Ligand Pharmaceuticals (LGND) 10-K 28 Feb 17 2016 FY Annual report Financial data

Document and Entity Information

Document and Entity Information - USD ($) $ in Billions	12 Months Ended
	Dec. 31, 2016	Feb. 09, 2017	Jun. 30, 2016
Document and Entity Information [Abstract]
Entity Registrant Name	LIGAND PHARMACEUTICALS INC
Entity Central Index Key	886,163
Document Type	10-K
Document Period End Date	Dec. 31, 2016
Amendment Flag	false
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	FY
Current Fiscal Year End Date	--12-31
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		20,919,894
Entity Public Float			$ 2.3
Entity Voluntary Filers	No
Entity Well-known Seasoned Issuer	No
Entity Current Reporting Status	Yes

CONSOLIDATED BALANCE SHEETS

CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 18,752	$ 97,428
Short-term investments	122,296	102,791
Accounts receivable, net	14,700	6,170
Note receivable from Viking	3,207	4,782
Inventory	1,923	1,633
Other current assets	2,175	1,908
Total current assets	163,053	214,712
Deferred income taxes	123,891	189,083
Investment in Viking	8,345	29,728
Intangible assets, net	204,705	48,347
Goodwill	72,207	12,238
Commercial license rights	25,821	8,554
Property and equipment, net	1,819	372
Other assets	1,744	27
Total assets	601,585	503,061
Current liabilities:
Accounts payable	2,734	4,083
Accrued liabilities	6,397	5,405
Current contingent liabilities	5,088	10,414
Current lease exit obligations		934
2019 convertible senior notes, net	212,910	201,985
Total current liabilities	227,129	222,821
Long-term contingent liabilities	2,916	3,033
Other long-term liabilities	687	297
Total liabilities	230,732	226,151
Commitments and contingencies
Equity component of currently redeemable convertible notes (Note 5)	29,563	39,628
Stockholders’ equity:
Common stock, $0.001 par value; 33,333,333 shares authorized; 20,909,301 and 19,949,012 shares issued and outstanding at December 31, 2016 and 2015, respectively	21	20
Additional paid-in capital	769,653	661,850
Accumulated other comprehensive income	2,743	4,903
Accumulated deficit	(431,127)	(429,491)
Total stockholders’ equity	341,290	237,282
Total liabilities and stockholders’ equity	$ 601,585	$ 503,061

CONSOLIDATED BALANCE SHEETS (Pa

CONSOLIDATED BALANCE SHEETS (Parenthetical) - $ / shares	Dec. 31, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
Common stock, par value (in USD per share)	$ 0.001	$ 0.001
Common stock, shares authorized (shares)	33,333,333	33,333,333
Common stock, shares issued (shares)	20,909,301	19,949,012
Common stock, shares outstanding (shares)	20,909,301	19,949,012

CONSOLIDATED STATEMENTS OF OPER

CONSOLIDATED STATEMENTS OF OPERATIONS - USD ($) shares in Thousands, $ in Thousands		12 Months Ended
		Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Revenues:
Royalties		$ 59,423	$ 38,194	$ 29,994
Material sales		22,502	27,662	28,488
License fees, milestones and other revenues		27,048	6,058	6,056
Total revenues		108,973	71,914	64,538
Operating costs and expenses:
Cost of sales	[1]	5,571	5,807	9,136
Amortization of intangibles		10,643	2,375	2,375
Research and development		21,221	11,005	9,747
General and administrative		26,621	24,378	22,570
Lease exit and termination costs		1,032	1,020	1,084
Total operating costs and expenses		65,088	44,585	44,912
Income from operations		43,885	27,329	19,626
Other (expense) income:
Interest expense, net		(12,178)	(11,802)	(4,860)
Increase in contingent liabilities		(3,334)	(5,013)	(5,135)
Gain on deconsolidation of Viking		0	28,190	0
Loss from Viking		(23,132)	(5,143)	0
Other income, net		2,719	1,768	1,671
Total other income (expense), net		(35,925)	8,000	(8,324)
Income before income tax benefit (expense)		7,960	35,329	11,302
Income tax benefit (expense)		(10,327)	192,115	(410)
Income (loss) from operations		(2,367)	227,444	10,892
Discontinued operations:
Gain on sale of Oncology Product Line before income taxes		1,139	0	0
Income tax expense on discontinued operations		(408)	0	0
Income from discontinued operations		731	0	0
Net (loss) income including noncontrolling interests:		(1,636)	227,444	10,892
Less: Net loss attributable to noncontrolling interests		0	(2,380)	(1,132)
Net (loss) income		$ (1,636)	$ 229,824	$ 12,024
Basic per share amounts(1):
Income (loss) from continuing operations (in usd per share)	[2]	$ (0.11)	$ 11.61	$ 0.59
Income from discontinued operations (in usd per share)	[2]	0.04	0	0
Net income (in usd per share)	[2]	$ (0.08)	$ 11.61	$ 0.59
Weighted average shares outstanding (shares):		20,831	19,790	20,419
Diluted per share amounts(1):
Income (loss) from continuing operations (in usd per share)	[2]	$ (0.11)	$ 10.83	$ 0.56
Income from discontinued operations (in usd per share)	[2]	0.04	0	0
Net (loss) income (in usd per share)	[2]	$ (0.08)	$ 10.83	$ 0.56
Weighted average number of common shares-diluted (shares)		20,831	21,228	21,433
[1]	Excludes amortization of intangibles
[2]	The sum of net income per share amounts may not equal the total due to rounding

CONSOLIDATED STATEMENTS OF COMP

CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Statement of Comprehensive Income [Abstract]
Net (loss) income	$ (1,636)	$ 229,824	$ 12,024
Unrealized net gain on available-for-sale securities, net of tax	93	1,933	3,872
Less:Reclassification of net realized gains included in net income, net of tax	(2,253)	(1,965)	(1,833)
Comprehensive (loss) income	$ (3,796)	$ 229,792	$ 14,063

CONSOLIDATED STATEMENT OF STOCK

CONSOLIDATED STATEMENT OF STOCKHOLDERS' EQUITY - USD ($) $ in Thousands	Total	Common Stock	Additional paid-in capital	Accumulated other comprehensive income (loss)	Accumulated deficit	Noncontrolling interest
Balance at beginning of period at Dec. 31, 2013	$ 49,613	$ 21	$ 718,017	$ 2,914	$ (671,339)
Balance at beginning of period (in shares) at Dec. 31, 2013		20,468,521
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Consolidation of Viking	(778)					$ (778)
Issuance of common stock under employee stock compensation plans, net	4,561		4,561
Issuance of common stock under employee stock compensation plans (in shares)		360,054
Shares issued in OMT acquisition	0
Stock-based compensation	11,270		11,270
Repurchase of common stock	$ (67,955)	$ (1)	(67,954)
Repurchase of common stock (in shares)	(1,253,425)	(1,253,425)
Sale of warrants	$ 11,638		11,638
Purchase of convertible bond hedge	(48,143)		(48,143)
Equity component of convertible debt issuance, net of issuance costs	51,271		51,271
Other comprehensive income	2,039			2,039
Net income	12,024				12,024
Net loss in noncontrolling interests	(1,132)					(1,132)
Balance at end of period at Dec. 31, 2014	24,408	$ 20	680,660	4,953	(659,315)	(1,910)
Balance at end of period (in shares) at Dec. 31, 2014		19,575,150
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock under employee stock compensation plans, net	8,849		8,849
Issuance of common stock under employee stock compensation plans (in shares)		379,982
Shares issued in OMT acquisition	0
Stock-based compensation	12,458		12,458
Repurchase of common stock	$ (489)		(489)
Repurchase of common stock (in shares)	(6,120)	(6,120)
Equity component of convertible debt issuance, net of issuance costs	$ (39,628)		(39,628)
Other comprehensive income	(50)			(50)
Net income	229,824				229,824
Net loss in noncontrolling interests	(2,380)					(2,380)
Deconsolidation of Viking	4,290					$ 4,290
Balance at end of period at Dec. 31, 2015	237,282	$ 20	661,850	4,903	(429,491)
Balance at end of period (in shares) at Dec. 31, 2015		19,949,012
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock under employee stock compensation plans, net	5,416		5,416
Issuance of common stock under employee stock compensation plans (in shares)		210,626
Shares issued in OMT acquisition	77,331	$ 1	77,330
Shares issued in OMT acquisition (shares)		790,163
Stock-based compensation	18,893		18,893
Repurchase of common stock	$ (3,901)		(3,901)
Repurchase of common stock (in shares)	(40,500)	(40,500)
Equity component of convertible debt issuance, net of issuance costs	$ 10,065		10,065
Other comprehensive income	(2,160)			(2,160)
Net income	(1,636)				(1,636)
Net loss in noncontrolling interests	0
Balance at end of period at Dec. 31, 2016	$ 341,290	$ 21	$ 769,653	$ 2,743	$ (431,127)
Balance at end of period (in shares) at Dec. 31, 2016		20,909,301

CONSOLIDATED STATEMENTS OF CASH

CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Operating activities
Net (loss) income	$ (1,636)	$ 227,444	$ 10,892
Less: gain from discontinued operations	731	0	0
Income (loss) from continuing operations	(2,367)	227,444	10,892
Adjustments to reconcile net income to net cash used in operating activities:
Change in estimated fair value of contingent liabilities	3,334	5,013	5,135
Realized gain on sale of short-term investment	(2,352)	(2,603)	(1,538)
Gain on disposal of assets	183	0	0
Depreciation and amortization	11,290	2,627	2,657
Gain on deconsolidation of Viking	0	(28,190)	0
Loss on equity investment in Viking	23,132	5,143	0
Change in fair value of the convertible debt receivable from Viking and warrants	(462)	765	0
Amortization of Premium (discount) on investments, net	348	0	0
Amortization of debt discount and issuance fees	10,925	10,274	3,694
Non-cash milestone revenue	0	0	(1,211)
Stock-based compensation	18,893	12,458	11,270
Deferred income taxes	10,697	(192,132)	410
Other	0	107	206
Changes in operating assets and liabilities, net of acquisition:
Accounts receivable, net	(8,525)	6,489	(10,412)
Inventory	(244)	(401)	4,369
Restricted cash	0	1,261	0
Other current assets	558	51	(426)
Other long term assets	(32)	(325)	(1,439)
Accounts payable and accrued liabilities	(2,369)	(4,027)	(3,121)
Deferred revenue	(8)	(2,227)	80
Net cash provided by operating activities of continuing operations	63,001	41,727	20,566
Net cash used in operating activities of discontinued operations	0	0	0
Net cash provided by operating activities	63,001	41,727	20,566
Investing activities
Purchase of commercial license rights	(17,695)	(4,030)	(1,000)
Reduction of cash due to deconsolidation of Viking	0	(247)	0
Purchase of commercial license rights	(92,502)	0	0
Payments to CVR holders and other contingency payments	(8,777)	(6,740)	(3,493)
Purchases of property and equipment	(1,850)	(93)	(6)
Purchases of short-term investments	(164,438)	(166,025)	0
Proceeds from sale of short-term investments	24,596	16,039	2,342
Proceeds from maturity of short-term investments	118,874	57,234	0
Proceeds received from repayment of Viking note receivable	300	0	0
Other, net	0	0	130
Net cash used in investing activities	(143,192)	(112,862)	(2,027)
Financing activities
Repayment of debt	0	0	(9,366)
Gross proceeds from issuance of 2019 Convertible Senior Notes	0	0	245,000
Payment of debt issuance costs	0	0	(5,711)
Proceeds from issuance of warrants	0	0	11,638
Purchase of convertible bond hedge	0	0	(48,143)
Net proceeds from stock option exercises and ESPP	6,415	8,849	4,561
Taxes paid related to net share settlement of equity awards	(999)	0	0
Share repurchases	(3,901)	(489)	(67,954)
Net cash provided by financing activities	1,515	8,360	130,025
Net (decrease) increase in cash and cash equivalents	(78,676)	(62,775)	148,564
Cash and cash equivalents at beginning of year	97,428	160,203	11,639
Cash and cash equivalents at end of year	18,752	97,428	160,203
Supplemental disclosure of cash flow information
Interest paid	1,838	1,822	494
Taxes paid	38	28	18
Supplemental schedule of non-cash investing and financing activities
Stock issued for acquisition, net of issuance cost	(77,331)	0	0
Stock and warrant received for repayment of Viking notes receivable	1,200	0	0
Accrued inventory purchases	646	1,333	3,246
Unrealized gain on AFS investments	(1,109)	3,005	3,872
Viking Therapeutics, Inc.
Investing activities
Purchase of Viking common stock and warrant	(700)	(9,000)	0
Purchase of Common Stock [Member]
Investing activities
Purchase of Viking common stock and warrant	$ (1,000)	$ 0	$ 0

