption did not have a material impact on our condensed consolidated financial statements. Collaborative Arrangements - In November 2018, the FASB issued ASU 2018-18, Collaborative Arrangements: Clarifying the Interaction between Topic 808 and Topic 606 (Topic 808) . The new standard clarifies that certain transactions between participants in a collaborative arrangement should be accounted for under Topic 606, Revenue from Contracts with Customers , when the counterparty is a customer for a good or service that is a distinct unit of account. The amendments also preclude entities from presenting consideration from transactions with a collaborator that is not a customer together with revenue recognized from contracts with customers. We adopted this standard on January 1, 2020, and the adoption did not have a material impact on our condensed consolidated financial statements. Income Taxes - In December 2019, the FASB issued ASU 2019-12, Simplifying the Accounting for Income Taxes . The standard is expected to reduce cost and complexity related to accounting for income taxes. The new guidance eliminates certain exceptions and clarifies and amends existing guidance to promote consistent application among reporting entities. This standard is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2020, with early adoption permitted. Depending on the amendment, adoption may be applied on a retrospective, modified retrospective or prospective basis. We adopted this standard on a prospective basis on January 1, 2020, and the adoption did not have a material impact on our condensed consolidated financial statements. Accounting Standards Not Yet Adopted We do not believe that any other recently issued, but not yet effective accounting pronouncements, if adopted, would have a material impact on our condensed consolidated financial statements or disclosures. Revenue Our revenue is generated primarily from royalties on sales of products commercialized by our partners, Captisol material sales, service revenue, and contract revenue for license fees and development, regulatory and sales based milestone payments. Royalties, Service Revenue, and Contract Revenue We receive royalty revenue on sales by our partners of products covered by patents that we own. We do not have future performance obligations under these license arrangements. We generally satisfy our obligation to grant intellectual property rights on the effective date of the contract. However, we apply the royalty recognition constraint required under the guidance for sales-based royalties which requires a sales-based royalty to be recorded when the underlying sale occurs. Therefore, royalties on sales of products commercialized by our partners are recognized in the quarter the product is sold. Our partners generally report sales information to us on a one quarter lag. Thus, we estimate the expected royalty proceeds based on an analysis of historical experience and interim data provided by our partners including their publicly announced sales. Differences between actual and estimated royalty revenues are adjusted for in the period in which they become known, typically the following quarter. We recognize service revenue for contracted R&D services performed for our customers over time. We measure our progress using an input method based on the effort we expend or costs we incur toward the satisfaction of our performance obligation. We estimate the amount of effort we expend, including the time we estimate it will take us to complete the activities, or costs we incur in a given period, relative to the estimated total effort or costs to satisfy the performance obligation. This results in a percentage that we multiply by the transaction price to determine the amount of revenue we recognize each period. This approach requires us to make estimates and use judgement. If our estimates or judgements change over the course of the collaboration, they may affect the timing and amount of revenue that we recognize in the current and future periods. Our contract revenue includes license fees and future contingent milestone based payments. We include contingent milestone based payments in the estimated transaction price when there is a basis to reasonably estimate the amount of the payment. These estimates are based on historical experience, anticipated results and our best judgment at the time. If the contingent milestone based payment is sales-based, we apply the royalty recognition constraint and record revenue when the underlying sale has taken place. Significant judgments must be made in determining the transaction price for our sales of intellectual property. Because of the risk that products in development with our partners will not reach development based milestones or receive regulatory approval, we generally recognize any contingent payments that would be due to us upon or after the development milestone or regulatory approval. Captisol Sales We recognize revenue when control of Captisol material is transferred to our customers in an amount that reflects the consideration we expect to receive from our customers in exchange for those products. This process involves identifying the contract with a customer, determining the performance obligations in the contract, determining the contract price, allocating the contract price to the distinct performance obligations in the contract, and recognizing revenue when the performance obligations have been satisfied. A performance obligation is considered distinct from other obligations in a contract when it provides a benefit to the customer either on its own or together with other resources that are readily available to the customer and is separately identified in the contract. We consider a performance obligation satisfied once we have transferred control of the product, meaning the customer has the ability to use and obtain the benefit of the Captisol material or intellectual property license right. We recognize revenue for satisfied performance obligations only when we determine there are no uncertainties regarding payment terms or transfer of control. We have elected to recognize the cost for freight and shipping when or after control over Captisol material has transferred to the customer as an expense in cost of Captisol. Sales tax and other taxes we collect concurrent with revenue-producing activities are excluded from revenue. We expense incremental costs of obtaining a contract when incurred if the expected amortization period of the asset that we would have recognized is one year or less or the amount is immaterial. We did not incur any incremental costs of obtaining a contract during the periods reported. Deferred Revenue Depending on the terms of the arrangement, we may also defer a portion of the consideration received because we have to satisfy a future obligation. We use an observable price to determine the stand-alone selling price for separate performance obligations or a cost plus margin approach when one is not available. The timing of revenue recognition, billings and cash collections results in billed accounts receivable, unbilled receivables (contract assets), and customer advances and deposits (contract liabilities) on the condensed consolidated balance sheet. Except for royalty revenue and certain service revenue, we generally receive payment at the point we satisfy our obligation or soon after. Therefore, we do not generally carry a contract asset balance. Any fees billed in advance of being earned are recorded as deferred revenue. During the three and six months ended June 30, 2020, the amount recognized as revenue that was previously deferred was $2.0 million and $2.4 million, respectively. During the three and six months ended June 30, 2019, the amount recognized as revenue that was previously deferred was $2.7 million and $4.1 million, respectively. Disaggregation of Revenue The following table represents disaggregation of royalties, Captisol, service revenue and contract revenue (in thousands): Three months ended Six months ended June 30, June 30, 2020 2019 2020 2019 Royalties Kyprolis $ 5,481 $ 4,882 $ 9,886 $ 8,715 Evomela 1,199 1,144 2,775 2,055 Other 501 600 1,085 1,201 Promacta — — — 14,193 $ 7,181 $ 6,626 $ 13,746 $ 26,164 Captisol $ 24,468 $ 8,549 $ 45,577 $ 17,508 Service Revenue $ 4,582 $ 4,559 $ 7,939 $ 8,442 Contract Revenue License Fees $ 660 $ 1,990 $ 1,635 $ 2,840 Milestone 3,472 2,497 3,806 12,751 Other 1,057 766 1,878 766 $ 5,189 $ 5,253 $ 7,319 $ 16,357 Total $ 41,420 $ 24,987 $ 74,581 $ 68,471 Short-term Investments Our investments, excluding investment in Viking, consist of the following at June 30, 2020 and December 31, 2019 (in thousands): June 30, 2020 December 31, 2019 Amortized cost Gross unrealized gains Gross unrealized losses Estimated fair value Amortized cost Gross unrealized gains Gross unrealized losses Estimated fair value Short-term investments Bank deposits $ 269,114 $ 221 $ (56) $ 269,279 $ 411,690 $ 188 $ (3) $ 411,875 Corporate bonds 55,380 125 (94) 55,411 63,818 161 — 63,979 Commercial paper 163,590 134 — 163,724 210,525 43 (16) 210,552 Corporate equity securities 4,506 634 (2,484) 2,656 4,506 416 (1,850) 3,072 Mutual fund 151,223 — (97) 151,126 250,635 — (249) 250,386 Warrants — 177 — 177 — 125 — 125 $ 643,813 $ 1,291 $ (2,731) $ 642,373 $ 941,174 $ 933 $ (2,118) $ 939,989 In addition, as of June 30, 2020 and December 31, 2019, we recorded shares of Viking common stock we own at fair value of $43.5 million and $48.4 million, respectively, in “Short-term investments” in our consolidated balance sheets. We also own warrants to purchase up to 1.5 million shares of Viking's common stock at an exercise price of $1.50 per share. We recorded the warrants in “Short-term investments” in our consolidated balance sheet at fair value of $8.8 million and $9.9 million at June 30, 2020 and December 31, 2019, respectively. Gain (loss) from short-term investments on our condensed consolidated statements of operations includes both realized and unrealized gain (loss) from our short-term investments in public equity and warrant securities. For available-for-sale debt securities with unrealized losses, the new credit losses standard (Topic 326) now requires allowances to be recorded instead of reducing the amortized cost of the investment. This standard limits the amount of credit losses to be recognized for available-for-sale debt securities to be the amount by which carrying value exceeds fair value and requires the reversal of previously recognized credit losses if fair value increases. The provisions of the new credit losses standard did not have a material impact on our available-for-sale debt securities during the three and six months ended June 30, 2020. The following table summarizes our available-for-sale debt securities by contractual maturity (in thousands): June 30, 2020 Amortized Cost Fair Value Within one year $ 414,505 $ 414,905 After one year through five years 73,579 73,509 After five years — — Total $ 488,084 $ 488,414 The following table summarizes our available-for-sale debt securities in an unrealized loss position (in thousands): Less than 12 months 12 months or greater Total Gross Estimated Gross Estimated Gross Estimated June 30, 2020 Bank deposits $ (56) $ 30,015 $ — $ — $ (56) $ 30,015 Corporate bonds (94) 16,022 — — (94) 16,022 Total $ (150) $ 46,037 $ — $ — $ (150) $ 46,037 December 31, 2019 Bank deposits $ (3) $ 58,584 $ — $ — $ (3) $ 58,584 Commercial paper (16) 79,363 — — (16) 79,363 Total $ (19) $ 137,947 $ — $ — $ (19) $ 137,947 Our investment policy is capital preservation and we only invested in U.S.-dollar denominated investments. We held a total of 7 positions which were in an unrealized loss position as of June 30, 2020. We believe that we will collect the principal and interest due on our debt securities that have an amortized cost in excess of fair value. The unrealized losses are largely due to changes in interest rates and not to unfavorable changes in the credit quality associated with these securities that impacted our assessment on collectability of principal and interest. We do not intend to sell these securities nor do we believe that we will be required to sell these securities before the recovery of the amortized cost basis. Accordingly, no credit losses were recognized for the three and six months ended June 30, 2020. Accounts Receivable and Allowance for Credit Losses Our accounts receivable arise primarily from sales on credit to customers. We establish an allowance for credit losses to present the net amount of accounts receivable expected to be collected. The allowance is determined by using the loss-rate method, which requires an estimation of loss rates based upon historical loss experience adjusted for factors that are relevant to determining the expected collectability of accounts receivable. Some of these factors include macroeconomic conditions that correlate with historical loss experience, delinquency trends, aging behavior of receivables and credit and liquidity quality indicators for industry groups, customer classes or individual customers. During the three and six months ended June 30, 2020, we considered the current and expected future economic and market conditions including, but not limited to, the anticipated unfavorable impacts of the surrounding novel coronavirus (COVID-19) pandemic on our business and recorded an additional $0.1 million and $0.3 million, of allowance for credit losses, respectively, as of June 30, 2020. Inventory Inventory, which consists of finished goods, is stated at the lower of cost or net realizable value. We determine cost using the first-in, first-out method or the specific identification method. Goodwill and Other Identifiable Intangible Assets Goodwill and other identifiable intangible assets consist of the following (in thousands): June 30, December 31, 2020 2019 Goodwill $ 103,369 $ 95,229 Definite lived intangible assets Complete technology 244,513 242,813 Less: accumulated amortization (1) (57,053) (50,203) Trade name 2,642 2,642 Less: accumulated amortization (1,246) (1,180) Customer relationships 40,700 29,600 Less: accumulated amortization (14,261) (13,224) Total goodwill and other identifiable intangible assets, net $ 318,664 $ 305,677 (1) accumulated amortization for complete technology includes immaterial amount of foreign currency translation adjustments for the complete technology acquired from the Vernalis acquisition. Commercial License and Other Economic Rights Commercial license and other economic rights consist of the following (in thousands): June 30, 2020 December 31, 2019 Gross Adjustments (1) Net Gross Adjustments (2) Net Aziyo and CorMatrix $ 17,696 $ (9,698) $ 7,998 $ 17,696 $ (5,500) $ 12,196 Palvella 10,000 (10,000) — 10,000 (7,492) 2,508 Selexis and Dianomi 10,602 (7,994) 2,608 10,602 (5,216) 5,386 Total $ 38,298 $ (27,692) $ 10,606 $ 38,298 $ (18,208) $ 20,090 (1) Amounts represent accumulated amortization to principal or research and development expenses of $21.7 million and credit loss adjustments of $6.0 million as of June 30, 2020. (2) Amounts represent accumulated amortization to principal or research and development expenses as of December 31, 2019. Commercial license and other economics rights represent a portfolio of future milestone and royalty payment rights acquired from Selexis in April 2013 and April 2015, CorMatrix in May 2016, Palvella in December 2018 and Dianomi in January 2019. Commercial license rights acquired are accounted for as financial assets and other economic rights are accounted for as funded research and developments as further discussed below. In May 2017, we entered into a Royalty Agreement with Aziyo pursuant to which we will receive royalties from certain marketed products that Aziyo acquired from CorMatrix. We account for the Aziyo commercial license right as a financial asset, and in accordance with ASC 310, Receivables , we amortize the commercial license right using the effective interest method whereby we forecast expected cash flows over the term of the arrangement to arrive at an annualized effective interest. The annual effective interest associated with the forecasted cash flows from the Royalty Agreement with Aziyo as of June 30, 2020 is 23%. Revenue is calculated by multiplying the carrying value of the commercial license right by the effective interest. In December 2018, we entered into a development funding and royalties agreement with Palvella. Pursuant to the agreement, we may receive up to $8.0 million of milestone payments upon the achievement by Palvella of certain corporate, financing and regulatory milestones for PTX-022, a product candidate being developed to treat pachyonychia congentia. In addition to the milestone payments, Palvella will pay us tiered royalties from 5.0% to 9.8% based on any aggregate annual worldwide net sales of any PTX-022 products, subject to Palvella’s right to reduce the royalty rates by making payments in certain circumstances. We paid Palvella an upfront payment of $10.0 million, which Palvella is required to use to fund the development of PTX-022. We are not obligated to provide additional funding to Palvella for the development or commercialization of PTX-022. We determined the economic rights related to Palvella should be characterized as a funded research and development arrangement, thus we account for it in accordance with ASC 730-20, Research and Development Arrangements , and reduce our asset as the funds are expended by Palvella. As of June 30, 2020, the fund has been fully expended by Palvella and our cost basis for the asset has been reduced to zero, we will recognize milestones and royalties as revenue when earned. During the three and six months ended June 30, 2020, we recorded a $3.0 million milestone from Palvella under contract revenue in our condensed consolidated statement of operations. We recorded a $5.5 million pre-tax reserve for credit losses upon adoption of the new credit losses on January 1, 2020. We estimated the credit losses at the individual asset level by considering the performance against the programs, the company operating performance and the macroeconomic forecast. In addition, we have judgmentally applied credit loss risk factors to the future expected payments with consideration given to the timing of the payment. Given the higher inherent credit risk associated with longer term receivables, we applied a lower risk factor to the earlier years and progressively higher risk factors to the later years. During the six months ended June 30, 2020, we further considered the current and expected future economic and market conditions surrounding novel coronavirus (COVID-19) pandemic and recorded an additional $0.5 million reserve for credit losses in other expense, net, in our condensed consolidated statement of operations. See further detail described in Note 1, Basis of Presentation and Summary of Significant Accounting Policies , of Notes to Consolidated Financial Statements in our 2019 Annual Report. Accrued Liabilities Accrued liabilities consist of the following (in thousands): June 30, December 31, 2020 2019 Compensation $ 3,457 $ 1,986 Professional fees 964 1,135 Amounts owed to former licensees 413 381 Royalties owed to third parties 1,038 — Return reserve 2,899 3,027 Current operating lease liabilities 1,728 1,242 Accrued interest 471 690 Other 1,858 1,375 Total accrued liabilities $ 12,828 $ 9,836 Share-Based Compensation Share-based compensation expense for awards to employees and non-employee directors is a non-cash expense and is recognized on a straight-line basis over the vesting period until the last tranche vests. The following table summarizes share-based compensation expense recorded as components of research and development expenses and general and administrative expenses for the periods indicated (in thousands): Three months ended Six months ended June 30, June 30, 2020 2019 2020 2019 SBC - Research and development expenses $ 3,019 $ 2,528 $ 5,416 $ 4,655 SBC - General and administrative expenses 4,340 4,043 7,596 7,263 $ 7,359 $ 6,571 $ 13,012 $ 11,918 The fair-value for options that were awarded to employees and directors was estimated at the date of grant using the Black-Scholes option valuation model with the following weighted-average assumptions: Three months ended Six months ended June 30, June 30, 2020 2019 2020 2019 Risk-free interest rate 0.4% 1.9% 1.1% 2.4% Dividend yield — — — — Expected volatility 69% 40% 55% 43% Expected term 5.1 5.9 4.8 5.2 Net Income (loss) Per Share Basic net income (loss) per share is calculated by dividing net income (loss) by the weighted-average number of common shares outstanding during the period. Diluted net income per share is computed based on the sum of the weighted average number of common shares and potentially dilutive common shares outstanding during the period. For the six months ended June 30, 2020, all of the 0.6 million weighted average shares of outstanding equity awards as of June 30, 2020 were anti-dilutive due to the net loss for the period. For the three months ended June 30, 2019, all of the 0.8 million weighted average shares of outstanding equity awards as of June 30, 2019 were anti-dilutive due to the net loss for the period Potentially dilutive common shares consist of shares issuable under the 2023 Notes, stock options and restricted stock. The 2023 Notes have a dilutive impact when the average market price of our common stock exceeds the applicable conversion price of the respective notes. It is our intent and policy to settle conversions through combination settlement, which involves payment in cash equal to the principal portion and delivery of shares of common stock for the excess of the conversion value over the principal portion. Potentially dilutive common shares from stock options and restricted stock are determined using the average share price for each period under the treasury stock method. In addition, the following amounts are assumed to be used to repurchase shares: proceeds from exercise of stock options and the average amount of unrecognized compensation expense for the awards. See Note 4 - Convertible Senior Notes and Note 6 - Stockholders’ Equity . The following table presents the calculation of weighted average shares used to calculate basic and diluted earnings per share (in thousands): Three months ended Six months ended June 30, June 30, 2020 2019 2020 2019 Weighted average shares outstanding: 16,055 19,558 16,292 20,000 Dilutive potential common shares: Restricted stock 40 — — 38 Stock options 599 — — 761 Shares used to compute diluted income per share 16,694 19,558 16,292 20,799 Potentially dilutive shares excluded from calculation due to anti-dilutive effect 7,832 7,457 8,988 7,243