Basis of Presentation and Summa

Basis of Presentation and Summary of Significant Accounting Policies	12 Months Ended
	Dec. 31, 2016
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 Business Ligand is a biopharmaceutical company with a business model based on developing or acquiring assets which generate royalty, milestone or other passive revenue for the Company and using a lean corporate cost structure. We operate in one business segment: development and licensing of biopharmaceutical assets. Principles of Consolidation The accompanying consolidated financial statements include Ligand and its wholly owned subsidiaries. All significant intercompany accounts and transactions have been eliminated in consolidation. Basis of Presentation The Company’s accompanying consolidated financial statements have been prepared in accordance with U.S. GAAP and include the accounts of the Company and its wholly-owned subsidiaires. All intercompany transactions and balances have been eliminated in consolidation. Upon the occurrence of certain circumstances, holders of the 2019 Convertible Senior Notes may redeem all or a portion of their notes, which may require the use of a substantial amount of cash. At December 31, 2016, we had a working capital deficit of $64.1 million , which includes the 2019 Convertible Senior notes that are currently redeemable as of December 31, 2016 but excludes another $29.6 million that is classified as mezzanine equity. As noted in Note 6, the debt may change from current to non-current period over period, primarily as a result of changes in the Company’s stock price. Management believes that it is remote that holders of the notes would choose to convert their notes early because the fair value of the security that a noteholder can currently realize in an active market is greater than the conversion value the noteholder would realize upon early conversion. In the unlikely event that all the debt was converted, we have 3 business days following a 50 trading day observation period from the convert date to pay the principal in cash. We have positive operating income and positive cash flow from operations for the three years ended December 31, 2016 and, accordingly, while there can be no assurance, we believe we have the ability to raise additional capital through our active S-3, by liquidating assets, or via alternative financing arrangements such as convertible or high yield debt. Reclassifications Certain reclassifications have been made to the previously issued statement of operations for comparability purposes. These reclassifications had no effect on the reported net income, stockholders' equity and operating cash flows as previously reported. Use of Estimates The preparation of consolidated financial statements in conformity with U.S. 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 Recent Accounting Pronouncements I n May 2014, the FASB issued new guidance related to revenue recognition, Accounting Standards Update 2014-09, Revenue from Contracts with Customers (“ASC 606”), which outlines a comprehensive revenue recognition model and supersedes most current revenue recognition guidance. The new guidance requires a company to recognize revenue upon transfer of goods or services to a customer at an amount that reflects the expected consideration to be received in exchange for those goods or services. ASC 606 defines a five-step approach for recognizing revenue, which may require a company to use more judgment and make more estimates than under the current guidance. The new guidance becomes effective in calendar year 2018 and early adoption in calendar year 2017 is permitted. Two methods of adoption are permitted: (a) full retrospective adoption, meaning the standard is applied to all periods presented; or (b) modified retrospective adoption, meaning the cumulative effect of applying the new guidance is recognized at the date of initial application as an adjustment to the opening retained earnings balance. We are undertaking a substantial effort to be ready for adoption of ASC 606. Some of our contracts have distinct terms which will need to be evaluated separately. We have started our preliminary assessment of these contracts and although we have not completed our assessment and are in the process of reviewing our contracts, we anticipate this standard will have a material impact on our consolidated financial statements by accelerating the timing of revenue recognition for revenues related to royalties, and potentially certain contingent milestone based payments. We intend to adopt ASC 606 starting as of January 1, 2018 using the modified retrospective method. In August 2014, the FASB issued Accounting Standards Update No. 2014-15, Presentation of Financial Statements -Going Concern (Subtopic 205-40). This accounting standard requires management to perform interim and annual assessments of the entity's ability to continue its business operations within one year of the date of issuance of its financial statements. The Company must then provide certain disclosure if there is substantial doubt about its ability to continue as a going concern. As of December 31, 2016, the Company has adopted this standard with no impact to the financial statements. In March 2016, the FASB issued ASU 2016-09 amending several aspects of share-based payment accounting. This guidance requires all excess tax benefits and tax deficiencies to be recorded in the income statement when the awards vest or are settled, with prospective application required. The guidance also changes the classification of such tax benefits or tax deficiencies on the statement of cash flows from a financing activity to an operating activity, with retrospective or prospective application allowed. The guidance requires the classification of employee taxes paid when an employer withholds shares for tax-withholding purposes as a financing activity on the statement of cash flows, with retrospective application required. In addition, the guidance provides for an option to recognize gross stock compensation expense with actual forfeitures recognized as they occur. The updated guidance is effective in fiscal year 2018 and early adoption in fiscal year 2017 is permitted. We are currently evaluating the adoption timing as well as the impact of the new guidance on our consolidated financial statements and related disclosures. In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses: Measurement of Credit Losses on Financial Instruments which requires that expected credit losses relating to financial assets measured on an amortized cost basis and available-for-sale debt securities be recorded through an allowance for credit losses. ASU 2016-13 limits the amount of credit losses to be recognized for available-for-sale debt securities to the amount by which carrying value exceeds fair value and also requires the reversal of previously recognized credit losses if fair value increases. The new standard will be effective for us in fiscal year 2020 and early adoption in fiscal 2019 is permitted. We are currently evaluating the effect that the updated standard will have on our consolidated financial statements. In August 2016 the FASB issued ASU No. 2016-15 Statement of Cash Flows (Topic 230) , Classification of Certain Cash Receipts and Cash Payments. The guidance addresses the classification of cash flows related to (1) debt prepayment or extinguishment costs, (2) settlement of zero-coupon debt instruments or other debt instruments with coupon rates that are insignificant in relation to the effective interest rate of the borrowing, (3) contingent consideration payments made after a business combination, (4) proceeds from the settlement of insurance claims, (5) proceeds from the settlement of corporate-owned life insurance, including bank-owned life insurance, (6) distributions received from equity method investees and (7) beneficial interests in securitization transactions. The guidance also clarifies how the predominance principle should be applied when cash receipts and cash payments have aspects of more than one class of cash flows. The new guidance will be effective for fiscal year 2018 and early adoption is permitted. We are currently evaluating the effect that the updated standard will have on our consolidated financial statements. We expect contingent consideration payment presentation will change to conform to the standard. We do not believe that any other recently issued, but not yet effective accounting pronouncements, if adopted, would have a material impact on our consolidated financial statements or disclosures. Concentrations of Business Risk Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash equivalents and investments. The Company invests its excess cash principally in United States government debt securities, investment grade corporate debt securities and certificates of deposit. The Company has established guidelines relative to diversification and maturities that maintain safety and liquidity. These guidelines are periodically reviewed and modified to take advantage of trends in yields and interest rates. A relatively small number of partners accounts for a significant percentage of our revenue. Revenue from significant partners, which is defined as 10% or more of our total revenue, was as follows: December 31, 2016 2015 2014 Partner A 41 % 27 % 37 % Partner B 14 % 23 % 31 % Partner C — 18 % 10 % The Company obtains Captisol from a single supplier, Hovione. If this supplier were not able to supply the requested amounts of Captisol, the Company would be unable to continue to derive revenues from the sale of Captisol until it obtained an alternative source, which could take a considerable length of time. Cash Equivalents & Short Term Investments Cash equivalents consist of all investments with maturities of three months or less from the date of acquisition. Short-term investments primarily consist of investments in debt securities that have effective maturities greater than three months and less than twelve months from the date of acquisition. The Company classifies its short-term investments as "available-for-sale". Such investments are carried at fair value, with unrealized gains and losses included in the statement of comprehensive income (loss). The Company determines the cost of investments based on the specific identification method. Accounts Receivable Trade accounts receivable are recorded at the net invoice value and are not interest bearing. The Company considers receivables past due based on the contractual payment terms which range from 30 to 90 days. The Company reserves specific receivables if collectibility is no longer reasonably assured. The Company re-evaluates such reserves on a regular basis and adjusts its reserves as needed. Once a receivable is deemed to be uncollectible, such balance is charged against the reserve. Inventory Inventory, which consists of finished goods, is stated at the lower of cost or market value. The Company determines cost using the first-in, first-out method. The Company analyzes its inventory levels periodically and writes down inventory to its net realizable value if it has become obsolete, has a cost basis in excess of its expected net realizable value or is in excess of expected requirements. There were no write downs related to obsolete inventory recorded for the years ended December 31, 2016 and 2015 . Property and Equipment Property and equipment are stated at cost, subject to review for impairment, and depreciated over the estimated useful lives of the assets, which generally range from three to ten years, using the straight-line method. Amortization of leasehold improvements is recorded over the shorter of the lease term or estimated useful life of the related asset. Maintenance and repairs are charged to operations as incurred. When assets are sold, or otherwise disposed of, the cost and related accumulated depreciation are removed from the accounts and any gain or loss is included in operating expense. Goodwill and Intangible Assets Goodwill, which has an indefinite useful life, represents the excess of cost over fair value of net assets acquired. The change in the carrying value of goodwill during the year ended December 31, 2016, was due to the acquisition of OMT. Goodwill is reviewed for impairment at least annually during the fourth quarter, or more frequently if an event occurs indicating the potential for impairment. During its goodwill impairment review, the Company may assess qualitative factors to determine whether it is more likely than not that the fair value of its reporting unit is less than its carrying amount, including goodwill. The qualitative factors include, but are not limited to, macroeconomic conditions, industry and market considerations, and the overall financial performance of the Company. If, after assessing the totality of these qualitative factors, the Company determines that it is not more likely than not that the fair value of its reporting unit is less than its carrying amount, then no additional assessment is deemed necessary. Otherwise, the Company proceeds to perform the two-step test for goodwill impairment. The first step involves comparing the estimated fair value of the reporting unit with its carrying value, including goodwill. If the carrying amount of the reporting unit exceeds its fair value, the Company performs the second step of the goodwill impairment test to determine the amount of loss, which involves comparing the implied fair value of the goodwill to the carrying value of the goodwill. The Company may also elect to bypass the qualitative assessment in a period and elect to proceed to perform the first step of the goodwill impairment test. The Company performed its annual assessment for goodwill impairment in the fourth quarter of 2016 by assessing qualitative factors, noting no impairment. Intangible assets related to acquired IPR&D are considered to be indefinite-lived until the completion or abandonment of the associated research and development efforts. During the period the assets are considered to be indefinite-lived, they are not amortized but are tested for impairment on an annual basis and between annual tests if the Company becomes aware of any events occurring or changes in circumstances that would indicate a reduction in the fair value of the IPR&D projects below their respective carrying amounts. If and when development is complete, which generally occurs if and when regulatory approval to market a product is obtained, the associated assets would be deemed finite-lived and would then be amortized based on their respective estimated useful lives at that point in time. The Company performed its annual assessment for IPR&D impairment in 2016, noting no impairment. Commercial license rights Commercial license rights represent a portfolio of future milestone and royalty payment rights acquired from Selexis in April 2013 and April 2015 and Cormatrix in May 2016. Individual commercial license rights acquired are carried at allocated cost and approximate fair value. The carrying value of the license rights will be reduced on a pro-rata basis as revenue is realized over the term of the agreement. Declines in the fair value of license rights below their carrying value that are deemed to be other than temporary are reflected in earnings in the period such determination is made. As of December 31, 2016 , management does not believe there have been any events or circumstances indicating that the carrying amount of its commercial license rights may not be recoverable. Royalty income earned from Cormatrix were $1.5 million for the year ended December 31, 2016. Accounts receivable due from Cormatrix were $0.2 million at December 31, 2016. Relationships between the CorMatrix Parties As previously disclosed in Ligand’s filings, Jason Aryeh is a director of both Ligand and CorMatrix. Mr. Aryeh beneficially owns equity of CorMatrix representing less than 1% of CorMatrix’s outstanding equity. Mr. Aryeh recused himself from all of the board’s consideration of the purchase agreement between the Company and CorMatrix, including any financial analysis, the terms of the purchase agreement and the vote to approve the Purchase Agreement and the related transactions. Contingent Liabilities In connection with the Company’s acquisition of CyDex in January 2011 , the Company recorded a contingent liability for amounts potentially due to holders of the CyDex CVRs and former license holders. See footnote 7, Other Balance Sheet Details. The liability is periodically assessed based on events and circumstances related to the underlying milestones, royalties and material sales. In connection with the Company’s acquisition of Metabasis in January 2010 , the Company issued Metabasis stockholders four tradable CVRs for each Metabasis share. The fair values of the CVRs are remeasured at each reporting date through the term of the related agreement. Any change in fair value is recorded in the Company's consolidated statement of operations. Revenue Recognition We recognize revenue when persuasive evidence of an arrangement exists, delivery has occurred or service has been provided, title has transferred or access has been given, the price is fixed or determinable, there are no remaining customer acceptance requirements, and collectability of the resulting receivable is reasonably assured. Royalties on sales of products commercialized by the Company’s partners are recognized in the quarter reported by the respective partner. Generally, the Company receives royalty reports from its licensees approximately one quarter in arrears due to the fact that its agreements require partners to report product sales between 30 and 60 days after the end of the quarter. The Company recognizes royalty revenues when it can reliably estimate such amounts and collectability is reasonably assured. Under this accounting policy, the royalty revenues reported are not based upon estimates and such royalty revenues are typically reported to the Company by its partners in the same period in which payment is received. Revenue from material sales of Captisol is recognized upon transfer of title, which normally passes upon shipment to the customer, provided all other revenue recognition criteria have been met. All product returns are subject to the Company's credit and exchange policy, approval by the Company and a 20% restocking fee. To date, product returns have not been material to net material sales in any related period. The Company records revenue net of product returns, if any, and sales tax collected and remitted to government authorities during the period. The Company analyzes its revenue arrangements and other agreements to determine whether there are multiple elements that should be separated and accounted for individually or as a single unit of accounting. For multiple element contracts, arrangement consideration is allocated at the inception of the arrangement to all deliverables on the basis of relative selling price, using a hierarchy to determine selling price. Management first considers VSOE, then TPE and if neither VSOE nor TPE exist, the Company uses its best estimate of selling price. Many of the Company's revenue arrangements for Captisol involve a license agreement and the supply of manufactured Captisol product. Licenses may be granted to pharmaceutical companies for the use of Captisol product in the development of pharmaceutical compounds. The supply of the Captisol product may be for all phases of clinical trials and through commercial availability of the host drug or may be limited to certain phases of the clinical trial process. Management believes that the Company's licenses have stand-alone value at the outset of an arrangement because the customer obtains the right to use Captisol in its formulations without any additional input by the Company, and in a hypothetical stand-alone transaction, the customer would be able to procure inventory from another manufacturer in the absence of contractual provisions for exclusive supply by the Company. Other nonrefundable, up-front license fees are recognized as revenue upon delivery of the license, if the license is determined to have standalone value that is not dependent on any future performance by the Company under the applicable collaboration agreement. Nonrefundable contingent event-based payments are recognized as revenue when the contingent event is met, which is usually the earlier of when payments are received or collections are assured, provided that it does not require future performance by the Company. The Company occasionally has sub-license obligations related to arrangements for which it receives license fees, milestones and royalties. Management evaluates the determination of gross versus net reporting based on each individual agreement. Sales-based contingent payments from partners are accounted for similarly to royalties, with revenue recognized upon achievement of the sales targets assuming all other revenue recognition criteria for milestones are met. Revenue from development and regulatory milestones is recognized when earned, as evidenced by written acknowledgement from the collaborator, provided that (1) the milestone event is substantive, its achievability was not reasonably assured at the inception of the agreement, and the Company has no further performance obligations relating to that event, and (2) collectability is reasonably assured. If these criteria are not met, the milestone payment is recognized over the remaining period of the Company’s performance obligations under the arrangement. Preclinical Study and Clinical Trial Accruals Substantial portions of the Company’s preclinical studies and all of the Company’s clinical trials have been performed by third-party laboratories, CROs. The Company accounts for a significant portion of its clinical study costs according to the terms of its contracts with CROs. The terms of its CRO contracts may result in payment flows that do not match the periods over which services are provided to us under such contracts. The Company's objective is to reflect the appropriate preclinical and clinical trial expenses in its financial statements in the same period as the services occur. As part of the process of preparing its financial statements, the Company relies on cost information provided by its CROs. The Company is also required to estimate certain of its expenses resulting from its obligations under its CRO contracts. Accordingly, the Company's preclinical study and clinical trial accrual is dependent upon the timely and accurate reporting of CROs and other third-party vendors. The Company periodically evaluates its estimates to determine if adjustments are necessary or appropriate as more information becomes available concerning changing circumstances, and conditions or events that may affect such estimates. No material adjustments to preclinical study and clinical trial accrued expenses have been recognized to date. Research and Development Expenses Research and development expense consists of labor, material, equipment, and allocated facilities costs of the Company’s scientific staff who are working pursuant to the Company’s collaborative agreements and other research and development projects. Also included in research and development expenses are third-party costs incurred for the Company’s research programs including in-licensing costs, CRO costs and costs incurred by other research and development service vendors. We expense these costs as they are incurred. When we make payments for research and development services prior to the services being rendered, we record those amounts as prepaid assets on our consolidated balance sheet and we expense them as the services are provided Stock-Based Compensation The Company incurs share-based compensation expense related to restricted stock, its ESPP, and stock options Restricted stock units (RSU) and performance stock units (PSU) are all considered restricted stock. The fair value of restricted stock is determined by the closing market price of the Company’s common stock on the date of grant. The Company recognizes share-based compensation expense based on the fair value on a straight-line basis over the requisite service periods of the awards, taking into consideration estimated forfeitures. PSU represents a right to receive a certain number of shares of common stock based on the achievement of corporate performance goals and continued employment during the vesting period. At each reporting period, the Company reassesses the probability of the achievement of such corporate performance goals and any expense change resulting from an adjustment in the estimated shares to be released are treated as a cumulative catch-up in the period of adjustment. The Company uses the Black-Scholes-Merton option-pricing model to estimate the fair value of stock purchases under ESPP and stock options granted. The model assumptions include expected volatility, term, dividends, and the risk-free interest rate. The Company looks to historical volatility of the Company's stock to determine the expected volatility. The expected term of an award is based on historical forfeiture experience, exercise activity, and on the terms and conditions of the stock awards. The expected dividend yield is determined to be 0% given that the Company has never declared or paid regular cash dividends on its common stock and does not anticipate paying such cash dividends. The risk-free interest rate is based upon U.S. Treasury securities with remaining terms similar to the expected term of the share-based awards The Company grants options and restricted stock awards to employees and non-employee directors. Non-employee directors are accounted for as employees. Options and restricted stock awards granted to certain non-employee directors vest in equal monthly installments over one year from the date of grant. Options granted to employees vest 1/8 on the six month anniversary of the date of grant, and 1/48 each month thereafter for forty-two months. Restricted stock awards granted to employees vest over three years. All option awards generally expire ten years from the date of grant. Stock-based compensation expense for awards to employees and non-employee directors is recognized on a straight-line basis over the vesting period until the last tranche vests. Income Taxes The provision for income taxes is computed using the asset and liability method, under which deferred tax assets and liabilities are recognized for the expected future tax consequences of temporary differences between the financial reporting and tax bases of assets and liabilities, and for the expected future tax benefit to be derived from tax loss and credit carryforwards. Deferred tax assets and liabilities are determined using the enacted tax rates in effect for the years in which those tax assets are expected to be realized. The effect of a change in tax rates on deferred tax assets and liabilities is recognized in the provision for income taxes in the period that includes the enactment date. Deferred tax assets are regularly assessed to determine the likelihood they will be recovered from future taxable income. A valuation allowance is established when the Company believes it is more likely than not the future realization of all or some of a deferred tax asset will not be achieved. In evaluating the ability to recover deferred tax assets within the jurisdiction which they arise the Company considers all available positive and negative evidence. Factors reviewed include the cumulative pre-tax book income for the past three years, scheduled reversals of deferred tax liabilities, history of earnings and reliable forecasting, projections of pre-tax book income over the foreseeable future, and the impact of any feasible and prudent tax planning strategies. The Company recognizes the impact of a tax position in the financial statements only if that position is more likely than not of being sustained upon examination by taxing authorities, based on the technical merits of the position. Any interest and penalties related to uncertain tax positions will be reflected in income tax expense. Discontinued Operations In 2006, we entered into a purchase agreement with Eisai pursuant to which Eisai agreed to acquire our Oncology product line which included four marketed oncology drugs: ONTAK, Targretin capsules, Targretin gel and Panretin gel. Certain liabilities were recorded associated with the disposal of the product line. During the year ended December 31, 2016 we recognized a $1.1 million gain due to subsequent changes in certain estimates and liabilities previously recorded. We recorded a provision for income taxes related to the gain of $0.4 million . Income Per Share Basic income (loss) per share is calculated by dividing net income by the weighted-average number of common shares outstanding during the period. Diluted income (loss) 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 Potentially dilutive common shares consist of shares issuable under 2019 convertible senior notes, stock options and restricted stock. 2019 convertible senior notes have a dilutive impact when the average market price of the Company’s common stock exceeds the applicable conversion price of the respective notes. 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; the average amount of unrecognized compensation expense for restricted stock; and estimated tax benefits that will be recorded in additional paid-in capital when expenses related to equity awards become deductible. In loss periods, basic net loss per share and diluted net loss per share are identical since the effect of otherwise dilutive potential common shares is anti-dilutive and therefore excluded The following table presents the calculation of weighted average shares used to calculate basic and diluted earnings per share (in thousands): Year Ended December 31, 2016 2015 2014 Weighted average shares outstanding: 20,831 19,790 20,419 Dilutive potential common shares: Restricted stock — 56 36 Stock options — 882 978 2019 Convertible Senior Notes — 499 — Shares used to compute diluted income per share 20,831 21,228 21,433 Potentially dilutive shares excluded from calculation due to anti-dilutive effect 3,544 3,333 5,104 Comprehensive Income (Loss) Comprehensive income (loss) represents net income (loss) adjusted for the change during the periods presented in unrealized gains and losses on available-for-sale securities less reclassification adjustments for realized gains or losses included in net income (loss). The unrealized gains or losses are reported on the Consolidated Statements of Comprehensive Income (Loss).

Investment in Viking

Investment in Viking	12 Months Ended
	Dec. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Investment in Viking	Investment in Viking In 2014, the Company entered into a MLA with Viking to license the rights to five of the Company's programs to Viking. Under the terms of the MLA, no consideration was exchanged upon execution, but rather Viking agreed to issue shares of Viking common stock with an aggregate value of approximately $29.2 million upon consummation of Viking's IPO. As part of this transaction, the Company also extended a $2.5 million convertible loan to Viking under a LSA. As a result of these transactions, the Company determined it held a variable interest in Viking. The Company considered certain criteria in the accounting guidance for VIEs, and determined that Viking was a VIE and Ligand was the primary beneficiary of Viking. As a result, the Company consolidated Viking on its financial statements from May 2014 through May 2015, the effective date of Viking's IPO. The Company recorded 100% of the losses incurred as net loss attributable to noncontrolling interest because it was the primary beneficiary with no equity interest in the VIE. In May 2015, Viking completed the Viking IPO and issued the Company approximately 3.7 million shares of Viking common stock with an aggregate value of $29.2 million based on the IPO price of $8.00 per share. In connection with the Viking IPO, the Company purchased 1.1 million shares of Viking common stock for an aggregate price of $9.0 million at the initial public offering price. Upon completion of Viking’s IPO, the Company determined that Viking was no longer a VIE and the Company did not have any other element of control that would require consolidation of Viking. In May 2015, the Company deconsolidated Viking and began to account for its equity investment in Viking under the equity method and records its proportional share of Viking gains and losses in Loss from Viking Therapeutics in the Company's consolidated statement of operations. Viking is considered a related party as the Company maintains a seat on Viking's board of directors. In January 2016, the Company entered into an amendment to the LSA with Viking to extend the maturity of the convertible loan to May 2017, reduce the interest rate from 5.0% to 2.5% , and extend the lock up period by one year such that the Company may not sell, transfer, or dispose of any Viking securities prior to January 23, 2017. Additionally, upon the consummation of a subsequent capital financing transaction, Viking will be required to repay $1.5 million of the Viking Note obligation to the Company, with at least $0.3 million to be paid in cash and the remaining amount to be paid in the form and at the price of the Viking equity securities sold in the financing transaction. Upon maturity or further payments, the Company may elect to receive equity of Viking common stock or cash equal to 200% of the principal amount plus accrued and unpaid interest. The Company has opted to account for the Viking convertible note receivable at fair value. In April 2016, Viking closed its underwritten public offering of 7.5 million shares of common stock and warrants to purchase up to 7.5 million shares of its common stock at a price of $1.25 per share of its common stock and related warrants. The warrant has an exercise price of $1.50 per share, immediately exercisable and will expire on April 13, 2021. As part of this public offering, the Company purchased 560,000 shares of common stock and warrants to purchase 560,000 shares of Viking's common stock for a total purchase price of $0.7 million . The purchased shares of common stock and warrants are subject to the same terms as the shares issued in this offering. In addition, on April 13, 2016, pursuant to the terms of the amendment to the LSA that was entered in January 2016 between Ligand and Viking, Viking repaid $0.3 million of the convertible notes in cash, and issued the Company 960,000 shares of its common stock and warrants to purchase 960,000 shares of its common stock as repayment of $1.2 million of the convertible notes. The shares received as part of the repayment, like all Viking securities held by the Company, are subject to a lock-up period that ends on January 23, 2017 in accordance with the amended LSA. A gain of $0.3 million representing the fair market value of the warrants is included within other income for the year ended December 31, 2016. As of December 31, 2016, the aggregate fair value of the note receivable was 3.2 million . The Company's ownership in Viking decreased to 32.7% after the public offering and the repayment of the convertible notes and further decreased to 30.3% as of December 31, 2016. Accordingly, the book value of the Company's equity method investment in Viking decreased by $10.7 million . The resulting net loss was recognized in Loss from Viking in the Company's consolidated statement of operations for the year ended December 31, 2016. The Company reviews its investment in Viking on a regular basis and assesses whether events, changes in circumstances or the passage of time, in management's judgment, indicate that a loss in the market value of the investment may be other than temporary. This might include, but would not necessarily be limited to, the period of time during which the carrying value of our investment is significantly above the observed market value, a deterioration in Viking's financial condition, or an adverse event relating to its lead clinical programs. Based on the sustained low Viking common stock unit price during the year ended December 31, 2016, the Company determined that an other than temporary decrease in the value of its investment in Viking had occurred. The Company wrote down the value of its investment in Viking to its estimated fair value which resulted in impairment charges of $7.4 million for the year ended December 31, 2016.

Business Combinations

Business Combinations	12 Months Ended
	Dec. 31, 2016
Business Combinations [Abstract]
Business Combinations	Business Combinations On January 8, 2016, the Company acquired substantially all of the assets and liabilities of OMT. OMT is a biotechnology company engaged in the genetic engineering of animals for the generation of human therapeutic antibodies through its OmniAb® technology, which currently offers three transgenic animal platforms for license, including OmniRat®, OmniMouse® and OmniFlic®. The transaction, which was accounted for as a business combination, initially added 16 partnerships to the Company's portfolio and provides the Company with opportunities for further licensing and collaborations in the area. The aggregate acquisition consideration was $173.4 million , consisting of (in thousands, except per share amounts): Cash consideration $ 96,006 Total share consideration: Actual number of shares issued 790 Multiplied by: Ligand closing share price on January 8, 2016 98 Total share consideration $ 77,373 Total consideration $ 173,379 The acquisition consideration was allocated to the acquisition date fair values of acquired assets and assumed liabilities as follows (in thousands): Cash and cash equivalents $ 3,504 Accounts receivable 5 Income tax receivable 136 Prepaid expenses and other current assets 1 Deferred tax liabilities, net (55,708 ) Intangible asset with finite life - core technology 167,000 Liabilities assumed (1,528 ) Goodwill 59,969 Total consideration $ 173,379 The fair value of the core technology, or OMT's OmniAb technology, was based on the discounted cash flow method that estimated the present value of a hypothetical royalty stream derived from the licensing of the OmniAb technology. These projected cash flows were discounted to present value using a discount rate of 15.5% . The fair value of the core technology is being amortized on a straight-line basis over the estimated useful life of 20 years. The excess of the acquisition date consideration over the fair values assigned to the assets acquired and the liabilities assumed was $60.0 million and was recorded as goodwill, which is not deductible for tax purposes and is primarily attributable to OMT’s potential revenue growth from combining the OMT and Ligand businesses and workforce, as well as the benefits of access to different markets and customers. The following table presents supplemental pro forma information for the three and twelve months ended December 31, 2016 and December 31, 2015 , as if the acquisition of OMT had occurred on January 1, 2015 (in thousands except for income per share): Three months ended Twelve months ended December 31, December 31, 2016 2015 2016 2015 Revenue $ 38,185 $ 24,571 $ 111,449 $ 80,365 Net (loss) income $ (3,126 ) 5,888 $ 632 $ 222,788 Basic (loss) income per share: $ (0.15 ) $ 0.30 $ 0.03 $ 11.26 Diluted (loss) income per share: $ (0.15 ) $ 0.27 $ 0.03 $ 10.50 The unaudited pro forma consolidated results include pro forma adjustments that assume the acquisition occurred on January 1, 2015. The primary adjustments include: (i) the $0.3 million and $0.9 million for the three and twelve months ended December 31, 2015 , respectively, for share based compensation expenses related to the stock awards issued to the retained OMT employees after the acquisition, (ii) additional intangible amortization expense of $2.1 million and $6.3 million was included in the three and twelve months ended December 31, 2015 , respectively and (iii) a platform license fee of $3.0 million paid by OMT during the twelve months ended December 31, 2015 . The license agreement was terminated upon acquisition by Ligand. The adjustments also include $2.5 million license revenue recognized by OMT from January 1, 2016 to the acquisition date. The unaudited pro forma consolidated results are not necessarily indicative of what our consolidated results of operations actually would have been had we completed the acquisition on January 1, 2015. In addition, the unaudited pro forma consolidated results do not purport to project the future results of operations of the combined company nor do they reflect the expected realization of any cost savings associated with the acquisition.