Fair Value Measurements

Fair Value Measurements	6 Months Ended
	Jun. 30, 2020
Fair Value Disclosures [Abstract]
Fair Value Measurements	Fair Value Measurements Assets and Liabilities Measured on a Recurring Basis The following table presents the hierarchy for our assets and liabilities measured at fair value (in thousands): June 30, 2020 December 31, 2019 Level 1 Level 2 Level 3 Total Level 1 Level 2 Level 3 Total Assets: Short-term investments, excluding Viking (1) $ 2,655 $ 639,541 $ 177 $ 642,373 $ 3,073 $ 936,791 $ 125 $ 939,989 Investment in Viking common stock 43,535 — — 43,535 48,425 — — 48,425 Investment in Viking warrants (2) 8,816 — — 8,816 9,910 — — 9,910 Total assets $ 55,006 $ 639,541 $ 177 $ 694,724 $ 61,408 $ 936,791 $ 125 $ 998,324 Liabilities: Crystal contingent liabilities (3) $ — $ — $ 859 $ 859 $ — $ — $ 2,659 $ 2,659 CyDex contingent liabilities — — 413 413 — — 348 348 Metabasis contingent liabilities (4) — 5,349 — 5,349 — 5,935 — 5,935 Icagen contingent liabilities (5) — — 4,800 4,800 — — — — Amounts owed to former licensor 107 — — 107 75 — — 75 Total liabilities $ 107 $ 5,349 $ 6,072 $ 11,528 $ 75 $ 5,935 $ 3,007 $ 9,017 1. Excluding our investment in Viking, our short-term investments in marketable debt and equity securities are classified as available-for-sale securities based on management's intentions and are at level 2 of the fair value hierarchy, as these investment securities are valued based upon quoted prices for identical or similar instruments in markets that are not active, and model-based valuation techniques for which all significant assumptions are observable in the market. Short-term investments in mutual funds are valued at their net asset value (NAV) on the last day of the period. We have classified marketable securities with original maturities of greater than one year as short-term investments based upon our ability and intent to use any and all of those marketable securities to satisfy the liquidity needs of our current operations. In addition, we have investment in warrants resulting from Seelos Therapeutics Inc. milestone payments that were settled in shares during the first quarter of 2019 and are at level 3 of the fair value hierarchy, based on black scholes value estimated by management on the last day of the period. 2. Investment in warrants, which we received as a result of Viking’s partial repayment of the Viking note receivable and our purchase of Viking common stock and warrants in April 2016, are classified as level 1 as the fair value is determined using quoted market prices in active markets for the same securities. The change of the fair value is recorded in "Gain (loss) from short-term investments" in our condensed consolidated statement of operations. 3. The fair value of Crystal contingent liabilities was determined using a probability weighted income approach. Most of the contingent payments are based on development or regulatory milestones as defined in the merger agreement with Crystal. The fair value is subjective and is affected by changes in inputs to the valuation model including management’s estimates regarding the timing and probability of achievement of certain developmental and regulatory milestones. Changes in these estimates may materially affect the fair value. During the first quarter of 2020, we paid a $1.8 million contingent liability on development milestones to former Crystal shareholders. 4. In connection with our acquisition of Metabasis in January 2010, we issued Metabasis stockholders four tradable CVRs, one CVR from each of four respective series of CVR, for each Metabasis share. The CVRs entitle Metabasis stockholders to cash payments as frequently as every six months as cash is received by us from proceeds from the sale or partnering of any of the Metabasis drug development programs, among other triggering events. The liability for the CVRs is determined using quoted prices in a market that is not active for the underlying CVR. The carrying amount of the liability may fluctuate significantly based upon quoted market prices and actual amounts paid under the agreements may be materially different than the carrying amount of the liability. Several of the Metabasis drug development programs have been outlicensed to Viking, including VK2809. VK2809 is a novel selective TR-β agonist with potential in multiple indications, including hypercholesterolemia, dyslipidemia, NASH, and X-ALD. Under the terms of the agreement with Viking, we may be entitled to up to $375 million of development, regulatory and commercial milestones and tiered royalties on potential future sales including a $10 million payment upon initiation of a Phase 3 clinical trial. 5. The fair value of Icagen contingent liabilities was determined using a probability weighted income approach. Most of the contingent payments are based on certain revenue milestones as defined in the asset purchase agreement with Icagen. The fair value is subjective and is affected by changes in inputs to the valuation model including management’s estimates regarding the timing and probability of achievement of certain developmental and regulatory milestones. Changes in these estimates may materially affect the fair value. Assets Measured on a Non-Recurring Basis We apply fair value techniques on a non-recurring basis associated with valuing potential impairment losses related to our goodwill, indefinite-lived intangible assets and long-lived assets. We evaluate goodwill and indefinite-lived intangible assets annually for impairment and whenever circumstances occur indicating that goodwill might be impaired. We determine the fair value of our reporting unit based on a combination of inputs, including the market capitalization of Ligand, as well as Level 3 inputs such as discounted cash flows, which are not observable from the market, directly or indirectly. We determine the fair value of our indefinite-lived intangible assets using the income approach based on Level 3 inputs.