Fair Value Measurement

Fair Value Measurement	12 Months Ended
	Dec. 31, 2016
Fair Value Disclosures [Abstract]
Fair Value Measurement	Fair Value Measurement The Company measures certain financial assets and liabilities at fair value on a recurring basis. Fair value is a market-based measurement that should be determined using assumptions that market participants would use in pricing an asset or liability. The Company establishes a three-level hierarchy to prioritize the inputs used in measuring fair value. The levels are described in the below with level 1 having the highest priority and level 3 having the lowest: Level 1 - Observable inputs such as quoted prices in active markets Level 2 - Inputs other than the quoted prices in active markets that are observable either directly or indirectly Level 3 - Unobservable inputs in which there is little or no market data, which require the Company to develop its own assumptions The following table provide a summary of the assets and liabilities that are measured at fair value on a recurring basis as of December 31, 2016 and 2015 (in thousands): Fair Value Measurements at Reporting Date Using December 31, 2016 Quoted Prices in Active Markets for Identical Assets Significant Other Observable Inputs Significant Unobservable Inputs Total (Level 1) (Level 2) (Level 3) Assets: Short-term investments (1) $ 122,296 $ 3,054 $ 119,242 $ — Note receivable Viking (2) 3,207 — — 3,207 Investment in warrants (3) 684 684 — — Total assets $ 126,187 $ 3,054 $ 119,242 $ 3,207 Liabilities: Current contingent liabilities - CyDex (4a) $ 101 $ — $ — $ 101 Long-term contingent liabilities - Metabasis (5) 1,413 — 1,413 — Long-term contingent liabilities - CyDex (4) 1,503 — — 1,503 Liability for amounts owed to former licensees (6) 371 371 — — Total liabilities $ 3,388 $ 371 $ 1,413 $ 1,604 Fair Value Measurements at Reporting Date Using December 31, 2015 Quoted Prices in Active Markets for Identical Assets Significant Other Observable Inputs Significant Unobservable Inputs Total (Level 1) (Level 2) (Level 3) Assets: Cash equivalents (7) $ 3,015 $ — $ 3,015 $ — Short-term investments (1) 92,775 6,786 85,989 — Note receivable Viking (2) 4,782 — — 4,782 Total assets $ 100,572 $ 6,786 $ 89,004 $ 4,782 Liabilities: Current contingent liabilities - CyDex (4) $ 7,812 $ — $ — $ 7,812 Current contingent liabilities-Metabasis (5) 2,602 — 2,602 — Long-term contingent liabilities - Metabasis (5) 1,355 — 1,355 — Long-term contingent liabilities - CyDex (4) 1,678 — — 1,678 Liability for amounts owed to former licensees (6) 794 794 — — Total liabilities $ 14,241 $ 794 $ 3,957 $ 9,490 (1) Investments in equity securities, are classified as level 1 as the fair value is determined using quoted market prices in active markets for the same securities. Short-term investments in marketable securities with maturities greater than 90 days are classified as 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. (2) The fair value of the convertible note receivable from Viking at December 31, 2015 was determined using a probability weighted option pricing model. The fair value is subjective and is affected by certain significant input to the valuation model such as the estimated volatility of the common stock, which was estimated to be 75% at December 31, 2016 and 65% at December 31, 2015 . Changes in these assumptions may materially affect the fair value estimate. For the year ended December 31, 2016 and December 31, 2015 , the Company reported a decrease in the fair value of the Viking convertible notes of $0.2 million and $0.8 million respectively in "Other, net" of the consolidated statement of operations. (3) Investment in warrants, which the Company received as a result of Viking’s partial repayment of the Viking note receivable and the Company’s 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. (4) The fair value of the liabilities for CyDex contingent liabilities were determined based on the income approach using a Monte Carlo analysis. The fair value is subjective and is affected by changes in inputs to the valuation model including management’s assumptions regarding revenue volatility, probability of commercialization of products, estimates of timing and probability of achievement of certain revenue thresholds and developmental and regulatory milestones which may be achieved and affect amounts owed to former license holders and CVR holders. Changes in these assumptions can materially affect the fair value estimate. (4a) The fair value of the liabilities for short-term CyDex contingent liabilities at December 31, 2016 disclosed herein represents the fair value of the estimated contingent considerations owed to former license holder only, which is determined based on the methodology described in (4) above. The contingent considerations owed to the Cydex CVR holders at December 31, 2016 is determined based on actual amount owed at December 31, 2016 as the Cydex CVR agreement ended at December 31, 2016. (5) The liability for CVRs for Metabasis are determined using quoted market prices in a market that is not active for the underlying CVR. (6) The liability for amounts owed to former licensees are determined using quoted market prices in active markets for the underlying investment received from a partner, a portion of which is owed to former licensees. (7) Highly liquid investments with maturities less than 90 days from the purchase date are recorded as cash equivalents that are classified as 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. The following table represents significant unobservable inputs used in determining the fair value of contingent liabilities assumed in the acquisition of CyDex: December 31, 2016 2015 Range of annual revenue subject to revenue sharing (1) N/A $22.5 million Revenue volatility 25% 25% Average of probability of commercialization 12.5% 73% Sales beta N/A 0.40 Credit rating BB BB Equity risk premium 6% 6% Market price of risk 3.2% N/A (1) For the December 31, 2015 valuation date, revenue subject to revenue sharing represent management’s estimate of the range of total annual revenue subject to revenue sharing (i.e. annual revenues in excess of $15 million ) through December 31, 2016, which is the term of the CVR agreement. For the December 31, 2016 valuation date, the Cydex CVR was determined based on the actual $5.0 million amount owed to Cydex CVR holders as the Cydex CVR agreement ended at December 31, 2016. This amount was subsequently paid in February 2017. A reconciliation of the level 3 financial instruments as of December 31, 2016 is as follows (in thousands): Assets: Fair value of level 3 financial instruments as of December 31, 2015 $ 4,782 Viking note receivable fair market value adjustment (215 ) Cash payment received as partial repayment of note receivable (300 ) Fair market value of stock received as partial repayment of note receivable (1,060 ) Fair value of level 3 financial instrument assets as of December 31, 2016 $ 3,207 Liabilities Fair value of level 3 financial instruments as of December 31, 2015 $ 9,490 Payments to CVR holders and other contingency payments (6,158 ) Fair value adjustments to contingent liabilities 3,259 Other (1) (4,987 ) Fair value of level 3 financial instruments as of December 31, 2016 $ 1,604 (1) Balance represents Cydex CVR obligation, which was determined based on actual amount owed to Cydex CVR holders as the Cydex CVR agreement ended at December 31, 2016. Other Fair Value Measurements-2019 Convertible Senior Notes In August 2014, the Company issued the 2019 Convertible Senior Notes. The Company uses a quoted market rate in an inactive market, which is classified as a Level 2 input, to estimate the current fair value of its 2019 Convertible Senior Notes. The estimated fair value of the 2019 Senior Convertible Notes was $331.7 million as of December 31, 2016 . The carrying value of the notes does not reflect the market rate. See Note 7 Financing Arrangements for additional information. Viking The Company records its investment in Viking under the equity method of accounting. The investment is subsequently adjusted for the Company’s share of Viking's operating results, and if applicable, cash contributions and distributions. See Note 2 Investment in Viking for additional information. The market value of the Company's investment in Viking was $7.5 million as of December 31, 2016 .

Lease Obligations

Lease Obligations	12 Months Ended
	Dec. 31, 2016
Leases [Abstract]
Lease Obligations	Lease Obligations The Company leases office facilities in California and Kansas. These leases expire between 2017 and 2023 . Total rent expense, net under all office leases for 2016 , 2015 and 2014 was $0.3 million , $0.4 million and $0.7 million , respectively. The following table provides a summary of operating lease obligations and payments expected to be received from sublease agreements as of December 31, 2016 (in thousands): Operating lease obligations: Lease Termination Date Less than 1 year 1-2 years 3-4 years Thereafter Total Corporate headquarters-San Diego, CA April 2023 $ 128 $ 267 $ 283 $ 197 $ 875 Office and research facility-La Jolla, CA June 2019 718 1,111 — — 1,829 Bioscience and Technology Business Center-Lawrence, KS December 2017 54 — — — 54 Total operating lease obligations $ 900 $ 1,378 $ 283 $ 197 $ 2,758 Sublease payments expected to be received: Office and research facility-La Jolla, CA June 2019 656 1,002 — — 1,658 Net operating lease obligations $ 244 $ 376 $ 283 $ 197 $ 1,100 Lease termination In November 2015, the Company entered into a lease termination agreement with its current lessor for the corporate headquarters facility located in La Jolla, California. The termination agreement accelerated the expiration date of the lease to April 2016, through which date, the Company is obligated to pay all base rent, operating expenses and other obligations due under the current lease. In conjunction with the execution of the termination agreement, the Company entered into a new lease agreement with a different lessor for its corporate headquarters located in San Diego, California. The new lease has an initial term of approximately 7 years and commenced in May 2016. The base rent under the new facility lease agreement is approximately $0.1 million per year for the first year, escalating 3.0% annually thereafter over the initial term. The Company has an option to extend the term of the lease for an additional five years. The lease is subject to additional charges for property management, common area maintenance and other costs. Lease exit obligations As of December 31, 2016 and 2015, the Company had lease exit obligations of $0 million and $0.9 million , respectively. The Company no longer records a lease obligation with respect to its vacated space expiring in June 2019 as the sublease proceeds offset the estimated lease exit obligations. For the years ended December 31, 2016 and 2015, the Company made cash payments, net of sublease payments received of $1.7 million and $3.3 million , respectively. The Company recognized adjustments for accretion and changes in leasing assumptions of $0.7 million , $0.9 million and $1.1 million for the years ended December 31, 2016, 2015 and 2014, respectively.

Financing Arrangements

Financing Arrangements	12 Months Ended
	Dec. 31, 2016
Debt Disclosure [Abstract]
Financing Arrangements	Financing Arrangements 2019 Convertible Senior Notes In August 2014, the Company issued $245.0 million aggregate principal amount of its 2019 Convertible Senior Notes, resulting in net proceeds of $239.3 million . The 2019 Convertible Senior Notes are convertible into common stock at an initial conversion rate of 13.3251 shares per $1,000 principal amount of convertible notes, subject to adjustment upon certain events, which is equivalent to an initial conversion price of approximately $75.05 per share of common stock. The notes bear cash interest at a rate of 0.75% per year, payable semi-annually. Holders of the 2019 Convertible Senior Notes may convert the notes at any time prior to the close of business on the business day immediately preceding May 15, 2019, under any of the following circumstances: (1) during any fiscal quarter (and only during such fiscal quarter) commencing after December 31, 2014 , 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 the Company's 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 the Company's 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. As of December 31 2016, the Company's last reported sale price exceeded the 130% threshold described above and accordingly the Convertible Notes have been classified as a current liability as of December 31, 2016. As a result, the related unamortized discount of $29.6 million was classified as temporary equity component of currently redeemable convertible notes on our consolidated balance sheet. The determination of whether or not the Convertible Notes are convertible as described above is made each quarter until maturity, conversion or repurchase. It is possible that the Convertible Notes may not be convertible in future periods, in which case the Convertible Notes would be classified as long-term debt, and the unamortized discount would be classified as permanent equity unless one of the other conversion events described above were to occur. On or after May 15, 2019 until the close of business on the second scheduled trading day immediately preceding August 15, 2019 , holders of the notes may convert all or a portion of their notes at any time. Upon conversion, Ligand must deliver cash to settle the principal and may deliver cash or shares of common stock, at the option of the Company, to settle any premium due upon conversion. The Company accounted for the debt and equity components of the 2019 Convertible Senior Notes by allocating the $245.0 million total proceeds between the debt component and the embedded conversion option, or equity component, due to Ligand's ability to settle the 2019 Convertible Senior Notes in cash for the principal portion and to settle any premium in cash or common stock, at the Company's election. The debt allocation was performed in a manner that reflected the Company's non-convertible borrowing rate for similar debt of 5.83% derived from independent valuation analysis. The initial debt value of $192.5 million accretes at 5.83% to reach $245.0 million at the maturity date. The equity component of the 2019 Convertible Senior Notes was recognized as a debt discount and represents the difference between the $245.0 million proceeds at issuance of the 2019 Convertible Senior Notes and the fair value of the debt allocation on their respective issuance dates. The debt discount is amortized to interest expense using the effective interest method over the expected life of a similar liability without an equity component. As of December 31, 2016 , the “if-converted value” exceeded the principal amount of the 2019 Convertible Senior Notes by $86.7 million . In connection with the issuance of the 2019 Convertible Senior Notes, the Company incurred $5.7 million of issuance costs, which primarily consisted of underwriting, legal and other professional fees. The portions of these costs allocated to the equity components totaling $1.2 million were recorded as a reduction to additional paid-in capital. The portions of these costs allocated to the liability components totaling $4.5 million were recorded as assets on the balance sheet at the time the debt was issued. Beginning in 2016, the unamortized issuance costs allocated to the liability components are recorded as part of debt discount on the consolidated balance sheet upon the Company's respective adoption of ASU 2015-03, Interest-Imputation of Interest: Simplifying the Presentation of Debt Issuance Costs . Issuance cost included in the unamortized debt discount was $2.5 million and $3.4 million as of December 31, 2016 and 2015, respectively. The Company determined the expected life of the debt discount for the 2019 Convertible Senior Notes to be equal to the original five -year term of the notes. The carrying value of the equity component related to the 2019 Convertible Senior Notes as of December 31, 2016 , net of issuance costs, was $51.3 million . Convertible Bond Hedge and Warrant Transactions In August 2014, to minimize the impact of potential dilution to the Company's common stock upon conversion of the 2019 Convertible Senior Notes, in August 2014, the Company entered into convertible bond hedges and sold warrants covering 3,264,643 shares of its common stock. The convertible bond hedges have an exercise price of $75.05 per share and are exercisable when and if the 2019 Convertible Senior Notes are converted. If upon conversion of the 2019 Convertible Senior Notes, the price of the Company's 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 the Company and are not part of the terms of the 2019 Convertible Senior Notes. Holders of the 2019 Convertible Senior Notes and warrants will not have any rights with respect to the convertible bond hedges. The Company paid $48.1 million for these convertible bond hedges and recorded the amount as a reduction to additional paid-in capital. Concurrently with the convertible bond hedge transactions, the Company entered into warrant transactions whereby it sold warrants to acquire approximately 3,264,643 shares of common stock with an exercise price of approximately $125.08 per share, subject to certain adjustments. None of the warrants have been exercised as of December 31, 2016. The warrants have various expiration dates ranging from November 13, 2019 to April 22, 2020. 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 Company received $11.6 million for these warrants and recorded this amount to additional paid-in capital. The common stock issuable upon exercise of the warrants will be in unregistered shares, and the Company does not have the obligation and does not intend to file any registration statement with the Securities and Exchange Commission registering the issuance of the shares under the warrants. The following table summarizes information about the liability components the Company's financing arrangement (dollars in thousands): December 31, 2016 December 31, 2015 2019 Convertible Senior Notes Principal amount outstanding $ 245,000 $ 245,000 Unamortized discount (32,090 ) (43,015 ) Total current portion of notes payable $ 212,910 $ 201,985 As of December 31, 2016 , there were no events of default or violation of any covenants under the Company's financing obligations.