Business Combination

Business Combination	6 Months Ended
	Jun. 30, 2020
Business Combinations [Abstract]
Business Combination	Business Combination As set forth below, we completed two acquisitions from January 1, 2019 through June 30, 2020, and both were accounted for as business combinations. We applied the acquisition method of accounting. Accordingly, we record the tangible and intangible assets acquired and liabilities assumed at their estimated fair values as of the applicable date of acquisition. For each acquisition, we did not incur any material acquisition related costs. Icagen Acquisition On April 1, 2020, we acquired the core assets, including its partnered programs and ion channel technology from Icagen and certain of its affiliates. The purchase price of $19.9 million included $15.1 million cash consideration paid upon acquisition, and a contingent earn-out payment of up to $25.0 million of cash payments based on certain revenue milestones with an estimated fair value of $4.8 million. The fair value of the earn-out liability was determined using a probability weighted income approach incorporating the estimated future cash flows from expected future milestones. These cash flows were then discounted to present value using a discount rate based on the market participants' cost of debt reflective of Icagen. Refer to Note 2, Fair Value Measurement , for further discussion. The liability will be periodically assessed based on events and circumstances related to the underlying milestones, and any change in fair value will be recorded in our consolidated statements of operations. The carrying amount of the liability may fluctuate significantly and actual amount paid may be materially different than the carrying amount of the liability. There was no change in the fair value of the continent liabilities during the second quarter of 2020. As the acquisition is not considered significant, pro forma information has not been provided. The results of Icagen have been included in our results of operations since the date of acquisition. The preliminary allocation of the purchase price consisted of (1) $1.8 million of fair value of tangible assets acquired, (2) $(0.8) million of liabilities assumed, (3) $12.8 million of acquired intangibles, (4) $(3.7) million of deferred revenue in connection with assumed performance obligations under a collaboration agreement, (5) $0.8 million of deferred tax asset associated with the deferred revenue, and (6) $9.0 million of goodwill, the majority of which is deductible for tax purposes. Acquired intangibles include $11.1 million of customer relationships and $1.7 million of core technology. The fair values of the customer relationships were based on a discounted cash flow analysis incorporating the estimated future cash flows from these relationships during the contractual term. These cash flows were then discounted to present value using a discount rate of 17%. The fair value of the customer relationships is being amortized on a straight-line basis over the weighted average estimated useful life of 9.6 years The fair value of the core technology was based on the discounted cash flow method that estimated the present value of the potential royalties, milestones, and collaboration revenue streams derived from the licensing of the related technologies. These projected cash flows were discounted to present value using a discount rate of 17%. The fair value of the core technology is being amortized on a straight-line basis over the estimated useful life of 10 years. The total acquired intangibles are being amortized on a straight-line basis over the estimated useful life of 9.7 years. The estimated fair values of assets acquired and liabilities assumed, including deferred tax assets and liabilities, and purchased intangibles are provisional. The accounting for these amounts falls within the measurement period and therefore we may adjust these provisional amounts to reflect new information obtained about facts and circumstances that existed as of the acquisition date. Ab Initio Acquisition On July 23, 2019, we acquired privately-held Ab Initio Biotherapeutics, Inc., an antigen-discovery company located in South San Francisco, California. The purchase price of $12.0 million included $11.84 million cash consideration paid upon acquisition, net of cash acquired, and $0.15 million cash holdback for potential indemnification claims. As the acquisition is not considered significant, pro forma information has not been provided. The results of Ab Initio have been included in our results of operations since the date of acquisition. The preliminary allocation of the purchase price consisted of (1) $0.03 million of fair value of tangible assets acquired, (2) $(0.08) million of liabilities assumed, (3) $7.4 million of acquired technologies, (4) $(1.6) million of deferred tax liability in connection with the acquired intangibles, and (5) $6.3 million of goodwill, none of which is deductible for tax purposes. The fair value of the core technology was based on the discounted cash flow method that estimated the present value of the potential royalties, milestones, and collaboration revenue streams derived from the licensing of the related technologies. These projected cash flows were discounted to present value using a discount rate of 12%. The fair value of the core technology is being amortized on a straight-line basis over the weighted average estimated useful life of the approximately 20 years. The estimated fair values of deferred tax assets and liabilities are provisional. The accounting for these amounts falls within the measurement period and therefore we may adjust these provisional amounts to reflect new information obtained about facts and circumstances that existed as of the acquisition date.

Convertible Senior Notes

Convertible Senior Notes	6 Months Ended
	Jun. 30, 2020
Debt Disclosure [Abstract]
Convertible Senior Notes	Convertible Senior Notes 0.75% Convertible Senior Notes due 2023 In May 2018, we issued $750.0 million aggregate principal amount of 0.75% convertible senior notes. The net proceeds from the offering, after deducting the initial purchasers' discount and offering expenses, were approximately $733.1 million. The 2023 Notes will be convertible into cash, shares of common stock, or a combination of cash and shares of common stock, at our election, based on an initial conversion rate, subject to adjustment, of 4.0244 shares per $1,000 principal amount of the 2023 Notes which represents an initial conversion price of approximately $248.48 per share. Holders of the 2023 Notes may convert the notes at any time prior to the close of business on the business day immediately preceding November 15, 2022, under any of the following circumstances: (1) during any fiscal quarter (and only during such fiscal quarter) commencing after September 30, 2018, if, for at least 20 trading days (whether or not consecutive) during the 30 consecutive trading day period ending on the last trading day of the immediately preceding fiscal quarter, the last reported sale price of our common stock on such trading day is greater than 130% of the conversion price on such trading day; (2) during the five business day period immediately following any 10 consecutive trading day period, in which the trading price per $1,000 principal amount of notes was less than 98% of the product of the last reported sale price of our common stock on such trading day and the conversion rate on each such trading day; or (3) upon the occurrence of certain specified corporate events as specified in the indenture governing the notes. The notes will have a dilutive effect to the extent the average market price per share of common stock for a given reporting period exceeds the conversion price of $248.48. As of June 30, 2020, the “if-converted value” did not exceed the principal amount of the 2023 Notes. In connection with the issuance of the 2023 Notes, we incurred $16.9 million of issuance costs, which primarily consisted of underwriting, legal and other professional fees. The portion of these costs allocated to the liability component totaling $13.7 million is amortized to interest expense using the effective interest method over the five year expected life of the 2023 Notes. It is our intent and policy to settle conversions through combination settlement, which essentially involves payment in cash equal to the principal portion and delivery of shares of common stock for the excess of the conversion value over the principal portion. In March 2020, we repurchased $234.4 million in principal of the 2023 Notes for $203.8 million in cash, including accrued interest of $0.6 million. We accounted for the repurchase as a debt extinguishment, which resulted (1) a gain of $0.7 million reflected in other income (expense), net, in our condensed consolidated statement of operations for the six months ended June 30, 2020; (2) a $32.7 million reduction in debt discount, and (3) a $2.7 million reduction to additional paid in capital, net of tax, related to the reacquisition of the equity component in our condensed consolidated balance sheet as of June 30, 2020. After the repurchases, approximately $515.6 million in principal amount of the 2023 Notes remain outstanding. Convertible Bond Hedge and Warrant Transactions In conjunction with the 2023 Notes, in May 2018, we entered into convertible bond hedges and sold warrants covering 3,018,327 shares of our common stock to minimize the impact of potential dilution to our common stock and/or offset the cash payments we are required to make in excess of the principal amount upon conversion of the 2023 Notes. The convertible bond hedges have an exercise price of $248.48 per share and are exercisable when and if the 2023 Notes are converted. We paid $140.3 million for these convertible bond hedges. If upon conversion of the 2023 Notes, the price of our common stock is above the exercise price of the convertible bond hedges, the counterparties will deliver shares of common stock and/or cash with an aggregate value approximately equal to the difference between the price of common stock at the conversion date and the exercise price, multiplied by the number of shares of common stock related to the convertible bond hedge transaction being exercised. The convertible bond hedges and warrants described below are separate transactions entered into by us and are not part of the terms of the 2023 Notes. Holders of the 2023 Notes and warrants will not have any rights with respect to the convertible bond hedges. Concurrently with the convertible bond hedge transactions, we entered into warrant transactions whereby we sold warrants covering approximately 3,018,327 shares of common stock with an exercise price of approximately $315.38 per share, subject to certain adjustments. We received $90.0 million for these warrants. The warrants have various expiration dates ranging from August 15, 2023 to February 6, 2024. The warrants will have a dilutive effect to the extent the market price per share of common stock exceeds the applicable exercise price of the warrants, as measured under the terms of the warrant transactions. The common stock issuable upon exercise of the warrants will be in unregistered shares, and we do not have the obligation and do not intend to file any registration statement with the SEC registering the issuance of the shares under the warrants. In April 2020, in connection with the repurchases of $234.4 million in principal of the 2023 Notes for $203.8 million in cash, including accrued interest of $0.6 million, during the quarter ended March 31, 2020, we entered into amendments with Barclays Bank PLC, Deutsche Bank AG, London Branch, and Goldman Sachs & Co. LLC to the convertible note hedges transactions we initially entered into in connection with the issuance of the 2023 Notes. The amendments provide that the options under the convertible note hedges corresponding to such repurchased 2023 Notes will remain outstanding notwithstanding such repurchase. The following table summarizes information about the 2023 Notes (in thousands): June 30, 2020 December 31, 2019 Principal amount of the 2023 Notes outstanding $ 515,560 $ 750,000 Unamortized discount (including unamortized debt issuance cost) (65,888) (111,041) Total long-term portion of notes payable $ 449,672 $ 638,959 Carrying value of equity component of the 2023 Notes $ 60,181 $ 101,422 Fair value of the 2023 Notes outstanding (Level 2) $ 452,167 $ 647,280

Income Tax

Income Tax	6 Months Ended
	Jun. 30, 2020
Income Tax Disclosure [Abstract]
Income Tax	Income TaxOur effective tax rate may vary from the U.S. federal statutory tax rate due to the change in the mix of earnings in various state jurisdictions with different statutory rates, benefits related to tax credits, and the tax impact of non-deductible expenses, stock award activities and other permanent differences between income before income taxes and taxable income. The effective tax rate for the three and six months ended June 30, 2020 was 21.5% and 10.9%, respectively. The variances from the U.S. federal statutory tax rate of 21% for the three and six months ended June 30, 2020 were primarily attributable to the mix of earnings in the jurisdictions with lower statutory rates than the U.S. offset by tax deductions related to stock award activities and tax deductions related to foreign derived intangible income tax credits. The effective tax rate for the three and six months ended June 30, 2019 was 20.0% and 20.9%, respectively. The variances from the U.S. federal statutory tax rate of 21% for the three months ended June 30, 2019 were primarily attributable to the mix of earnings in the jurisdictions with lower statutory tax rates than the U.S..