Other Balance Sheet Details

Other Balance Sheet Details	12 Months Ended
	Dec. 31, 2016
Other Balance Sheet Details [Abstract]
Other Balance Sheet Details	Balance Sheet Account Details Short-term Investments The following table summarizes the various investment categories at December 31, 2016 and 2015 (in thousands): Cost Gross unrealized gains Gross unrealized losses Estimated fair value December 31, 2016 Short-term investments Bank deposits $ 40,715 $ 19 $ — $ 40,734 Corporate bonds 11,031 — (5 ) 11,026 Corporate equity securities 1,512 1,542 — 3,054 Commercial paper 33,074 2 (9 ) 33,067 Agency bonds 7,294 1 — 7,295 U.S. Government bonds 7,508 — (1 ) 7,507 Municipal bonds 19,624 — (11 ) 19,613 $ 120,758 $ 1,564 $ (26 ) $ 122,296 December 31, 2015 Short-term investments Bank deposits $ 43,043 $ — $ (4 ) $ 43,039 Corporate bonds 41,238 — (35 ) 41,203 Commercial paper 1,747 — — 1,747 Asset backed securities 10,020 — (5 ) 10,015 Corporate equity securities 1,843 4,944 — 6,787 $ 97,891 $ 4,944 $ (44 ) $ 102,791 Other current assets consist of the following (in thousands): December 31, 2016 2015 Prepaid expenses $ 1,864 $ 1,177 Other receivables 311 731 $ 2,175 $ 1,908 Property and equipment is stated at cost and consists of the following (in thousands): December 31, 2016 2015 Lab and office equipment $ 1,067 $ 2,248 Leasehold improvements 1,754 273 Computer equipment and software 569 632 3,390 3,153 Less accumulated depreciation and amortization (1,571 ) (2,781 ) $ 1,819 $ 372 Depreciation of equipment is computed using the straight-line method over the estimated useful lives of the assets which range from three to ten years. Leasehold improvements are amortized using the straight-line method over their estimated useful lives or their related lease term, whichever is shorter. Depreciation expense of $ 0.2 million , $0.2 million , and $0.3 million was recognized for the years ended December 31, 2016 , 2015 , and 2014 , respectively and is included in operating expenses. Goodwill and identifiable intangible assets consist of the following (in thousands): December 31, 2016 2015 Indefinite lived intangible assets IPR&D $ 12,246 $ 12,556 Goodwill 72,207 12,238 Definite lived intangible assets Complete technology 182,577 15,267 Less: Accumulated amortization (12,792 ) (3,762 ) Trade name 2,642 2,642 Less: Accumulated amortization (784 ) (652 ) Customer relationships 29,600 29,600 Less: Accumulated amortization (8,784 ) (7,304 ) Total goodwill and other identifiable intangible assets, net $ 276,912 $ 60,585 Amortization of finite lived intangible assets is computed using the straight-line method over the estimated useful life of the asset of 20 years. Amortization expense of $10.6 million , $2.4 million , and $2.4 million was recognized for the years ended December 31, 2016 and 2015 , and 2014 . Estimated amortization expense for the years ending December 31, 2017 through 2021 is $10.6 million per year. For each of the years ended December 31, 2016 , 2015 , and 2014 , there was no impairment of intangible assets with finite lives. Commercial license rights consist of the following (in thousands): December 31, December 31, 2016 2015 CorMatrix $ 17,696 $ — Selexis 8,602 8,602 26,298 8,602 Less: accumulated amortization (477 ) (48 ) Total commercial rights, net $ 25,821 $ 8,554 Accrued liabilities consist of the following (in thousands): December 31, 2016 2015 Compensation $ 2,603 $ 1,711 Legal 829 726 Amounts owed to former licensees 899 915 Royalties owed to third parties 942 823 Other 1,124 1,230 $ 6,397 $ 5,405 In connection with the acquisition of CyDex in January 2011, we issued a series of CVRs and also assumed certain contingent liabilities. We may be required to make additional payments upon achievement of certain clinical and regulatory milestones to the CyDex shareholders and former license holders. We pay CyDex shareholders, through 2016, 20% of all CyDex-related revenue, but only to the extent that, and beginning only when, CyDex-related revenue for the year exceeds $15.0 million ; plus an additional 10% of all CyDex-related revenue recognized during such year, but only to the extent, and beginning only when aggregate CyDex-related revenue for such year exceeds $35.0 million . In connection with the acquisition of Metabasis in January 2010, we entered into four CVR agreements with Metabasis shareholders. The CVRs entitle the holders to cash payments as frequently as every six months as proceeds are received by us upon the sale or licensing of any of the Metabasis drug development programs and upon the achievement of specified milestones. Contingent liabilities consist of the following (in millions): December 31, 2014 Payments Fair Value Adjustment December 31, 2015 Payments Fair Value Adjustment December 31, 2016 Cydex $ 11.5 $ (5.8 ) $ 3.8 $ 9.5 (6.2 ) $ 3.3 $ 6.6 Metabasis 3.7 (0.9 ) 1.2 4.0 (2.6 ) 0.1 1.5 Total 15.2 (6.7 ) 5.0 13.5 (8.8 ) 3.4 8.1 Other long-term liabilities consist of the following (in thousands): December 31, 2016 2015 Deferred rent $ 357 $ — Deposits 43 268 Other 287 29 $ 687 $ 297

Stockholders' Equity

Stockholders' Equity	12 Months Ended
	Dec. 31, 2016
Equity [Abstract]
Stockholders' Equity	Stockholders’ Equity Share-based Compensation Expense The following table summarizes stock-based compensation expense (in thousands): December 31, 2016 2015 2014 Stock-based compensation expense as a component of: Research and development expenses $ 8,836 $ 4,080 $ 3,595 General and administrative expenses 10,057 8,378 7,675 $ 18,893 $ 12,458 $ 11,270 Stock Plans In May 2009, the Company’s stockholders approved the amendment and restatement of the Company’s 2002 Stock Incentive Plan (the “Amended 2002 Plan”). The Company’s 2002 Stock Incentive Plan was amended to (i) increase the number of shares available for issuance under the Amended 2002 Plan by 1.3 million shares, (ii) revise the list of performance criteria that may be used by the compensation committee for purposes of granting awards under the Amended 2002 Plan that are intended to qualify as performance-based compensation under Section 162(m) of the Internal Revenue Code, as amended, and (iii) eliminate the automatic option grant program for non-employee directors, the director fee stock issuance program and the director fee option grant program, which programs have been superseded by the Company’s amended and restated Director Compensation Policy. Additionally, in May 2012 and May 2016, the Company’s stockholders approved an amendment and restatement of the Company’s 2002 Stock Incentive Plan to increase the number of shares available for issuance by 1.8 million and 0.9 million shares, respectively. As of December 31, 2016 , there were 1.0 million shares available for future option grants or direct issuance under the Amended 2002 Plan. Following is a summary of the Company’s stock option plan activity and related information: Shares Weighted Average Exercise Price Weighted Average Remaining Contractual Term in Years Aggregate Intrinsic Value (In thousands) Balance at December 31, 2015 1,683,341 $ 34.19 6.48 $ 124,800 Granted 263,489 92.09 Exercised (164,440 ) 38.08 Forfeited (28,115 ) 60.17 Balance at December 31, 2016 1,754,275 42.12 6.19 104,247 Exercisable at December 31, 2016 1,298,561 30.21 5.44 92,723 Options vested and expected to vest as of December 31, 2016 1,752,275 $ 42.12 6.19 $ 104,247 The weighted-average grant-date fair value of all stock options granted during 2016 , 2015 and 2014 was $46.53 , $35.39 and $46.20 per share, respectively. The total intrinsic value of all options exercised during 2016 , 2015 and 2014 was approximately $12.0 million , $20.7 million and $15.3 million , respectively. Cash received from options exercised, net of fees paid, in 2016 , 2015 and 2014 was $6.2 million , $8.7 million and $4.4 million , respectively. Following is a further breakdown of the options outstanding as of December 31, 2016 : Range of exercise prices Options outstanding Weighted average remaining life in years Weighted average exercise price Options exercisable Weighted average exercise price $8.58 - $12.53 247,574 3.94 $ 9.98 247,574 $ 9.98 $10.12 - $12.81 76,100 4.92 11.38 76,100 11.38 $14.47 - $14.47 288,887 5.11 14.47 274,887 14.47 $16.14 - $21.00 106,242 1.85 17.76 106,242 17.76 $21.92 - $21.92 225,105 6.13 21.92 213,199 21.92 $32.00 - $53.34 72,330 6.02 36.18 62,747 34.73 $56.26 - $59.26 183,595 8.11 56.26 70,877 56.26 $63.58 - $68.62 26,382 7.50 67.20 21,976 67.50 $74.42 - $74.42 227,856 7.12 74.42 162,233 74.42 $85.79 - $138.53 298,204 9.03 93.19 62,726 89.71 $8.58 – $138.53 1,752,275 6.19 $ 42.12 1,298,561 $ 30.21 The assumptions used for the specified reporting periods and the resulting estimates of weighted-average grant date fair value per share of options granted: Year Ended December 31, 2016 2015 2014 Risk-free interest rate 1.3%-1.9% 1.7%-2.0% 1.9% Expected volatility 48%-50% 50%-58% 62%-69% Expected term 6.6 to 6.7 years 6.5 years 6.0 years Forfeiture rate 5.00% 8.52% 8.6%-9.7% As of December 31, 2016 , there was $17.5 million of total unrecognized compensation cost related to non-vested stock options. That cost is expected to be recognized over a weighted average period of 2.22 years . Restricted Stock Activity The following is a summary of the Company’s restricted stock activity and related information: Shares Weighted-Average Grant Date Fair Value Outstanding at December 31, 2015 130,749 $ 60.36 Granted 234,855 95.31 Vested (54,421 ) 66.79 Forfeited (2,483 ) 67.95 Outstanding at December 31, 2016 308,700 $ 86.61 As of December 31, 2016 , unrecognized compensation cost related to non-vested stock awards amounted to $13.8 million . That cost is expected to be recognized over a weighted average period of 1.14 years. Employee Stock Purchase Plan As of December 31, 2016, 70,406 shares of the Company's common stock are available for future issuance under it's Amended Employee Stock Purchase Plan, or ESPP. The ESPP permits eligible employees to purchase up to 1,250 shares of Ligand common stock per calendar year at a discount through payroll deductions. The price at which stock is purchased under the ESPP is equal to 85% of the fair market value of the common stock on the first of a six month offering period or purchase date, whichever is lower. There were 1,961 , 3,374 and 3,774 shares issued under the ESPP in 2016, 2015 and 2014, respectively. Share Repurchases During the years ended December 31, 2016 , 2015 and 2014 the Company repurchased 40,500 shares for $3.9 million , 6,120 shares for $0.5 million , and 1,253,425 shares for $68.0 million , respectively. In September 2015, the Company's Board of Directors authorized the Company to repurchase up to $200.0 million of its own stock in privately negotiated and open market transactions for a period of up to three years, subject to the Company's evaluation of market conditions. Authorization to repurchase up to an additional $195.6 million of its common stock remained as of December 31, 2016.

Litigation

Litigation	12 Months Ended
	Dec. 31, 2016
Commitments and Contingencies Disclosure [Abstract]
Litigation	Litigation The Company records 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, The Company records the minimum estimated liability related to the claim in accordance with FASB ASC Topic 450 Contingencies. As additional information becomes available, the Company assesses the potential liability related to its pending litigation and revises its estimates. Revisions in the Company's estimates of potential liability could materially impact its results of operations. Securities Litigation In 2012, a federal securities class action and shareholder derivative lawsuit was filed in Pennsylvania alleging that the Company and its chief executive officer assisted various breaches of fiduciary duties based on the Company’s purchase of a licensing interest in a development-stage pharmaceutical program from the Genaera Liquidating Trust in 2010 and the Company’s subsequent sale of half of its interest in the transaction to Biotechnology Value Fund, Inc. Plaintiff filed a second amended complaint in February 2015, which the Company moved to dismiss in March 2015. The district court granted the motion to dismiss on November 11, 2015. The plaintiff has appealed that ruling to the U.S. Third Circuit Court of Appeals. The Company intends to continue to vigorously defend against the claims against the Company and its chief executive officer. The outcome of the matter is not presently determinable. Paragraph IV Certification by Par Pharmaceuticals On January 7, 2016, the Company received a paragraph IV certification from Par Sterile Products, LLC, a subsidiary of Par Pharmaceuticals, Inc., or Par, advising us that it had filed an ANDA with the FDA seeking approval to market a generic version of Merck’s NOXAFIL-IV product. On February 19, 2016, Merck filed an action against Par in the United States District Court for the District of New Jersey, asserting that Par's manufacture, use or sale of the product for which the ANDA was submitted would infringe Merck's U.S. Patent No. 9,023,790. On October 31, 2016, the parties entered into a consent judgment dismissing all claims, counterclaims, affirmative defenses and demands. The parties have reported to the court that they entered into a confidential settlement agreement, and that they submitted the agreement to the Federal Trade Commission and the United States Department of Justice pursuant to Section 112(a) of the Medicare Prescription Drug, Improvement and Modernization Act of 2003. Class Action Lawsuit In November 2016, a putative shareholder class action lawsuit was filed in the United States District Court for the Southern District of California against the Company, its chief executive officer and chief financial officer. The complaint alleges violations of Sections 10(b) and 20(a) of the Securities Exchange Act of 1934, and Rule 10b-5 promulgated thereunder, and seeks unspecified compensatory damages and other relief on behalf of a purported class of purchasers of the Company’s securities between November 9, 2015 and November 14, 2016, inclusive. The complaint’s allegations relate generally to the Company’s November 2016 restatement of certain prior period financial statements. In January 2017, a purported Company shareholder filed a motion for appointment of lead counsel and lead plaintiff. The motion is scheduled to be heard by the Court in March 2017. No trial date has been set. The Company believes that the lawsuit is without merit and intends to vigorously defend against the lawsuit.