Stockholders' Equity

Stockholders' Equity	6 Months Ended
	Jun. 30, 2020
Equity [Abstract]
Stockholders' Equity	Stockholders’ Equity We grant options and awards to employees and non-employee directors pursuant to a stockholder approved stock incentive plan, which is described in further detail in Note 9, Stockholders’ Equity , of Notes to Consolidated Financial Statements in our 2019 Annual Report. The following is a summary of our stock option and restricted stock activity and related information: Stock Options Restricted Stock Awards Shares Weighted-Average Exercise Price Shares Weighted-Average Grant Date Fair Value Balance as of December 31, 2019 1,956,379 $ 77.54 147,259 $ 125.11 Granted 458,750 $ 89.43 101,156 $ 89.25 Options exercised/RSUs vested (93,570) $ 19.19 (49,749) $ 122.14 Forfeited (3,500) $ 68.28 — $ — Balance as of June 30, 2020 2,318,059 $ 82.26 198,666 $ 107.59 As of June 30, 2020, outstanding options to purchase 1.5 million shares were exercisable with a weighted average exercise price per share of $69.79. Employee Stock Purchase Plan The price at which common stock is purchased under the Amended Employee Stock Purchase Plan, or ESPP, is equal to 85% of the fair market value of the common stock on the first or last day of the offering period, whichever is lower. As of June 30, 2020, 56,079 shares were available for future purchases under the ESPP. Share Repurchases During the first quarter of 2020, we repurchased $73.3 million of our common stock under our stock repurchase programs as discussed below. We did not have any share repurchases during the second quarter of 2020. On September 11, 2019, our Board of Directors approved a stock repurchase program authorizing, but not obligating, the repurchase of up to $500.0 million of our common stock from time to time over the next three years. We expect to acquire shares primarily through open-market transactions and may enter into Rule 10b5-1 trading plans, to facilitate open-market repurchases. The timing and amount of repurchase transactions will be determined by management based on our evaluation of

Commitment and Contingencies_ L

Commitment and Contingencies: Legal Proceedings	6 Months Ended
	Jun. 30, 2020
Commitments and Contingencies Disclosure [Abstract]
Commitment and Contingencies: Legal Proceedings	Commitment and Contingencies: Legal Proceedings We record an estimate of a loss when the loss is considered probable and estimable. Where a liability is probable and there is a range of estimated loss and no amount in the range is more likely than any other number in the range, we record the minimum estimated liability related to the claim in accordance with ASC 450, Contingencies. As additional information becomes available, we assess the potential liability related to our pending litigation and revises our estimates. Revisions in our estimates of potential liability could materially impact our results of operations. In November 2017, CyDex, our wholly-owned subsidiary, received a Paragraph IV certification Notice Letter from Teva stating that Teva had submitted an ANDA to the FDA, seeking approval to manufacture, offer to sell, and sell a generic version of EVOMELA® prior to the expiration of any of U.S. Patent Nos. 8,410,077 (“the ’077 patent”); 9,200,088 (“the ’088 patent”), or 9,493,582 (“the ’582 patent”), and alleging that these patents, each of which relates to Captisol®, are invalid, unenforceable, and/or will not be infringed by Teva’s ANDA product. On December 20, 2017, CyDex filed a complaint against Teva in the U.S. District Court for the District of Delaware, asserting that the filing of Teva’s ANDA constitutes infringement of each of the ’077 patent, the ’088 patent, and the ’582 patent. On March 22, 2018, Teva filed an answer and counterclaims seeking declarations of non-infringement and invalidity as to each of the asserted patents and, on April 12, 2018, CyDex filed an answer to Teva’s counterclaims. On October 31, 2019, CyDex, Teva, and Acrotech Biopharma L.L.C. (the holder of the NDA for EVOMELA®) entered into a Confidential Settlement Agreement, settling this patent litigation. As a result of the settlement, Teva will be permitted to market a generic version of EVOMELA® in the United States on June 1, 2026 or earlier under certain circumstances. The terms of the settlement agreement are otherwise confidential. On April 9, 2019, CyDex received a Paragraph IV certification Notice Letter from Alembic Global Holdings SA (“Alembic”) stating that Alembic had submitted an ANDA to the FDA, seeking approval to manufacture, offer to sell, and sell a generic version of EVOMELA® prior to the expiration of any of the ’077 patent; the ’088 patent, the ’582 patent, or U.S. Patent No. 10,040,872 (“the ’872 patent”), and alleging that these patents, each of which relates to Captisol®, are invalid, unenforceable, and/or would not be infringed by Alembic’s ANDA product. On May 23, 2019, CyDex filed a complaint against Alembic, Alembic Pharmaceuticals, Ltd., and Alembic Pharmaceuticals, Inc. in the U.S. District Court for the District of Delaware, asserting that the filing of Alembic’s ANDA constitutes infringement of each of the ’088 patent and the ’582 patent. On July 29, 2019, Alembic filed an answer and counterclaims seeking declarations of non-infringement and invalidity as to each of the asserted patents and, on August 19, 2019, CyDex filed an answer to Alembic’s counterclaims. On April 7, 2020, the Court ordered that the Scheduling Order be amended such that, inter alia , the fact discovery cut off was set for November 2, 2020, the close of expect discovery was set for March 22, 2021, and that May 17, 2021 would remain the first day of a five-to-six-day bench trial. On September 16, 2019, CyDex received a Paragraph IV certification Notice Letter from Lupin Ltd. (“Lupin”) stating that Lupin had submitted an ANDA to the FDA, seeking approval to manufacture, offer to sell, and sell a generic version of EVOMELA® prior to the expiration of any of the ’077 patent; the ’088 patent, the ’582 patent, or the ’872 patent, and alleging that these patents, each of which relates to Captisol®, are invalid, unenforceable, and/or would not be infringed by Lupin’s ANDA product. CyDex filed a complaint on October 29, 2019, alleging patent infringement against Lupin. Lupin filed an answer on December 11, 2019 and counterclaimed for declaratory judgments of invalidity and non-infringement as to all four patents and CyDex filed its answer to Lupin’s counterclaims on January 2, 2020. The Court’s scheduling order sets close of discovery on May 7, 2021 and a five day bench trial starting on December 13, 2021. On October 31, 2019, we received three civil complaints filed in the US District Court for the Northern District of Ohio on behalf of several Indian tribes. The Northern District of Ohio is the Court that the Judicial Panel on Multi-District Litigation (“JPML”) has assigned more than one thousand civil cases which have been designated as a Multi-District Litigation (“MDL”) and captioned In Re: National Prescription Opiate Litigation. The allegations in these complaints focus on the activities of defendants other than the company and no individualized factual allegations have been advanced against us in any of the three complaints. We reject all claims raised in the complaints and intend to vigorously defend these matters.

Leases

Leases	6 Months Ended
	Jun. 30, 2020
Leases [Abstract]
Leases	LeasesWe lease certain office facilities and equipment primarily under various operating leases. Our leases have remaining contractual terms up to seven seven contain any material residual value guarantees, material restrictive covenants, or material termination options. Our operating lease costs are primarily related to facility leases for administration offices and research and development facilities, and our finance leases are immaterial. Lease assets and lease liabilities are recognized at the commencement of an arrangement where it is determined at inception that a lease exists. Lease assets represent the right to use an underlying asset for the lease term, and lease liabilities represent the obligation to make lease payments arising from the lease. These assets and liabilities are initially recognized based on the present value of lease payments over the lease term calculated using our incremental borrowing rate generally applicable to the location of the lease asset, unless the implicit rate is readily determinable. Lease assets also include any upfront lease payments made and lease incentives. Lease terms include options to extend or terminate the lease when it is reasonably certain that those options will be exercised. For leases with a term of 12 months or less, we elected to not recognize lease assets and lease liabilities and expense the leases over a straight-line basis for the term of those leases. In addition to base rent, certain of our operating leases require variable payments, such as insurance and common area maintenance. These variable lease costs, other than those dependent upon an index or rate, are expensed when the obligation for those payments is incurred. Leases with an initial term of 12 months or less are not recorded on the balance sheet, and the expense for these short-term leases and for operating leases is recognized on a straight-line basis over the lease term. The depreciable life of lease assets and leasehold improvements is limited by the expected lease term, unless there is a transfer of title or purchase option reasonably certain of exercise.

Basis of Presentation and Sum_2

Basis of Presentation and Summary of Significant Accounting Policies (Policies)	6 Months Ended
	Jun. 30, 2020
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Basis of Presentation	Basis of PresentationOur condensed consolidated financial statements include the financial statements of Ligand and its wholly-owned subsidiaries. All significant intercompany accounts and transactions have been eliminated in consolidation. We have included all adjustments, consisting only of normal recurring adjustments, which we considered necessary for a fair presentation of our financial results. These unaudited condensed consolidated financial statements and accompanying notes should be read together with the audited consolidated financial statements included in our 2019 Annual Report. Interim financial results are not necessarily indicative of the results that may be expected for the full year.
Reclassifications and Prior Period Immaterial Error	Reclassifications Certain amounts in the prior period condensed consolidated financial statements have been reclassified to conform with the current period presentation. Specifically, effective the first quarter of 2020, we began to present service revenue and contract revenue separately, which were combined in license fees, milestones and other revenues in prior years. As a result, service revenue and contract revenue in the condensed consolidated statements of operations for the three and six months ended June 30, 2019 have been reclassified to conform to the current period presentation. In addition, effective the second quarter of 2020, we began to include our investment in Viking in “short-term investments” in the condensed consolidated balance sheet as of June 30, 2020, and present “gain (loss) from short-term investments” in the condensed consolidated statements of operations for the three and six months ended June 30, 2020 to include both the gain (loss) from investment in Viking and other short-term investments, which was previously included in “other income, net”. As a result, the audited consolidated balance sheet as of December 31, 2019 and the condensed consolidated statements of operations for the three and six months ended June 30, 2019 have been reclassified to conform to the current period presentation.
Use of Estimates	Use of Estimates The preparation of condensed consolidated financial statements in conformity with GAAP requires the use of estimates and assumptions that affect the amounts reported in the condensed consolidated financial statements and the accompanying notes. Actual results may differ from those estimates.
Accounting Standards Recently Adopted and Accounting Standards Not Yet Adopted	Accounting Standards Recently Adopted Credit Losses - In June 2016, the FASB issued ASU 2016-13, Financial Instruments - Credit Losses: Measurement of Credit Losses on Financial Instruments (Topic 326) , which amends the impairment model by requiring entities to use a forward-looking approach based on expected losses to estimate credit losses on certain types of financial instruments, including trade receivables and available for sale debt securities. This standard includes our financial instruments, such as accounts receivable, investments that are generally of high credit quality, and commercial license rights. Previously, when credit losses were measured under GAAP, an entity generally only considered past events and current conditions in measuring the incurred loss. The new guidance requires us to identify, analyze, document and support new methodologies for quantifying expected credit loss estimates for our financial instruments, using information such as historical experience and current economic conditions, plus the use of reasonable supportable forecast information. We adopted ASU 2016-13 “Short-term Investments” , “Accounts Receivable and Allowance for Credit Losses” and “Commercial License and Other Economic Rights” discussed below. Goodwill Impairment Testing - In January 2017, the FASB issued ASU 2017-04, Simplifying the Test for Goodwill Impairment, which eliminates the requirement to perform a hypothetical purchase price allocation to measure goodwill impairment. Under the new standard the goodwill impairment test is performed by comparing the fair value of a reporting unit with its carrying amount, and recognizing an impairment charge for the amount by which the carrying amount of the reporting unit exceeds its fair value, although it cannot exceed the total amount of goodwill allocated to that reporting unit. We adopted this standard on January 1, 2020, and the adoption did not have a material impact on our condensed consolidated financial statements. Fair Value Measurement - In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement: Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement (Topic 820) , which modifies the disclosure requirements on fair value measurements. We adopted this standard on January 1, 2020, and the adoption did not have a material impact on our condensed consolidated financial statements. Collaborative Arrangements - In November 2018, the FASB issued ASU 2018-18, Collaborative Arrangements: Clarifying the Interaction between Topic 808 and Topic 606 (Topic 808) . The new standard clarifies that certain transactions between participants in a collaborative arrangement should be accounted for under Topic 606, Revenue from Contracts with Customers , when the counterparty is a customer for a good or service that is a distinct unit of account. The amendments also preclude entities from presenting consideration from transactions with a collaborator that is not a customer together with revenue recognized from contracts with customers. We adopted this standard on January 1, 2020, and the adoption did not have a material impact on our condensed consolidated financial statements. Income Taxes - In December 2019, the FASB issued ASU 2019-12, Simplifying the Accounting for Income Taxes . The standard is expected to reduce cost and complexity related to accounting for income taxes. The new guidance eliminates certain exceptions and clarifies and amends existing guidance to promote consistent application among reporting entities. This standard is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2020, with early adoption permitted. Depending on the amendment, adoption may be applied on a retrospective, modified retrospective or prospective basis. We adopted this standard on a prospective basis on January 1, 2020, and the adoption did not have a material impact on our condensed consolidated financial statements. Accounting Standards Not Yet Adopted We do not believe that any other recently issued, but not yet effective accounting pronouncements, if adopted, would have a material impact on our condensed consolidated financial statements or disclosures.
Revenue	Revenue Our revenue is generated primarily from royalties on sales of products commercialized by our partners, Captisol material sales, service revenue, and contract revenue for license fees and development, regulatory and sales based milestone payments. Royalties, Service Revenue, and Contract Revenue We receive royalty revenue on sales by our partners of products covered by patents that we own. We do not have future performance obligations under these license arrangements. We generally satisfy our obligation to grant intellectual property rights on the effective date of the contract. However, we apply the royalty recognition constraint required under the guidance for sales-based royalties which requires a sales-based royalty to be recorded when the underlying sale occurs. Therefore, royalties on sales of products commercialized by our partners are recognized in the quarter the product is sold. Our partners generally report sales information to us on a one quarter lag. Thus, we estimate the expected royalty proceeds based on an analysis of historical experience and interim data provided by our partners including their publicly announced sales. Differences between actual and estimated royalty revenues are adjusted for in the period in which they become known, typically the following quarter. We recognize service revenue for contracted R&D services performed for our customers over time. We measure our progress using an input method based on the effort we expend or costs we incur toward the satisfaction of our performance obligation. We estimate the amount of effort we expend, including the time we estimate it will take us to complete the activities, or costs we incur in a given period, relative to the estimated total effort or costs to satisfy the performance obligation. This results in a percentage that we multiply by the transaction price to determine the amount of revenue we recognize each period. This approach requires us to make estimates and use judgement. If our estimates or judgements change over the course of the collaboration, they may affect the timing and amount of revenue that we recognize in the current and future periods. Our contract revenue includes license fees and future contingent milestone based payments. We include contingent milestone based payments in the estimated transaction price when there is a basis to reasonably estimate the amount of the payment. These estimates are based on historical experience, anticipated results and our best judgment at the time. If the contingent milestone based payment is sales-based, we apply the royalty recognition constraint and record revenue when the underlying sale has taken place. Significant judgments must be made in determining the transaction price for our sales of intellectual property. Because of the risk that products in development with our partners will not reach development based milestones or receive regulatory approval, we generally recognize any contingent payments that would be due to us upon or after the development milestone or regulatory approval. Captisol Sales We recognize revenue when control of Captisol material is transferred to our customers in an amount that reflects the consideration we expect to receive from our customers in exchange for those products. This process involves identifying the contract with a customer, determining the performance obligations in the contract, determining the contract price, allocating the contract price to the distinct performance obligations in the contract, and recognizing revenue when the performance obligations have been satisfied. A performance obligation is considered distinct from other obligations in a contract when it provides a benefit to the customer either on its own or together with other resources that are readily available to the customer and is separately identified in the contract. We consider a performance obligation satisfied once we have transferred control of the product, meaning the customer has the ability to use and obtain the benefit of the Captisol material or intellectual property license right. We recognize revenue for satisfied performance obligations only when we determine there are no uncertainties regarding payment terms or transfer of control. We have elected to recognize the cost for freight and shipping when or after control over Captisol material has transferred to the customer as an expense in cost of Captisol. Sales tax and other taxes we collect concurrent with revenue-producing activities are excluded from revenue. We expense incremental costs of obtaining a contract when incurred if the expected amortization period of the asset that we would have recognized is one year or less or the amount is immaterial. We did not incur any incremental costs of obtaining a contract during the periods reported. Deferred Revenue Depending on the terms of the arrangement, we may also defer a portion of the consideration received because we have to satisfy a future obligation. We use an observable price to determine the stand-alone selling price for separate performance obligations or a cost plus margin approach when one is not available. The timing of revenue recognition, billings and cash collections results in billed accounts receivable, unbilled receivables (contract assets), and customer advances and deposits (contract liabilities) on the condensed consolidated balance sheet. Except for royalty revenue and certain service revenue, we generally receive payment at the point we satisfy our obligation or soon after. Therefore, we do not generally carry a contract asset balance. Any fees billed in advance of being earned are recorded as deferred revenue. During the three and six months ended June 30, 2020, the amount recognized as revenue that was previously deferred was $2.0 million and $2.4 million, respectively. During the three and six months ended June 30, 2019, the amount recognized as revenue that was previously deferred was $2.7 million and $4.1 million, respectively.
Share-Based Compensation	Share-Based Compensation Share-based compensation expense for awards to employees and non-employee directors is a non-cash expense and is recognized on a straight-line basis over the vesting period until the last tranche vests. The following table summarizes share-based compensation expense recorded as components of research and development expenses and general and administrative expenses for the periods indicated (in thousands): Three months ended Six months ended June 30, June 30, 2020 2019 2020 2019 SBC - Research and development expenses $ 3,019 $ 2,528 $ 5,416 $ 4,655 SBC - General and administrative expenses 4,340 4,043 7,596 7,263 $ 7,359 $ 6,571 $ 13,012 $ 11,918 The fair-value for options that were awarded to employees and directors was estimated at the date of grant using the Black-Scholes option valuation model with the following weighted-average assumptions: Three months ended Six months ended June 30, June 30, 2020 2019 2020 2019 Risk-free interest rate 0.4% 1.9% 1.1% 2.4% Dividend yield — — — — Expected volatility 69% 40% 55% 43% Expected term 5.1 5.9 4.8 5.2
Net Income (loss) Per Share	Net Income (loss) Per Share Basic net income (loss) per share is calculated by dividing net income (loss) by the weighted-average number of common shares outstanding during the period. Diluted net income per share is computed based on the sum of the weighted average number of common shares and potentially dilutive common shares outstanding during the period. For the six months ended June 30, 2020, all of the 0.6 million weighted average shares of outstanding equity awards as of June 30, 2020 were anti-dilutive due to the net loss for the period. For the three months ended June 30, 2019, all of the 0.8 million weighted average shares of outstanding equity awards as of June 30, 2019 were anti-dilutive due to the net loss for the period Potentially dilutive common shares consist of shares issuable under the 2023 Notes, stock options and restricted stock. The 2023 Notes have a dilutive impact when the average market price of our common stock exceeds the applicable conversion price of the respective notes. It is our intent and policy to settle conversions through combination settlement, which involves payment in cash equal to the principal portion and delivery of shares of common stock for the excess of the conversion value over the principal portion. Potentially dilutive common shares from stock options and restricted stock are determined using the average share price for each period under the treasury stock method. In addition, the following amounts are assumed to be used to repurchase shares: proceeds from exercise of stock options and the average amount of unrecognized compensation expense for the awards. See Note 4 - Convertible Senior Notes and Note 6 - Stockholders’ Equity .