Income Taxes

Income Taxes	12 Months Ended
	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The components of the income tax expense (benefit) for continuing operations are as follows (in thousands): Year Ended December 31, 2016 2015 2014 Current expense (benefit): Federal $ 21 $ 11 $ 15 State 12 7 19 33 18 34 Deferred expense (benefit): Federal 10,534 (167,413 ) 406 State (240 ) (24,720 ) (30 ) $ 10,327 $ (192,115 ) $ 410 A reconciliation of income tax expense (benefit) from continuing operations to the amount computed by applying the statutory federal income tax rate to the net income (loss) from continuing operations is summarized as follows: Year Ended December 31, 2016 2015 2014 Amounts computed at statutory federal rate $ 2,786 $ 13,198 $ 3,843 State taxes net of federal benefit 175 386 697 Meals & entertainment 16 16 9 Imputed interest (1 ) (161 ) 53 Section 162(m) limitation 94 197 490 Contingent liabilities 1,225 1,684 1,748 Stock-based compensation 263 140 89 Expired NOLs — 232 88 Research and development credits (1,525 ) 304 (113 ) Change in uncertain tax positions 1,423 27,188 7 Rate change for changes in state law 25 (5,756 ) 119 APIC Excess Tax Benefit True Up (622 ) — — Increase in deferred tax assets from completion of 382 analysis (120 ) 3,329 43 Avinza true up — (2,107 ) — Change in valuation allowance 6,283 (231,370 ) (7,243 ) Other 305 605 580 $ 10,327 $ (192,115 ) $ 410 Significant components of the Company’s deferred tax assets and liabilities as of December 31, 2016 and 2015 are shown below. The Company assesses the positive and negative evidence to determine if sufficient future taxable income will be generated to use the existing deferred tax assets. The Company's evaluation of evidence resulted in management concluding that the majority of the Company's deferred tax assets will be realized. However, the Company maintains a valuation allowance to offset certain net deferred tax assets as management believes realization of such assets are uncertain as of December 31, 2016 , 2015 and 2014 . The valuation allowance increased $6.3 million in 2016, decreased $231.7 million in 2015 and decreased $7.2 million in 2014. December 31, 2016 2015 (in thousands) Deferred assets: Net operating loss carryforwards $ 150,226 $ 160,595 Research credit carryforwards 26,878 25,613 Fixed assets and intangibles 4,385 8,839 Accrued expenses 943 1,523 Contingent liabilities 578 707 Deferred revenue — 3 Present value of royalties 591 3,007 Deferred rent 45 68 Capital Loss Carryforward 4,432 — Viking Equity Method Investment 5,692 1,840 Other 19,312 15,441 213,082 217,636 Valuation allowance for deferred tax assets (15,349 ) (9,066 ) Net deferred tax assets $ 197,733 $ 208,570 Deferred tax liabilities: Retrophin fair value adjustment $ (52 ) $ (1,256 ) Convertible debt (1,196 ) (1,844 ) Identified intangibles (68,631 ) (12,770 ) Identified indefinite lived intangibles (3,963 ) (3,617 ) Total $ 123,891 $ 189,083 Sections 382 and 383 of the U.S. tax code impose limitations (“382 and 383 limitations”) on the annual utilization of operating loss and credit carryforwards whenever a greater than fifty percent change in the ownership of a company occurs within a three year period. In addition to the annual limitations on operating loss and credit carryforwards, Section 382 can also restrict the utilization of certain post change losses if the tax basis in assets exceeds the fair value of assets (“net unrealized built in loss”) at the date of an ownership change. Companies with operating loss and credit carryforwards are required to test the cumulative three year change whenever there is an equity transaction that impacts the ownership of holders of more than five percent of the Company’s stock. During 2016, the Company completed a rollforward analysis through December 31, 2016. As a result of the rollforward analysis, it was determined that no additional ownership changes occurred at the Company within the meaning of section 382 since June 20, 2007 . Future changes in the ownership of the Company could place additional restrictions on the Company’s ability to utilize operating loss and credit carryforwards arising through December 31, 2016 . As of December 31, 2016 , the Company had federal and state net operating loss carryforwards set to expire through 2036 of $446.3 million and $140.5 million of state net operating loss carryforwards. The Company also has $21.9 million of federal research and development credit carryforwards, which expire through 2036 . The Company has $19.4 million of California research and development credit carryforwards that have no expiration date. The Company accounts for income taxes by evaluating a probability threshold that a tax position must meet before a financial statement benefit is recognized. The minimum threshold is a tax position that is more likely than not to be sustained upon examination by the applicable taxing authority, including resolution of any related appeals or litigation processes, based on the technical merits of the position. The Company’s remaining liabilities for uncertain tax positions are presented net of the deferred tax asset balances on the accompanying consolidated balance sheet. A reconciliation of the amount of unrecognized tax benefits at December 31, 2016 , 2015 and 2014 is as follows (in thousands): December 31, 2016 2015 2014 Balance at beginning of year $ 36,452 $ 8,524 $ 8,504 Additions based on tax positions related to the current year 70 154 40 Additions for tax positions of prior years 2,408 28,224 — Reductions for tax positions of prior years (160 ) (450 ) (20 ) Balance at end of year $ 38,770 $ 36,452 $ 8,524 Included in the balance of unrecognized tax benefits at December 31, 2016 is $35.5 million of tax benefits that, if recognized would impact the effective rate. There are no positions for which it is reasonably possible that the uncertain tax benefit will significantly increase or decrease within twelve months. The Company recognizes interest and penalties related to uncertain tax positions in income tax expense. As of December 31, 2016 and December 31, 2015 , the Company recognized an immaterial amount of interest and penalties. The Company files income tax returns in the United States and in various state jurisdictions with varying statutes of limitations. The federal statute of limitation remains open for the 2013 tax year to present. The state income tax returns generally remain open for the 2012 tax years through present. Net operating loss and research credit carryforwards arising prior to these years are also open to examination if and when utilized. In March 2016, the Financial Accounting Standards Board (the “FASB”) issued Accounting Standards Update No. 2016-09, Compensation - Stock Compensation (Topic 718): Improvements to Employee Shared-Based Payment Accounting (''ASU 2016-09''). ASU 2016-09 simplifies how several aspects of share-based payments are accounted for and presented in the financial statements. ASU 2016-09 is effective for public companies for annual reporting periods beginning after December 15, 2016. The Company will adopt this ASU in the first quarter of 2017. The Company has excess tax federal and state benefits for which a benefit could not be previously recognized of approximately $13.7 million and $11.5 million , respectively. Upon adoption the balance of the unrecognized excess tax benefits will be reversed with the impact recorded to retained earnings including any change to the valuation allowance as a result of the adoption.

Summary of Unaudited Quarterly

Summary of Unaudited Quarterly Financial Information	12 Months Ended
	Dec. 31, 2016
Quarterly Financial Information Disclosure [Abstract]
Summary of Unaudited Quarterly Financial Information	Summary of Unaudited Quarterly Financial Information The following financial information reflects all normal recurring adjustments, which are, in the opinion of management, necessary for a fair statement of the results and cash flows of interim periods. Summarized quarterly data for fiscal years 2016 and 2015 are as follows (in thousands, except per share amounts): First Quarter Second Quarter Third Quarter Fourth Quarter 2016 Total revenues $ 29,648 $ 19,521 $ 21,619 $ 38,185 Total operating costs and expenses 14,552 15,552 16,153 18,831 Income tax (expense) benefit (3,694 ) 3,881 (160 ) (10,354 ) Income (loss) from continuing operations 5,877 (6,170 ) 1,051 (3,125 ) Income from discontinued operations 731 — — — Net income (loss) 6,608 (6,170 ) 1,051 (3,125 ) Basic per share amounts: Net income (loss) $ 0.32 $ (0.30 ) $ 0.05 $ 0.15 Diluted per share amounts: Net income (loss) 0.30 (0.30 ) 0.05 0.15 Weighted average shares—basic 20,708 20,832 20,887 20,898 Weighted average shares—diluted 22,284 20,832 22,997 20,898 2015 Total revenues $ 14,602 $ 18,418 $ 17,701 $ 21,193 Total operating costs and expenses 11,253 14,053 9,104 10,175 Income tax (expense) benefit (15 ) (265 ) 191,881 514 (Loss) income from continuing operations (89 ) 22,027 199,165 6,341 Net loss attributable to noncontrolling interests (843 ) (1,537 ) — — Net income 754 23,564 199,165 6,341 Basic per share amounts: Net income $ 0.04 $ 1.19 $ 10.01 $ 0.32 Diluted per share amounts: Net income $ 0.04 $ 1.11 $ 9.28 $ 0.29 Weighted average shares—basic 19,612 19,725 19,887 19,933 Weighted average shares—diluted 20,631 21,276 21,460 21,542