Basis of Presentation and Sum_3

Basis of Presentation and Summary of Significant Accounting Policies (Tables)	6 Months Ended
	Jun. 30, 2020
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Schedule of Revenue by Source	The following table represents disaggregation of royalties, Captisol, service revenue and contract revenue (in thousands): Three months ended Six months ended June 30, June 30, 2020 2019 2020 2019 Royalties Kyprolis $ 5,481 $ 4,882 $ 9,886 $ 8,715 Evomela 1,199 1,144 2,775 2,055 Other 501 600 1,085 1,201 Promacta — — — 14,193 $ 7,181 $ 6,626 $ 13,746 $ 26,164 Captisol $ 24,468 $ 8,549 $ 45,577 $ 17,508 Service Revenue $ 4,582 $ 4,559 $ 7,939 $ 8,442 Contract Revenue License Fees $ 660 $ 1,990 $ 1,635 $ 2,840 Milestone 3,472 2,497 3,806 12,751 Other 1,057 766 1,878 766 $ 5,189 $ 5,253 $ 7,319 $ 16,357 Total $ 41,420 $ 24,987 $ 74,581 $ 68,471
Schedule of Short-Term Investments	Our investments, excluding investment in Viking, consist of the following at June 30, 2020 and December 31, 2019 (in thousands): June 30, 2020 December 31, 2019 Amortized cost Gross unrealized gains Gross unrealized losses Estimated fair value Amortized cost Gross unrealized gains Gross unrealized losses Estimated fair value Short-term investments Bank deposits $ 269,114 $ 221 $ (56) $ 269,279 $ 411,690 $ 188 $ (3) $ 411,875 Corporate bonds 55,380 125 (94) 55,411 63,818 161 — 63,979 Commercial paper 163,590 134 — 163,724 210,525 43 (16) 210,552 Corporate equity securities 4,506 634 (2,484) 2,656 4,506 416 (1,850) 3,072 Mutual fund 151,223 — (97) 151,126 250,635 — (249) 250,386 Warrants — 177 — 177 — 125 — 125 $ 643,813 $ 1,291 $ (2,731) $ 642,373 $ 941,174 $ 933 $ (2,118) $ 939,989
Schedule of Available-for-Sale Debt Securities	The following table summarizes our available-for-sale debt securities by contractual maturity (in thousands): June 30, 2020 Amortized Cost Fair Value Within one year $ 414,505 $ 414,905 After one year through five years 73,579 73,509 After five years — — Total $ 488,084 $ 488,414 The following table summarizes our available-for-sale debt securities in an unrealized loss position (in thousands): Less than 12 months 12 months or greater Total Gross Estimated Gross Estimated Gross Estimated June 30, 2020 Bank deposits $ (56) $ 30,015 $ — $ — $ (56) $ 30,015 Corporate bonds (94) 16,022 — — (94) 16,022 Total $ (150) $ 46,037 $ — $ — $ (150) $ 46,037 December 31, 2019 Bank deposits $ (3) $ 58,584 $ — $ — $ (3) $ 58,584 Commercial paper (16) 79,363 — — (16) 79,363 Total $ (19) $ 137,947 $ — $ — $ (19) $ 137,947
Schedule of Goodwill and Other Identifiable Intangible Assets	Goodwill and other identifiable intangible assets consist of the following (in thousands): June 30, December 31, 2020 2019 Goodwill $ 103,369 $ 95,229 Definite lived intangible assets Complete technology 244,513 242,813 Less: accumulated amortization (1) (57,053) (50,203) Trade name 2,642 2,642 Less: accumulated amortization (1,246) (1,180) Customer relationships 40,700 29,600 Less: accumulated amortization (14,261) (13,224) Total goodwill and other identifiable intangible assets, net $ 318,664 $ 305,677 (1) accumulated amortization for complete technology includes immaterial amount of foreign currency translation adjustments for the complete technology acquired from the Vernalis acquisition.
Schedule of Commercial License Rights	Commercial license and other economic rights consist of the following (in thousands): June 30, 2020 December 31, 2019 Gross Adjustments (1) Net Gross Adjustments (2) Net Aziyo and CorMatrix $ 17,696 $ (9,698) $ 7,998 $ 17,696 $ (5,500) $ 12,196 Palvella 10,000 (10,000) — 10,000 (7,492) 2,508 Selexis and Dianomi 10,602 (7,994) 2,608 10,602 (5,216) 5,386 Total $ 38,298 $ (27,692) $ 10,606 $ 38,298 $ (18,208) $ 20,090 (1) Amounts represent accumulated amortization to principal or research and development expenses of $21.7 million and credit loss adjustments of $6.0 million as of June 30, 2020. (2) Amounts represent accumulated amortization to principal or research and development expenses as of December 31, 2019.
Schedule of Accrued Liabilities	Accrued liabilities consist of the following (in thousands): June 30, December 31, 2020 2019 Compensation $ 3,457 $ 1,986 Professional fees 964 1,135 Amounts owed to former licensees 413 381 Royalties owed to third parties 1,038 — Return reserve 2,899 3,027 Current operating lease liabilities 1,728 1,242 Accrued interest 471 690 Other 1,858 1,375 Total accrued liabilities $ 12,828 $ 9,836
Schedule of Accounting for Share-Based Compensation	The following table summarizes share-based compensation expense recorded as components of research and development expenses and general and administrative expenses for the periods indicated (in thousands): Three months ended Six months ended June 30, June 30, 2020 2019 2020 2019 SBC - Research and development expenses $ 3,019 $ 2,528 $ 5,416 $ 4,655 SBC - General and administrative expenses 4,340 4,043 7,596 7,263 $ 7,359 $ 6,571 $ 13,012 $ 11,918
Schedule of Fair-Value Options Awarded to Employees and Directors	The fair-value for options that were awarded to employees and directors was estimated at the date of grant using the Black-Scholes option valuation model with the following weighted-average assumptions: Three months ended Six months ended June 30, June 30, 2020 2019 2020 2019 Risk-free interest rate 0.4% 1.9% 1.1% 2.4% Dividend yield — — — — Expected volatility 69% 40% 55% 43% Expected term 5.1 5.9 4.8 5.2
Schedule of Computation of Basic and Diluted Earnings per Share	The following table presents the calculation of weighted average shares used to calculate basic and diluted earnings per share (in thousands): Three months ended Six months ended June 30, June 30, 2020 2019 2020 2019 Weighted average shares outstanding: 16,055 19,558 16,292 20,000 Dilutive potential common shares: Restricted stock 40 — — 38 Stock options 599 — — 761 Shares used to compute diluted income per share 16,694 19,558 16,292 20,799 Potentially dilutive shares excluded from calculation due to anti-dilutive effect 7,832 7,457 8,988 7,243

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	6 Months Ended
	Jun. 30, 2020
Fair Value Disclosures [Abstract]
Schedule of Assets and Liabilities Measured at Fair Value	The following table presents the hierarchy for our assets and liabilities measured at fair value (in thousands): June 30, 2020 December 31, 2019 Level 1 Level 2 Level 3 Total Level 1 Level 2 Level 3 Total Assets: Short-term investments, excluding Viking (1) $ 2,655 $ 639,541 $ 177 $ 642,373 $ 3,073 $ 936,791 $ 125 $ 939,989 Investment in Viking common stock 43,535 — — 43,535 48,425 — — 48,425 Investment in Viking warrants (2) 8,816 — — 8,816 9,910 — — 9,910 Total assets $ 55,006 $ 639,541 $ 177 $ 694,724 $ 61,408 $ 936,791 $ 125 $ 998,324 Liabilities: Crystal contingent liabilities (3) $ — $ — $ 859 $ 859 $ — $ — $ 2,659 $ 2,659 CyDex contingent liabilities — — 413 413 — — 348 348 Metabasis contingent liabilities (4) — 5,349 — 5,349 — 5,935 — 5,935 Icagen contingent liabilities (5) — — 4,800 4,800 — — — — Amounts owed to former licensor 107 — — 107 75 — — 75 Total liabilities $ 107 $ 5,349 $ 6,072 $ 11,528 $ 75 $ 5,935 $ 3,007 $ 9,017 1. Excluding our investment in Viking, our short-term investments in marketable debt and equity securities are classified as available-for-sale securities based on management's intentions and are at level 2 of the fair value hierarchy, as these investment securities are valued based upon quoted prices for identical or similar instruments in markets that are not active, and model-based valuation techniques for which all significant assumptions are observable in the market. Short-term investments in mutual funds are valued at their net asset value (NAV) on the last day of the period. We have classified marketable securities with original maturities of greater than one year as short-term investments based upon our ability and intent to use any and all of those marketable securities to satisfy the liquidity needs of our current operations. In addition, we have investment in warrants resulting from Seelos Therapeutics Inc. milestone payments that were settled in shares during the first quarter of 2019 and are at level 3 of the fair value hierarchy, based on black scholes value estimated by management on the last day of the period. 2. Investment in warrants, which we received as a result of Viking’s partial repayment of the Viking note receivable and our purchase of Viking common stock and warrants in April 2016, are classified as level 1 as the fair value is determined using quoted market prices in active markets for the same securities. The change of the fair value is recorded in "Gain (loss) from short-term investments" in our condensed consolidated statement of operations. 3. The fair value of Crystal contingent liabilities was determined using a probability weighted income approach. Most of the contingent payments are based on development or regulatory milestones as defined in the merger agreement with Crystal. The fair value is subjective and is affected by changes in inputs to the valuation model including management’s estimates regarding the timing and probability of achievement of certain developmental and regulatory milestones. Changes in these estimates may materially affect the fair value. During the first quarter of 2020, we paid a $1.8 million contingent liability on development milestones to former Crystal shareholders. 4. In connection with our acquisition of Metabasis in January 2010, we issued Metabasis stockholders four tradable CVRs, one CVR from each of four respective series of CVR, for each Metabasis share. The CVRs entitle Metabasis stockholders to cash payments as frequently as every six months as cash is received by us from proceeds from the sale or partnering of any of the Metabasis drug development programs, among other triggering events. The liability for the CVRs is determined using quoted prices in a market that is not active for the underlying CVR. The carrying amount of the liability may fluctuate significantly based upon quoted market prices and actual amounts paid under the agreements may be materially different than the carrying amount of the liability. Several of the Metabasis drug development programs have been outlicensed to Viking, including VK2809. VK2809 is a novel selective TR-β agonist with potential in multiple indications, including hypercholesterolemia, dyslipidemia, NASH, and X-ALD. Under the terms of the agreement with Viking, we may be entitled to up to $375 million of development, regulatory and commercial milestones and tiered royalties on potential future sales including a $10 million payment upon initiation of a Phase 3 clinical trial. 5. The fair value of Icagen contingent liabilities was determined using a probability weighted income approach. Most of the contingent payments are based on certain revenue milestones as defined in the asset purchase agreement with Icagen. The fair value is subjective and is affected by changes in inputs to the valuation model including management’s estimates regarding the timing and probability of achievement of certain developmental and regulatory milestones. Changes in these estimates may materially affect the fair value.

Convertible Senior Notes (Table

Convertible Senior Notes (Tables)	6 Months Ended
	Jun. 30, 2020
Debt Disclosure [Abstract]
Schedule of Carrying Values and Coupon Rates on Financing Arrangements	The following table summarizes information about the 2023 Notes (in thousands): June 30, 2020 December 31, 2019 Principal amount of the 2023 Notes outstanding $ 515,560 $ 750,000 Unamortized discount (including unamortized debt issuance cost) (65,888) (111,041) Total long-term portion of notes payable $ 449,672 $ 638,959 Carrying value of equity component of the 2023 Notes $ 60,181 $ 101,422 Fair value of the 2023 Notes outstanding (Level 2) $ 452,167 $ 647,280

Stockholders' Equity (Tables)

Stockholders' Equity (Tables)	6 Months Ended
	Jun. 30, 2020
Equity [Abstract]
Schedule of Stock Option Plan Activity	The following is a summary of our stock option and restricted stock activity and related information: Stock Options Restricted Stock Awards Shares Weighted-Average Exercise Price Shares Weighted-Average Grant Date Fair Value Balance as of December 31, 2019 1,956,379 $ 77.54 147,259 $ 125.11 Granted 458,750 $ 89.43 101,156 $ 89.25 Options exercised/RSUs vested (93,570) $ 19.19 (49,749) $ 122.14 Forfeited (3,500) $ 68.28 — $ — Balance as of June 30, 2020 2,318,059 $ 82.26 198,666 $ 107.59
Schedule of Restricted Stock Activity	The following is a summary of our stock option and restricted stock activity and related information: Stock Options Restricted Stock Awards Shares Weighted-Average Exercise Price Shares Weighted-Average Grant Date Fair Value Balance as of December 31, 2019 1,956,379 $ 77.54 147,259 $ 125.11 Granted 458,750 $ 89.43 101,156 $ 89.25 Options exercised/RSUs vested (93,570) $ 19.19 (49,749) $ 122.14 Forfeited (3,500) $ 68.28 — $ — Balance as of June 30, 2020 2,318,059 $ 82.26 198,666 $ 107.59

Basis of Presentation and Sum_4

Basis of Presentation and Summary of Significant Accounting Policies - Narrative (Details)	1 Months Ended	3 Months Ended		6 Months Ended
	Dec. 31, 2018USD ($)	Jun. 30, 2020USD ($)position$ / sharesshares	Jun. 30, 2019USD ($)shares	Jun. 30, 2020USD ($)position$ / sharesshares	Jun. 30, 2019USD ($)shares	Jan. 01, 2020USD ($)	Dec. 31, 2019USD ($)
Property, Plant and Equipment [Line Items]
Accounting Standards Update				us-gaap:AccountingStandardsUpdate201613Member
Revenue recognized from milestone method revenue		$ 2,000,000	$ 2,700,000	$ 2,400,000	$ 4,100,000
Fair value of equity securities		$ 8,816,000		$ 8,816,000			$ 9,910,000
Number of positions in an unrealized loss position | position		7		7
Credit losses related to available-for-sale debt securities		$ 0		$ 0
Additional allowance for credit losses recorded related to COVID-19		100,000		$ 300,000
Allowance for credit loss						$ 5,500,000
Increase (decrease) to allowance for credit loss during period		$ 500,000
Potentially dilutive shares excluded from calculation due to anti-dilutive effect (shares) | shares		7,832,000	7,457,000	8,988,000	7,243,000
Warrants
Property, Plant and Equipment [Line Items]
Fair value of equity securities		$ 177,000		$ 177,000			125,000
Warrants | Short-term Investments
Property, Plant and Equipment [Line Items]
Fair value of equity securities		$ 8,800,000		$ 8,800,000			9,900,000
Share-based Compensation
Property, Plant and Equipment [Line Items]
Potentially dilutive shares excluded from calculation due to anti-dilutive effect (shares) | shares			800,000	600,000
Adjustment
Property, Plant and Equipment [Line Items]
Cumulative-effect adjustment from adoption of ASU 2016-13, net of tax							(5,167,000)
Viking Therapeutics, Inc.
Property, Plant and Equipment [Line Items]
Warrant exercise price (USD per share) | $ / shares		$ 1.50		$ 1.50
Viking Therapeutics, Inc. | Common Stock | Short-term Investments
Property, Plant and Equipment [Line Items]
Fair value of equity securities		$ 43,500,000		$ 43,500,000			48,400,000
Palvella
Property, Plant and Equipment [Line Items]
Revenue recognized from milestone method revenue		3,000,000		$ 3,000,000
Royalty Agreements | Aziyo
Property, Plant and Equipment [Line Items]
Effective interest rate for forecasted cash flows (as a percent)				23.00%
Commercial license rights
Property, Plant and Equipment [Line Items]
Up-front payment		38,298,000		$ 38,298,000			38,298,000
Commercial license rights | Palvella
Property, Plant and Equipment [Line Items]
Contract asset	$ 8,000,000
Up-front payment	$ 10,000,000	$ 10,000,000		$ 10,000,000			$ 10,000,000
Minimum | Royalty Agreements | Palvella
Property, Plant and Equipment [Line Items]
Tiered royalty rate (as a percent)	5.00%
Maximum | Viking Therapeutics, Inc.
Property, Plant and Equipment [Line Items]
Outstanding warrants to purchase shares of Viking's common stock (shares) | shares		1,500,000		1,500,000
Maximum | Royalty Agreements | Palvella
Property, Plant and Equipment [Line Items]
Tiered royalty rate (as a percent)	9.80%

Basis of Presentation and Sum_5

Basis of Presentation and Summary of Significant Accounting Policies - Revenue by Source (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Disaggregation of Revenue [Line Items]
Total revenue	$ 41,420	$ 24,987	$ 74,581	$ 68,471
Royalties
Disaggregation of Revenue [Line Items]
Total revenue	7,181	6,626	13,746	26,164
Kyprolis
Disaggregation of Revenue [Line Items]
Total revenue	5,481	4,882	9,886	8,715
Evomela
Disaggregation of Revenue [Line Items]
Total revenue	1,199	1,144	2,775	2,055
Other
Disaggregation of Revenue [Line Items]
Total revenue	501	600	1,085	1,201
Promacta
Disaggregation of Revenue [Line Items]
Total revenue	0	0	0	14,193
Captisol
Disaggregation of Revenue [Line Items]
Total revenue	24,468	8,549	45,577	17,508
Service Revenue
Disaggregation of Revenue [Line Items]
Total revenue	4,582	4,559	7,939	8,442
Contract Revenue
Disaggregation of Revenue [Line Items]
Total revenue	5,189	5,253	7,319	16,357
License Fees
Disaggregation of Revenue [Line Items]
Total revenue	660	1,990	1,635	2,840
Milestone
Disaggregation of Revenue [Line Items]
Total revenue	3,472	2,497	3,806	12,751
Other
Disaggregation of Revenue [Line Items]
Total revenue	$ 1,057	$ 766	$ 1,878	$ 766

Basis of Presentation and Sum_6

Basis of Presentation and Summary of Significant Accounting Policies - Investment Categories (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Equity Securities, FV-NI [Abstract]
Estimated fair value	$ 8,816	$ 9,910
Debt and Equity Securities, FV-NI [Abstract]
Amortized cost	643,813	941,174
Gross unrealized gains	1,291	933
Gross unrealized losses	(2,731)	(2,118)
Estimated fair value	642,373	939,989
Bank deposits
Debt Securities, Available-for-sale [Line Items]
Amortized cost	269,114	411,690
Gross unrealized gains	221	188
Gross unrealized losses	(56)	(3)
Estimated fair value	269,279	411,875
Corporate bonds
Debt Securities, Available-for-sale [Line Items]
Amortized cost	55,380	63,818
Gross unrealized gains	125	161
Gross unrealized losses	(94)	0
Estimated fair value	55,411	63,979
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Amortized cost	163,590	210,525
Gross unrealized gains	134	43
Gross unrealized losses	0	(16)
Estimated fair value	163,724	210,552
Corporate equity securities
Debt Securities, Available-for-sale [Line Items]
Amortized cost	4,506	4,506
Gross unrealized gains	634	416
Gross unrealized losses	(2,484)	(1,850)
Estimated fair value	2,656	3,072
Mutual fund
Debt Securities, Available-for-sale [Line Items]
Amortized cost	151,223	250,635
Gross unrealized gains	0	0
Gross unrealized losses	(97)	(249)
Estimated fair value	151,126	250,386
Warrants
Equity Securities, FV-NI [Abstract]
Amortized cost	0	0
Gross unrealized gains	177	125
Gross unrealized losses	0	0
Estimated fair value	$ 177	$ 125

Basis of Presentation and Sum_7

Basis of Presentation and Summary of Significant Accounting Policies - Available-for-Sale Debt Securities by Contractual Maturity (Details) $ in Thousands	Jun. 30, 2020USD ($)
Amortized Cost
Within one year	$ 414,505
After one year through five years	73,579
After five years	0
Total	488,084
Fair Value
Within one year	414,905
After one year through five years	73,509
After five years	0
Total	$ 488,414

Basis of Presentation and Sum_8

Basis of Presentation and Summary of Significant Accounting Policies - Available-for-Sale Debt Securities in an Unrealized Loss Position (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Gross Unrealized Losses
Less than 12 months	$ (150)	$ (19)
12 months or greater	0	0
Total	(150)	(19)
Estimated Fair Value
Less than 12 months	46,037	137,947
12 months or greater	0	0
Total	46,037	137,947
Bank deposits
Gross Unrealized Losses
Less than 12 months	(56)	(3)
12 months or greater	0	0
Total	(56)	(3)
Estimated Fair Value
Less than 12 months	30,015	58,584
12 months or greater	0	0
Total	30,015	58,584
Corporate bonds
Gross Unrealized Losses
Less than 12 months	(94)
12 months or greater	0
Total	(94)
Estimated Fair Value
Less than 12 months	16,022
12 months or greater	0
Total	$ 16,022
Commercial paper
Gross Unrealized Losses
Less than 12 months		(16)
12 months or greater		0
Total		(16)
Estimated Fair Value
Less than 12 months		79,363
12 months or greater		0
Total		$ 79,363

Basis of Presentation and Sum_9

Basis of Presentation and Summary of Significant Accounting Policies - Goodwill and Other Identifiable Intangible Assets (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Summary of Goodwill and Other Identifiable Intangible Assets
Goodwill	$ 103,369	$ 95,229
Total goodwill and other identifiable intangible assets, net	318,664	305,677
Complete technology
Summary of Goodwill and Other Identifiable Intangible Assets
Definite lived intangible assets	244,513	242,813
Less: accumulated amortization	(57,053)	(50,203)
Trade name
Summary of Goodwill and Other Identifiable Intangible Assets
Definite lived intangible assets	2,642	2,642
Less: accumulated amortization	(1,246)	(1,180)
Customer relationships
Summary of Goodwill and Other Identifiable Intangible Assets
Definite lived intangible assets	40,700	29,600
Less: accumulated amortization	$ (14,261)	$ (13,224)

Basis of Presentation and Su_10

Basis of Presentation and Summary of Significant Accounting Policies - Commercial License and Other Economic Rights (Details) - Commercial license rights - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019	Dec. 31, 2018
Commercial License and Other Economic Rights
Gross	$ 38,298	$ 38,298
Adjustments	(27,692)	(18,208)
Net	10,606	20,090
Accumulated amortization on finite-lived intangible assets	(21,700)
Credit loss adjustments of finite-lived intangible assets	(6,000)
Aziyo and CorMatrix
Commercial License and Other Economic Rights
Gross	17,696	17,696
Adjustments	(9,698)	(5,500)
Net	7,998	12,196
Palvella
Commercial License and Other Economic Rights
Gross	10,000	10,000	$ 10,000
Adjustments	(10,000)	(7,492)
Net	0	2,508
Selexis and Dianomi
Commercial License and Other Economic Rights
Gross	10,602	10,602
Adjustments	(7,994)	(5,216)
Net	$ 2,608	$ 5,386

Basis of Presentation and Su_11

Basis of Presentation and Summary of Significant Accounting Policies - Accrued Liabilities and Other Long-Term Liabilities (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Accrued Liabilities
Compensation	$ 3,457	$ 1,986
Professional fees	964	1,135
Amounts owed to former licensees	413	381
Royalties owed to third parties	1,038	0
Return reserve	2,899	3,027
Current operating lease liabilities	1,728	1,242
Accrued interest	471	690
Other	1,858	1,375
Total accrued liabilities	$ 12,828	$ 9,836

Basis of Presentation and Su_12

Basis of Presentation and Summary of Significant Accounting Policies - Accounting for Share-Based Compensation (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Basis of Presentation [Line Items]
Share-based compensation expense	$ 7,359	$ 6,571	$ 13,012	$ 11,918
SBC - Research and development expenses
Basis of Presentation [Line Items]
Share-based compensation expense	3,019	2,528	5,416	4,655
SBC - General and administrative expenses
Basis of Presentation [Line Items]
Share-based compensation expense	$ 4,340	$ 4,043	$ 7,596	$ 7,263

Basis of Presentation and Su_13

Basis of Presentation and Summary of Significant Accounting Policies - Fair Value Valuation Assumptions (Details)	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Risk-free interest rate (as a percent)	0.40%	1.90%	1.10%	2.40%
Dividend yield (as a percent)	0.00%	0.00%	0.00%	0.00%
Expected volatility (as a percent)	69.00%	40.00%	55.00%	43.00%
Expected term	5 years 1 month 6 days	5 years 10 months 24 days	4 years 9 months 18 days	5 years 2 months 12 days

Basis of Presentation and Su_14

Basis of Presentation and Summary of Significant Accounting Policies - Earnings (Loss) Per Share (Details) - shares	3 Months Ended		6 Months Ended		9 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	Sep. 30, 2018	Sep. 30, 2017
Summary of computation of basic and diluted net income (loss) per share
Weighted average shares outstanding (shares)	16,055,000	19,558,000	16,292,000	20,000,000
Dilutive potential common shares:
Restricted stock (in shares)	40,000	0	0	38,000
Stock options (in shares)	599,000	0	0	761,000
Shares used to compute diluted income per share (shares)	16,694,000	19,558,000	16,292,000	20,799,000	16,292,000	20,799,000
Potentially dilutive shares excluded from calculation due to anti-dilutive effect (shares)	7,832,000	7,457,000	8,988,000	7,243,000