Summary of Significant Accounti

Summary of Significant Accounting Policies (Policies)	12 Months Ended
	Dec. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Reclassifications	Reclassifications Certain reclassifications have been made to the previously issued statement of operations for comparability purposes. These reclassifications had no effect on the reported net income, stockholders' equity and operating cash flows as previously reported.
Principles of Consolidation	Principles of Consolidation The accompanying consolidated financial statements include Ligand and its wholly owned subsidiaries. All significant intercompany accounts and transactions have been eliminated in consolidation.
Use of Estimates	Use of Estimates The preparation of consolidated financial statements in conformity with U.S. 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
Recent Accounting Pronouncements	Recent Accounting Pronouncements I n May 2014, the FASB issued new guidance related to revenue recognition, Accounting Standards Update 2014-09, Revenue from Contracts with Customers (“ASC 606”), which outlines a comprehensive revenue recognition model and supersedes most current revenue recognition guidance. The new guidance requires a company to recognize revenue upon transfer of goods or services to a customer at an amount that reflects the expected consideration to be received in exchange for those goods or services. ASC 606 defines a five-step approach for recognizing revenue, which may require a company to use more judgment and make more estimates than under the current guidance. The new guidance becomes effective in calendar year 2018 and early adoption in calendar year 2017 is permitted. Two methods of adoption are permitted: (a) full retrospective adoption, meaning the standard is applied to all periods presented; or (b) modified retrospective adoption, meaning the cumulative effect of applying the new guidance is recognized at the date of initial application as an adjustment to the opening retained earnings balance. We are undertaking a substantial effort to be ready for adoption of ASC 606. Some of our contracts have distinct terms which will need to be evaluated separately. We have started our preliminary assessment of these contracts and although we have not completed our assessment and are in the process of reviewing our contracts, we anticipate this standard will have a material impact on our consolidated financial statements by accelerating the timing of revenue recognition for revenues related to royalties, and potentially certain contingent milestone based payments. We intend to adopt ASC 606 starting as of January 1, 2018 using the modified retrospective method. In August 2014, the FASB issued Accounting Standards Update No. 2014-15, Presentation of Financial Statements -Going Concern (Subtopic 205-40). This accounting standard requires management to perform interim and annual assessments of the entity's ability to continue its business operations within one year of the date of issuance of its financial statements. The Company must then provide certain disclosure if there is substantial doubt about its ability to continue as a going concern. As of December 31, 2016, the Company has adopted this standard with no impact to the financial statements. In March 2016, the FASB issued ASU 2016-09 amending several aspects of share-based payment accounting. This guidance requires all excess tax benefits and tax deficiencies to be recorded in the income statement when the awards vest or are settled, with prospective application required. The guidance also changes the classification of such tax benefits or tax deficiencies on the statement of cash flows from a financing activity to an operating activity, with retrospective or prospective application allowed. The guidance requires the classification of employee taxes paid when an employer withholds shares for tax-withholding purposes as a financing activity on the statement of cash flows, with retrospective application required. In addition, the guidance provides for an option to recognize gross stock compensation expense with actual forfeitures recognized as they occur. The updated guidance is effective in fiscal year 2018 and early adoption in fiscal year 2017 is permitted. We are currently evaluating the adoption timing as well as the impact of the new guidance on our consolidated financial statements and related disclosures. In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses: Measurement of Credit Losses on Financial Instruments which requires that expected credit losses relating to financial assets measured on an amortized cost basis and available-for-sale debt securities be recorded through an allowance for credit losses. ASU 2016-13 limits the amount of credit losses to be recognized for available-for-sale debt securities to the amount by which carrying value exceeds fair value and also requires the reversal of previously recognized credit losses if fair value increases. The new standard will be effective for us in fiscal year 2020 and early adoption in fiscal 2019 is permitted. We are currently evaluating the effect that the updated standard will have on our consolidated financial statements. In August 2016 the FASB issued ASU No. 2016-15 Statement of Cash Flows (Topic 230) , Classification of Certain Cash Receipts and Cash Payments. The guidance addresses the classification of cash flows related to (1) debt prepayment or extinguishment costs, (2) settlement of zero-coupon debt instruments or other debt instruments with coupon rates that are insignificant in relation to the effective interest rate of the borrowing, (3) contingent consideration payments made after a business combination, (4) proceeds from the settlement of insurance claims, (5) proceeds from the settlement of corporate-owned life insurance, including bank-owned life insurance, (6) distributions received from equity method investees and (7) beneficial interests in securitization transactions. The guidance also clarifies how the predominance principle should be applied when cash receipts and cash payments have aspects of more than one class of cash flows. The new guidance will be effective for fiscal year 2018 and early adoption is permitted. We are currently evaluating the effect that the updated standard will have on our consolidated financial statements. We expect contingent consideration payment presentation will change to conform to the standard. We do not believe that any other recently issued, but not yet effective accounting pronouncements, if adopted, would have a material impact on our consolidated financial statements or disclosures.
Concentrations of Credit Risk	Concentrations of Business Risk Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash equivalents and investments. The Company invests its excess cash principally in United States government debt securities, investment grade corporate debt securities and certificates of deposit. The Company has established guidelines relative to diversification and maturities that maintain safety and liquidity. These guidelines are periodically reviewed and modified to take advantage of trends in yields and interest rates.
Cash Equivalents and Short-term Investments	Cash Equivalents & Short Term Investments Cash equivalents consist of all investments with maturities of three months or less from the date of acquisition. Short-term investments primarily consist of investments in debt securities that have effective maturities greater than three months and less than twelve months from the date of acquisition. The Company classifies its short-term investments as "available-for-sale". Such investments are carried at fair value, with unrealized gains and losses included in the statement of comprehensive income (loss). The Company determines the cost of investments based on the specific identification method.
Accounts Receivable	Accounts Receivable Trade accounts receivable are recorded at the net invoice value and are not interest bearing. The Company considers receivables past due based on the contractual payment terms which range from 30 to 90 days. The Company reserves specific receivables if collectibility is no longer reasonably assured. The Company re-evaluates such reserves on a regular basis and adjusts its reserves as needed. Once a receivable is deemed to be uncollectible, such balance is charged against the reserve.
Inventory	Inventory Inventory, which consists of finished goods, is stated at the lower of cost or market value. The Company determines cost using the first-in, first-out method. The Company analyzes its inventory levels periodically and writes down inventory to its net realizable value if it has become obsolete, has a cost basis in excess of its expected net realizable value or is in excess of expected requirements.
Property and Equipment, net	Property and Equipment Property and equipment are stated at cost, subject to review for impairment, and depreciated over the estimated useful lives of the assets, which generally range from three to ten years, using the straight-line method. Amortization of leasehold improvements is recorded over the shorter of the lease term or estimated useful life of the related asset. Maintenance and repairs are charged to operations as incurred. When assets are sold, or otherwise disposed of, the cost and related accumulated depreciation are removed from the accounts and any gain or loss is included in operating expense.
Goodwill	Goodwill, which has an indefinite useful life, represents the excess of cost over fair value of net assets acquired. The change in the carrying value of goodwill during the year ended December 31, 2016, was due to the acquisition of OMT. Goodwill is reviewed for impairment at least annually during the fourth quarter, or more frequently if an event occurs indicating the potential for impairment. During its goodwill impairment review, the Company may assess qualitative factors to determine whether it is more likely than not that the fair value of its reporting unit is less than its carrying amount, including goodwill. The qualitative factors include, but are not limited to, macroeconomic conditions, industry and market considerations, and the overall financial performance of the Company. If, after assessing the totality of these qualitative factors, the Company determines that it is not more likely than not that the fair value of its reporting unit is less than its carrying amount, then no additional assessment is deemed necessary. Otherwise, the Company proceeds to perform the two-step test for goodwill impairment. The first step involves comparing the estimated fair value of the reporting unit with its carrying value, including goodwill. If the carrying amount of the reporting unit exceeds its fair value, the Company performs the second step of the goodwill impairment test to determine the amount of loss, which involves comparing the implied fair value of the goodwill to the carrying value of the goodwill. The Company may also elect to bypass the qualitative assessment in a period and elect to proceed to perform the first step of the goodwill impairment test. The Company performed its annual assessment for goodwill impairment in the fourth quarter of 2016 by assessing qualitative factors, noting no impairment.
Acquired in-process research and development	Intangible assets related to acquired IPR&D are considered to be indefinite-lived until the completion or abandonment of the associated research and development efforts. During the period the assets are considered to be indefinite-lived, they are not amortized but are tested for impairment on an annual basis and between annual tests if the Company becomes aware of any events occurring or changes in circumstances that would indicate a reduction in the fair value of the IPR&D projects below their respective carrying amounts. If and when development is complete, which generally occurs if and when regulatory approval to market a product is obtained, the associated assets would be deemed finite-lived and would then be amortized based on their respective estimated useful lives at that point in time. The Company performed its annual assessment for IPR&D impairment in 2016, noting no impairment.
Commercial license rights	Commercial license rights Commercial license rights represent a portfolio of future milestone and royalty payment rights acquired from Selexis in April 2013 and April 2015 and Cormatrix in May 2016. Individual commercial license rights acquired are carried at allocated cost and approximate fair value. The carrying value of the license rights will be reduced on a pro-rata basis as revenue is realized over the term of the agreement. Declines in the fair value of license rights below their carrying value that are deemed to be other than temporary are reflected in earnings in the period such determination is made.
Contingent Liabilities	Contingent Liabilities In connection with the Company’s acquisition of CyDex in January 2011 , the Company recorded a contingent liability for amounts potentially due to holders of the CyDex CVRs and former license holders. See footnote 7, Other Balance Sheet Details. The liability is periodically assessed based on events and circumstances related to the underlying milestones, royalties and material sales. In connection with the Company’s acquisition of Metabasis in January 2010 , the Company issued Metabasis stockholders four tradable CVRs for each Metabasis share. The fair values of the CVRs are remeasured at each reporting date through the term of the related agreement. Any change in fair value is recorded in the Company's consolidated statement of operations.
Revenue Recognition	Revenue Recognition We recognize revenue when persuasive evidence of an arrangement exists, delivery has occurred or service has been provided, title has transferred or access has been given, the price is fixed or determinable, there are no remaining customer acceptance requirements, and collectability of the resulting receivable is reasonably assured. Royalties on sales of products commercialized by the Company’s partners are recognized in the quarter reported by the respective partner. Generally, the Company receives royalty reports from its licensees approximately one quarter in arrears due to the fact that its agreements require partners to report product sales between 30 and 60 days after the end of the quarter. The Company recognizes royalty revenues when it can reliably estimate such amounts and collectability is reasonably assured. Under this accounting policy, the royalty revenues reported are not based upon estimates and such royalty revenues are typically reported to the Company by its partners in the same period in which payment is received. Revenue from material sales of Captisol is recognized upon transfer of title, which normally passes upon shipment to the customer, provided all other revenue recognition criteria have been met. All product returns are subject to the Company's credit and exchange policy, approval by the Company and a 20% restocking fee. To date, product returns have not been material to net material sales in any related period. The Company records revenue net of product returns, if any, and sales tax collected and remitted to government authorities during the period. The Company analyzes its revenue arrangements and other agreements to determine whether there are multiple elements that should be separated and accounted for individually or as a single unit of accounting. For multiple element contracts, arrangement consideration is allocated at the inception of the arrangement to all deliverables on the basis of relative selling price, using a hierarchy to determine selling price. Management first considers VSOE, then TPE and if neither VSOE nor TPE exist, the Company uses its best estimate of selling price. Many of the Company's revenue arrangements for Captisol involve a license agreement and the supply of manufactured Captisol product. Licenses may be granted to pharmaceutical companies for the use of Captisol product in the development of pharmaceutical compounds. The supply of the Captisol product may be for all phases of clinical trials and through commercial availability of the host drug or may be limited to certain phases of the clinical trial process. Management believes that the Company's licenses have stand-alone value at the outset of an arrangement because the customer obtains the right to use Captisol in its formulations without any additional input by the Company, and in a hypothetical stand-alone transaction, the customer would be able to procure inventory from another manufacturer in the absence of contractual provisions for exclusive supply by the Company. Other nonrefundable, up-front license fees are recognized as revenue upon delivery of the license, if the license is determined to have standalone value that is not dependent on any future performance by the Company under the applicable collaboration agreement. Nonrefundable contingent event-based payments are recognized as revenue when the contingent event is met, which is usually the earlier of when payments are received or collections are assured, provided that it does not require future performance by the Company. The Company occasionally has sub-license obligations related to arrangements for which it receives license fees, milestones and royalties. Management evaluates the determination of gross versus net reporting based on each individual agreement. Sales-based contingent payments from partners are accounted for similarly to royalties, with revenue recognized upon achievement of the sales targets assuming all other revenue recognition criteria for milestones are met. Revenue from development and regulatory milestones is recognized when earned, as evidenced by written acknowledgement from the collaborator, provided that (1) the milestone event is substantive, its achievability was not reasonably assured at the inception of the agreement, and the Company has no further performance obligations relating to that event, and (2) collectability is reasonably assured. If these criteria are not met, the milestone payment is recognized over the remaining period of the Company’s performance obligations under the arrangement.
Preclinical Study and Clinical Trial Accruals	Preclinical Study and Clinical Trial Accruals Substantial portions of the Company’s preclinical studies and all of the Company’s clinical trials have been performed by third-party laboratories, CROs. The Company accounts for a significant portion of its clinical study costs according to the terms of its contracts with CROs. The terms of its CRO contracts may result in payment flows that do not match the periods over which services are provided to us under such contracts. The Company's objective is to reflect the appropriate preclinical and clinical trial expenses in its financial statements in the same period as the services occur. As part of the process of preparing its financial statements, the Company relies on cost information provided by its CROs. The Company is also required to estimate certain of its expenses resulting from its obligations under its CRO contracts. Accordingly, the Company's preclinical study and clinical trial accrual is dependent upon the timely and accurate reporting of CROs and other third-party vendors. The Company periodically evaluates its estimates to determine if adjustments are necessary or appropriate as more information becomes available concerning changing circumstances, and conditions or events that may affect such estimates. No material adjustments to preclinical study and clinical trial accrued expenses have been recognized to date.
Research and Development Expenses	Research and Development Expenses Research and development expense consists of labor, material, equipment, and allocated facilities costs of the Company’s scientific staff who are working pursuant to the Company’s collaborative agreements and other research and development projects. Also included in research and development expenses are third-party costs incurred for the Company’s research programs including in-licensing costs, CRO costs and costs incurred by other research and development service vendors. We expense these costs as they are incurred. When we make payments for research and development services prior to the services being rendered, we record those amounts as prepaid assets on our consolidated balance sheet and we expense them as the services are provided
Share-Based Compensation	Stock-Based Compensation The Company incurs share-based compensation expense related to restricted stock, its ESPP, and stock options Restricted stock units (RSU) and performance stock units (PSU) are all considered restricted stock. The fair value of restricted stock is determined by the closing market price of the Company’s common stock on the date of grant. The Company recognizes share-based compensation expense based on the fair value on a straight-line basis over the requisite service periods of the awards, taking into consideration estimated forfeitures. PSU represents a right to receive a certain number of shares of common stock based on the achievement of corporate performance goals and continued employment during the vesting period. At each reporting period, the Company reassesses the probability of the achievement of such corporate performance goals and any expense change resulting from an adjustment in the estimated shares to be released are treated as a cumulative catch-up in the period of adjustment. The Company uses the Black-Scholes-Merton option-pricing model to estimate the fair value of stock purchases under ESPP and stock options granted. The model assumptions include expected volatility, term, dividends, and the risk-free interest rate. The Company looks to historical volatility of the Company's stock to determine the expected volatility. The expected term of an award is based on historical forfeiture experience, exercise activity, and on the terms and conditions of the stock awards. The expected dividend yield is determined to be 0% given that the Company has never declared or paid regular cash dividends on its common stock and does not anticipate paying such cash dividends. The risk-free interest rate is based upon U.S. Treasury securities with remaining terms similar to the expected term of the share-based awards The Company grants options and restricted stock awards to employees and non-employee directors. Non-employee directors are accounted for as employees. Options and restricted stock awards granted to certain non-employee directors vest in equal monthly installments over one year from the date of grant. Options granted to employees vest 1/8 on the six month anniversary of the date of grant, and 1/48 each month thereafter for forty-two months. Restricted stock awards granted to employees vest over three years. All option awards generally expire ten years from the date of grant. Stock-based compensation expense for awards to employees and non-employee directors is recognized on a straight-line basis over the vesting period until the last tranche vests.
Income Taxes	Income Taxes The provision for income taxes is computed using the asset and liability method, under which deferred tax assets and liabilities are recognized for the expected future tax consequences of temporary differences between the financial reporting and tax bases of assets and liabilities, and for the expected future tax benefit to be derived from tax loss and credit carryforwards. Deferred tax assets and liabilities are determined using the enacted tax rates in effect for the years in which those tax assets are expected to be realized. The effect of a change in tax rates on deferred tax assets and liabilities is recognized in the provision for income taxes in the period that includes the enactment date. Deferred tax assets are regularly assessed to determine the likelihood they will be recovered from future taxable income. A valuation allowance is established when the Company believes it is more likely than not the future realization of all or some of a deferred tax asset will not be achieved. In evaluating the ability to recover deferred tax assets within the jurisdiction which they arise the Company considers all available positive and negative evidence. Factors reviewed include the cumulative pre-tax book income for the past three years, scheduled reversals of deferred tax liabilities, history of earnings and reliable forecasting, projections of pre-tax book income over the foreseeable future, and the impact of any feasible and prudent tax planning strategies. The Company recognizes the impact of a tax position in the financial statements only if that position is more likely than not of being sustained upon examination by taxing authorities, based on the technical merits of the position. Any interest and penalties related to uncertain tax positions will be reflected in income tax expense.
Income Per Share	Income Per Share Basic income (loss) per share is calculated by dividing net income by the weighted-average number of common shares outstanding during the period. Diluted income (loss) 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 Potentially dilutive common shares consist of shares issuable under 2019 convertible senior notes, stock options and restricted stock. 2019 convertible senior notes have a dilutive impact when the average market price of the Company’s common stock exceeds the applicable conversion price of the respective notes. 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; the average amount of unrecognized compensation expense for restricted stock; and estimated tax benefits that will be recorded in additional paid-in capital when expenses related to equity awards become deductible. In loss periods, basic net loss per share and diluted net loss per share are identical since the effect of otherwise dilutive potential common shares is anti-dilutive and therefore excluded
Comprehensive Income (Loss)	Comprehensive Income (Loss) Comprehensive income (loss) represents net income (loss) adjusted for the change during the periods presented in unrealized gains and losses on available-for-sale securities less reclassification adjustments for realized gains or losses included in net income (loss). The unrealized gains or losses are reported on the Consolidated Statements of Comprehensive Income (Loss).