Fair Value Measurements - Asset

Fair Value Measurements - Assets and Liabilities at Fair Value (Details)	1 Months Ended	3 Months Ended
	Jan. 31, 2010contingentValueRightSeriescontingentValueRight	Mar. 31, 2020USD ($)	Jun. 30, 2020USD ($)	Dec. 31, 2019USD ($)
Assets:
Short-term investments			$ 642,373,000	$ 939,989,000
Investment in Viking common stock			43,535,000	48,425,000
Investment in warrants			8,816,000	9,910,000
Total assets			694,724,000	998,324,000
Liabilities:
Amounts owed to former licensor			107,000	75,000
Total liabilities			11,528,000	9,017,000
Repayments of related party debt		$ 1,800,000
Number of CVR Series | contingentValueRightSeries	4
Metabasis
Liabilities:
Number of CVRs issued per acquiree share | contingentValueRight	4
Number of CVRs issued from each CVR series | contingentValueRight	1
Frequency of cash payments to CVR holders	6 months
Transferred over Time | Phase 3 Clinical Trial
Liabilities:
Contract asset			10,000,000
Maximum | Transferred over Time | Development, Regulatory, & Commercial Milestones and Tiered Royalties
Liabilities:
Investments			375,000,000
Crystal contingent liabilities
Liabilities:
Contingent liabilities			859,000	2,659,000
CyDex contingent liabilities
Liabilities:
Contingent liabilities			413,000	348,000
Metabasis contingent liabilities
Liabilities:
Contingent liabilities			5,349,000	5,935,000
Icagen contingent liabilities
Liabilities:
Contingent liabilities			4,800,000	0
Level 1
Assets:
Short-term investments			2,655,000	3,073,000
Investment in Viking common stock			43,535,000	48,425,000
Investment in warrants			8,816,000	9,910,000
Total assets			55,006,000	61,408,000
Liabilities:
Amounts owed to former licensor			107,000	75,000
Total liabilities			107,000	75,000
Level 1 | Crystal contingent liabilities
Liabilities:
Contingent liabilities			0	0
Level 1 | CyDex contingent liabilities
Liabilities:
Contingent liabilities			0	0
Level 1 | Metabasis contingent liabilities
Liabilities:
Contingent liabilities			0	0
Level 1 | Icagen contingent liabilities
Liabilities:
Contingent liabilities			0	0
Level 2
Assets:
Short-term investments			639,541,000	936,791,000
Investment in Viking common stock			0	0
Investment in warrants			0	0
Total assets			639,541,000	936,791,000
Liabilities:
Amounts owed to former licensor			0	0
Total liabilities			5,349,000	5,935,000
Level 2 | Crystal contingent liabilities
Liabilities:
Contingent liabilities			0	0
Level 2 | CyDex contingent liabilities
Liabilities:
Contingent liabilities			0	0
Level 2 | Metabasis contingent liabilities
Liabilities:
Contingent liabilities			5,349,000	5,935,000
Level 2 | Icagen contingent liabilities
Liabilities:
Contingent liabilities			0	0
Level 3
Assets:
Short-term investments			177,000	125,000
Investment in Viking common stock			0	0
Investment in warrants			0	0
Total assets			177,000	125,000
Liabilities:
Amounts owed to former licensor			0	0
Total liabilities			6,072,000	3,007,000
Level 3 | Crystal contingent liabilities
Liabilities:
Contingent liabilities			859,000	2,659,000
Level 3 | CyDex contingent liabilities
Liabilities:
Contingent liabilities			413,000	348,000
Level 3 | Metabasis contingent liabilities
Liabilities:
Contingent liabilities			0	0
Level 3 | Icagen contingent liabilities
Liabilities:
Contingent liabilities			$ 4,800,000	$ 0

Business Combination - Narrativ

Business Combination - Narrative (Details)	Apr. 01, 2020USD ($)	Jul. 23, 2019USD ($)	Jun. 30, 2020USD ($)	Jun. 30, 2019USD ($)	Jun. 30, 2020USD ($)acquisition
Business Acquisition [Line Items]
Number of acquisitions | acquisition					2
Acquisition related costs					$ 0
Cash payments for acquisition			$ 15,140,000	$ 0
Icagen
Business Acquisition [Line Items]
Consideration transferred in acquisition	$ 19,900,000
Cash payments for acquisition	15,100,000
Contingent earn-out payment	25,000,000
Fair value of contingent earn-out payment	4,800,000
Tangible assets acquired	1,800,000
Liabilities assumed	(800,000)
Finite-lived intangible assets acquired	12,800,000
Deferred revenue acquired	(3,700,000)
Deferred tax assets acquired	800,000
Goodwill acquired	$ 9,000,000
Weighted-average estimated useful life of finite-lived intangible assets acquired	9 years 8 months 12 days
Icagen | Customer Relationships
Business Acquisition [Line Items]
Finite-lived intangible assets acquired	$ 11,100,000
Discount rate used to value intangible assets acquired (as a percent)	17.00%
Weighted-average estimated useful life of finite-lived intangible assets acquired	9 years 7 months 6 days
Icagen | Core Technology
Business Acquisition [Line Items]
Finite-lived intangible assets acquired	$ 1,700,000
Discount rate used to value intangible assets acquired (as a percent)	17.00%
Weighted-average estimated useful life of finite-lived intangible assets acquired	10 years
Ab Initio Biotherapeutics, Inc.
Business Acquisition [Line Items]
Consideration transferred in acquisition		$ 12,000,000
Cash payments for acquisition		11,840,000
Tangible assets acquired		30,000
Liabilities assumed		(80,000)
Goodwill acquired		6,300,000
Cash holdback for potential indemnification claims		150,000
Deferred tax liability acquired in connection with the acquired intangibles		(1,600,000)
Ab Initio Biotherapeutics, Inc. | Core Technology
Business Acquisition [Line Items]
Finite-lived intangible assets acquired		$ 7,400,000
Discount rate used to value intangible assets acquired (as a percent)		12.00%
Weighted-average estimated useful life of finite-lived intangible assets acquired		20 years

Convertible Senior Notes - Narr

Convertible Senior Notes - Narrative (Details)	Apr. 06, 2020USD ($)	May 31, 2018USD ($)d$ / sharesshares	Jun. 30, 2020USD ($)	Mar. 31, 2020USD ($)	Jun. 30, 2020USD ($)	Jun. 30, 2019USD ($)	Dec. 31, 2019USD ($)
Debt Instrument [Line Items]
Gain (loss) on extinguishment of debt					$ 659,000	$ 0
Adjustments to additional paid in capital, equity component of convertible debt			$ 23,000	$ 2,745,000
Convertible Notes | 2023 Convertible Senior Notes
Debt Instrument [Line Items]
Aggregate principal amount outstanding		$ 750,000,000	515,560,000		515,560,000		$ 750,000,000
Interest rate (as a percent)		0.75%
Proceeds from debt, net of issuance costs		$ 733,100,000
Initial conversion rate (shares per $1,000)		0.0040244
Initial conversion price (USD per share) | $ / shares		$ 248.48
Debt issuance costs			16,900,000		16,900,000
Debt premium			13,700,000		13,700,000
Long-term debt	$ 234,400,000		515,600,000		$ 515,600,000
Repayments of notes	$ 203,800,000
Accrued Interest				$ 600,000
Gain (loss) on extinguishment of debt			700,000
Increase (decrease) in debt discount			32,700,000
Adjustments to additional paid in capital, equity component of convertible debt			$ 2,700,000
Warrants issued in public offering (shares) | shares		3,018,327
Payments for convertible bond hedges		$ 140,300,000
Warrant exercise price (USD per share) | $ / shares		$ 315.38
Warrant derivative in connection with Notes		$ 90,000,000
Convertible Notes | 2023 Convertible Senior Notes | Debt Instrument, Redemption, Period One
Debt Instrument [Line Items]
Threshold trading days | d		20
Consecutive trading days | d		30
Stock price trigger to classify convertible debt as current (as a percent)		130.00%
Convertible Notes | 2023 Convertible Senior Notes | Debt Instrument, Redemption, Period Two
Debt Instrument [Line Items]
Threshold trading days | d		5
Consecutive trading days | d		10
Maximum threshold of debt trading price trigger (as a percent)		98.00%

Convertible Senior Notes - Note

Convertible Senior Notes - Notes Payable (Details) - Convertible Notes - 2023 Convertible Senior Notes - USD ($)	Jun. 30, 2020	Dec. 31, 2019	May 31, 2018
Notes Payable, Current and Noncurrent [Abstract]
Principal amount of the 2023 Notes outstanding	$ 515,560,000	$ 750,000,000	$ 750,000,000
Unamortized discount (including unamortized debt issuance cost)	(65,888,000)	(111,041,000)
Total long-term portion of notes payable	449,672,000	638,959,000
Carrying value of equity component of the 2023 Notes	60,181,000	101,422,000
Fair value of the 2023 Notes outstanding (Level 2)	$ 452,167,000	$ 647,280,000

Income Tax - Narrative (Details

Income Tax - Narrative (Details)	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Income Tax Disclosure [Abstract]
Effective income tax rate (as a percent)	21.50%	20.00%	10.90%	20.90%

Stockholders' Equity - Stock Op

Stockholders' Equity - Stock Option Plan and Restricted Stock Activity (Details)	6 Months Ended
	Jun. 30, 2020$ / sharesshares
Stock Options
Stock Options
Balance at beginning of period (shares) | shares	1,956,379
Granted (shares) | shares	458,750
Options exercised (shares) | shares	(93,570)
Forfeited (shares) | shares	(3,500)
Balance at end of period (shares) | shares	2,318,059
Weighted- Average Exercise Price
Balance at beginning of period (USD per share) | $ / shares	$ 77.54
Granted (USD per share) | $ / shares	89.43
Options exercised (USD per share) | $ / shares	19.19
Forfeited (USD per share) | $ / shares	68.28
Balance at end of period (USD per share) | $ / shares	$ 82.26
Restricted Stock Awards
Restricted Stock Awards
Nonvested at beginning of period (shares) | shares	147,259
Granted (shares) | shares	101,156
RSUs vested (shares) | shares	(49,749)
Forfeited (shares) | shares	0
Nonvested at end of period (shares) | shares	198,666
Weighted- Average Grant Date Fair Value
Nonvested at beginning of period (USD per share) | $ / shares	$ 125.11
Granted (USD per share) | $ / shares	89.25
RSUs vested (USD per share) | $ / shares	122.14
Forfeited (USD per share) | $ / shares	0
Nonvested at end of period (USD per share) | $ / shares	$ 107.59

Stockholders' Equity - Narrativ

Stockholders' Equity - Narrative (Details) - USD ($)	Sep. 11, 2019	Jun. 30, 2020	Mar. 31, 2020	Jun. 30, 2019	Mar. 31, 2019	Jun. 30, 2020
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Outstanding options that are exercisable (shares)		1,500,000				1,500,000
Outstanding options that are exercisable, weighted average exercise price (USD per share)		$ 69.79				$ 69.79
Employee Stock Purchase Plan
Stock repurchased during period		$ 0	$ 73,287,000	$ 33,717,000	$ 151,585,000
Authorized stock repurchase amount	$ 500,000,000
Period in force of stock repurchase program	3 years
Remaining authorized stock repurchase amount		$ 253,500,000				$ 253,500,000
Employee Stock Purchase Plan
Employee Stock Purchase Plan
Share purchase price as percent of market price (as a percent)						85.00%
Shares available for future purchases (shares)						56,079

Commitment and Contingencies__2

Commitment and Contingencies: Legal Proceedings - Narrative (Details)	Oct. 31, 2019civilComplaint	Oct. 29, 2019patent
Lupin Patent Infringement
Gain Contingencies [Line Items]
Number of patents allegedly infringed upon | patent		4
US District Court for the Northern District of Ohio [Member]
Gain Contingencies [Line Items]
Number of civil complaints filed against entity | civilComplaint	3

Leases - Narrative (Details)

Leases - Narrative (Details)	Jun. 30, 2020
Leases [Abstract]
Remaining lease term	7 years
Lease renewal term	7 years