Summary of Significant Accoun20

Summary of Significant Accounting Policies (Tables)	12 Months Ended
	Dec. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Schedule of major customers	A relatively small number of partners accounts for a significant percentage of our revenue. Revenue from significant partners, which is defined as 10% or more of our total revenue, was as follows: December 31, 2016 2015 2014 Partner A 41 % 27 % 37 % Partner B 14 % 23 % 31 % Partner C — 18 % 10 %
Summary of computation of basic and diluted net income (loss) per share	The following table presents the calculation of weighted average shares used to calculate basic and diluted earnings per share (in thousands): Year Ended December 31, 2016 2015 2014 Weighted average shares outstanding: 20,831 19,790 20,419 Dilutive potential common shares: Restricted stock — 56 36 Stock options — 882 978 2019 Convertible Senior Notes — 499 — Shares used to compute diluted income per share 20,831 21,228 21,433 Potentially dilutive shares excluded from calculation due to anti-dilutive effect 3,544 3,333 5,104

Business Combinations (Tables)

Business Combinations (Tables)	12 Months Ended
	Dec. 31, 2016
Business Combinations [Abstract]
Schedule of Business Acquisitions by Acquisition, Consideration Transferred	The aggregate acquisition consideration was $173.4 million , consisting of (in thousands, except per share amounts): Cash consideration $ 96,006 Total share consideration: Actual number of shares issued 790 Multiplied by: Ligand closing share price on January 8, 2016 98 Total share consideration $ 77,373 Total consideration $ 173,379
Schedule of Recognized Identified Assets Acquired and Liabilities Assumed	The acquisition consideration was allocated to the acquisition date fair values of acquired assets and assumed liabilities as follows (in thousands): Cash and cash equivalents $ 3,504 Accounts receivable 5 Income tax receivable 136 Prepaid expenses and other current assets 1 Deferred tax liabilities, net (55,708 ) Intangible asset with finite life - core technology 167,000 Liabilities assumed (1,528 ) Goodwill 59,969 Total consideration $ 173,379
Schedule of Pro Forma Information	The following table presents supplemental pro forma information for the three and twelve months ended December 31, 2016 and December 31, 2015 , as if the acquisition of OMT had occurred on January 1, 2015 (in thousands except for income per share): Three months ended Twelve months ended December 31, December 31, 2016 2015 2016 2015 Revenue $ 38,185 $ 24,571 $ 111,449 $ 80,365 Net (loss) income $ (3,126 ) 5,888 $ 632 $ 222,788 Basic (loss) income per share: $ (0.15 ) $ 0.30 $ 0.03 $ 11.26 Diluted (loss) income per share: $ (0.15 ) $ 0.27 $ 0.03 $ 10.50

Fair Value Measurement (Tables)

Fair Value Measurement (Tables)	12 Months Ended
	Dec. 31, 2016
Fair Value Disclosures [Abstract]
Schedule of assets and liabilities measured on recurring basis	The following table provide a summary of the assets and liabilities that are measured at fair value on a recurring basis as of December 31, 2016 and 2015 (in thousands): Fair Value Measurements at Reporting Date Using December 31, 2016 Quoted Prices in Active Markets for Identical Assets Significant Other Observable Inputs Significant Unobservable Inputs Total (Level 1) (Level 2) (Level 3) Assets: Short-term investments (1) $ 122,296 $ 3,054 $ 119,242 $ — Note receivable Viking (2) 3,207 — — 3,207 Investment in warrants (3) 684 684 — — Total assets $ 126,187 $ 3,054 $ 119,242 $ 3,207 Liabilities: Current contingent liabilities - CyDex (4a) $ 101 $ — $ — $ 101 Long-term contingent liabilities - Metabasis (5) 1,413 — 1,413 — Long-term contingent liabilities - CyDex (4) 1,503 — — 1,503 Liability for amounts owed to former licensees (6) 371 371 — — Total liabilities $ 3,388 $ 371 $ 1,413 $ 1,604 Fair Value Measurements at Reporting Date Using December 31, 2015 Quoted Prices in Active Markets for Identical Assets Significant Other Observable Inputs Significant Unobservable Inputs Total (Level 1) (Level 2) (Level 3) Assets: Cash equivalents (7) $ 3,015 $ — $ 3,015 $ — Short-term investments (1) 92,775 6,786 85,989 — Note receivable Viking (2) 4,782 — — 4,782 Total assets $ 100,572 $ 6,786 $ 89,004 $ 4,782 Liabilities: Current contingent liabilities - CyDex (4) $ 7,812 $ — $ — $ 7,812 Current contingent liabilities-Metabasis (5) 2,602 — 2,602 — Long-term contingent liabilities - Metabasis (5) 1,355 — 1,355 — Long-term contingent liabilities - CyDex (4) 1,678 — — 1,678 Liability for amounts owed to former licensees (6) 794 794 — — Total liabilities $ 14,241 $ 794 $ 3,957 $ 9,490 (1) Investments in equity securities, are classified as level 1 as the fair value is determined using quoted market prices in active markets for the same securities. Short-term investments in marketable securities with maturities greater than 90 days are classified as 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. (2) The fair value of the convertible note receivable from Viking at December 31, 2015 was determined using a probability weighted option pricing model. The fair value is subjective and is affected by certain significant input to the valuation model such as the estimated volatility of the common stock, which was estimated to be 75% at December 31, 2016 and 65% at December 31, 2015 . Changes in these assumptions may materially affect the fair value estimate. For the year ended December 31, 2016 and December 31, 2015 , the Company reported a decrease in the fair value of the Viking convertible notes of $0.2 million and $0.8 million respectively in "Other, net" of the consolidated statement of operations. (3) Investment in warrants, which the Company received as a result of Viking’s partial repayment of the Viking note receivable and the Company’s 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. (4) The fair value of the liabilities for CyDex contingent liabilities were determined based on the income approach using a Monte Carlo analysis. The fair value is subjective and is affected by changes in inputs to the valuation model including management’s assumptions regarding revenue volatility, probability of commercialization of products, estimates of timing and probability of achievement of certain revenue thresholds and developmental and regulatory milestones which may be achieved and affect amounts owed to former license holders and CVR holders. Changes in these assumptions can materially affect the fair value estimate. (4a) The fair value of the liabilities for short-term CyDex contingent liabilities at December 31, 2016 disclosed herein represents the fair value of the estimated contingent considerations owed to former license holder only, which is determined based on the methodology described in (4) above. The contingent considerations owed to the Cydex CVR holders at December 31, 2016 is determined based on actual amount owed at December 31, 2016 as the Cydex CVR agreement ended at December 31, 2016. (5) The liability for CVRs for Metabasis are determined using quoted market prices in a market that is not active for the underlying CVR. (6) The liability for amounts owed to former licensees are determined using quoted market prices in active markets for the underlying investment received from a partner, a portion of which is owed to former licensees. (7) Highly liquid investments with maturities less than 90 days from the purchase date are recorded as cash equivalents that are classified as 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.
Significant unobservable inputs used in determining the fair value of contingent liabilities	The following table represents significant unobservable inputs used in determining the fair value of contingent liabilities assumed in the acquisition of CyDex: December 31, 2016 2015 Range of annual revenue subject to revenue sharing (1) N/A $22.5 million Revenue volatility 25% 25% Average of probability of commercialization 12.5% 73% Sales beta N/A 0.40 Credit rating BB BB Equity risk premium 6% 6% Market price of risk 3.2% N/A (1) For the December 31, 2015 valuation date, revenue subject to revenue sharing represent management’s estimate of the range of total annual revenue subject to revenue sharing (i.e. annual revenues in excess of $15 million ) through December 31, 2016, which is the term of the CVR agreement. For the December 31, 2016 valuation date, the Cydex CVR was determined based on the actual $5.0 million amount owed to Cydex CVR holders as the Cydex CVR agreement ended at December 31, 2016. This amount was subsequently paid in February 2017.
Reconciliation of the level 3 financial instruments	A reconciliation of the level 3 financial instruments as of December 31, 2016 is as follows (in thousands): Assets: Fair value of level 3 financial instruments as of December 31, 2015 $ 4,782 Viking note receivable fair market value adjustment (215 ) Cash payment received as partial repayment of note receivable (300 ) Fair market value of stock received as partial repayment of note receivable (1,060 ) Fair value of level 3 financial instrument assets as of December 31, 2016 $ 3,207 Liabilities Fair value of level 3 financial instruments as of December 31, 2015 $ 9,490 Payments to CVR holders and other contingency payments (6,158 ) Fair value adjustments to contingent liabilities 3,259 Other (1) (4,987 ) Fair value of level 3 financial instruments as of December 31, 2016 $ 1,604

Lease Obligations (Tables)

Lease Obligations (Tables)	12 Months Ended
	Dec. 31, 2016
Leases [Abstract]
Payments expected to received from sublease agreements	The following table provides a summary of operating lease obligations and payments expected to be received from sublease agreements as of December 31, 2016 (in thousands): Operating lease obligations: Lease Termination Date Less than 1 year 1-2 years 3-4 years Thereafter Total Corporate headquarters-San Diego, CA April 2023 $ 128 $ 267 $ 283 $ 197 $ 875 Office and research facility-La Jolla, CA June 2019 718 1,111 — — 1,829 Bioscience and Technology Business Center-Lawrence, KS December 2017 54 — — — 54 Total operating lease obligations $ 900 $ 1,378 $ 283 $ 197 $ 2,758 Sublease payments expected to be received: Office and research facility-La Jolla, CA June 2019 656 1,002 — — 1,658 Net operating lease obligations $ 244 $ 376 $ 283 $ 197 $ 1,100

Financing Arrangements (Tables)

Financing Arrangements (Tables)	12 Months Ended
	Dec. 31, 2016
Debt Disclosure [Abstract]
Summary of carrying values and coupon rates on financing arrangements	The following table summarizes information about the liability components the Company's financing arrangement (dollars in thousands): December 31, 2016 December 31, 2015 2019 Convertible Senior Notes Principal amount outstanding $ 245,000 $ 245,000 Unamortized discount (32,090 ) (43,015 ) Total current portion of notes payable $ 212,910 $ 201,985

Other Balance Sheet Details (Ta

Other Balance Sheet Details (Tables)	12 Months Ended
	Dec. 31, 2016
Other Balance Sheet Details [Abstract]
Schedule of investment categories	The following table summarizes the various investment categories at December 31, 2016 and 2015 (in thousands): Cost Gross unrealized gains Gross unrealized losses Estimated fair value December 31, 2016 Short-term investments Bank deposits $ 40,715 $ 19 $ — $ 40,734 Corporate bonds 11,031 — (5 ) 11,026 Corporate equity securities 1,512 1,542 — 3,054 Commercial paper 33,074 2 (9 ) 33,067 Agency bonds 7,294 1 — 7,295 U.S. Government bonds 7,508 — (1 ) 7,507 Municipal bonds 19,624 — (11 ) 19,613 $ 120,758 $ 1,564 $ (26 ) $ 122,296 December 31, 2015 Short-term investments Bank deposits $ 43,043 $ — $ (4 ) $ 43,039 Corporate bonds 41,238 — (35 ) 41,203 Commercial paper 1,747 — — 1,747 Asset backed securities 10,020 — (5 ) 10,015 Corporate equity securities 1,843 4,944 — 6,787 $ 97,891 $ 4,944 $ (44 ) $ 102,791
Schedule of other current assets	Other current assets consist of the following (in thousands): December 31, 2016 2015 Prepaid expenses $ 1,864 $ 1,177 Other receivables 311 731 $ 2,175 $ 1,908
Schedule of property and equipment	Property and equipment is stated at cost and consists of the following (in thousands): December 31, 2016 2015 Lab and office equipment $ 1,067 $ 2,248 Leasehold improvements 1,754 273 Computer equipment and software 569 632 3,390 3,153 Less accumulated depreciation and amortization (1,571 ) (2,781 ) $ 1,819 $ 372
Summary of goodwill and other identifiable intangible assets	Goodwill and identifiable intangible assets consist of the following (in thousands): December 31, 2016 2015 Indefinite lived intangible assets IPR&D $ 12,246 $ 12,556 Goodwill 72,207 12,238 Definite lived intangible assets Complete technology 182,577 15,267 Less: Accumulated amortization (12,792 ) (3,762 ) Trade name 2,642 2,642 Less: Accumulated amortization (784 ) (652 ) Customer relationships 29,600 29,600 Less: Accumulated amortization (8,784 ) (7,304 ) Total goodwill and other identifiable intangible assets, net $ 276,912 $ 60,585
Schedule of commercial license rights	Commercial license rights consist of the following (in thousands): December 31, December 31, 2016 2015 CorMatrix $ 17,696 $ — Selexis 8,602 8,602 26,298 8,602 Less: accumulated amortization (477 ) (48 ) Total commercial rights, net $ 25,821 $ 8,554
Schedule of accrued liabilities	Accrued liabilities consist of the following (in thousands): December 31, 2016 2015 Compensation $ 2,603 $ 1,711 Legal 829 726 Amounts owed to former licensees 899 915 Royalties owed to third parties 942 823 Other 1,124 1,230 $ 6,397 $ 5,405
Schedule of contingent liabilities	Contingent liabilities consist of the following (in millions): December 31, 2014 Payments Fair Value Adjustment December 31, 2015 Payments Fair Value Adjustment December 31, 2016 Cydex $ 11.5 $ (5.8 ) $ 3.8 $ 9.5 (6.2 ) $ 3.3 $ 6.6 Metabasis 3.7 (0.9 ) 1.2 4.0 (2.6 ) 0.1 1.5 Total 15.2 (6.7 ) 5.0 13.5 (8.8 ) 3.4 8.1
Schedule of other long-term liabilities	Other long-term liabilities consist of the following (in thousands): December 31, 2016 2015 Deferred rent $ 357 $ — Deposits 43 268 Other 287 29 $ 687 $ 297

Stockholders' Equity (Tables)

Stockholders' Equity (Tables)	12 Months Ended
	Dec. 31, 2016
Equity [Abstract]
Schedule for accounting for share-based compensation	The following table summarizes stock-based compensation expense (in thousands): December 31, 2016 2015 2014 Stock-based compensation expense as a component of: Research and development expenses $ 8,836 $ 4,080 $ 3,595 General and administrative expenses 10,057 8,378 7,675 $ 18,893 $ 12,458 $ 11,270
Stock option plan activity	Following is a summary of the Company’s stock option plan activity and related information: Shares Weighted Average Exercise Price Weighted Average Remaining Contractual Term in Years Aggregate Intrinsic Value (In thousands) Balance at December 31, 2015 1,683,341 $ 34.19 6.48 $ 124,800 Granted 263,489 92.09 Exercised (164,440 ) 38.08 Forfeited (28,115 ) 60.17 Balance at December 31, 2016 1,754,275 42.12 6.19 104,247 Exercisable at December 31, 2016 1,298,561 30.21 5.44 92,723 Options vested and expected to vest as of December 31, 2016 1,752,275 $ 42.12 6.19 $ 104,247
Stock option plan activity, by exercise price range	Following is a further breakdown of the options outstanding as of December 31, 2016 : Range of exercise prices Options outstanding Weighted average remaining life in years Weighted average exercise price Options exercisable Weighted average exercise price $8.58 - $12.53 247,574 3.94 $ 9.98 247,574 $ 9.98 $10.12 - $12.81 76,100 4.92 11.38 76,100 11.38 $14.47 - $14.47 288,887 5.11 14.47 274,887 14.47 $16.14 - $21.00 106,242 1.85 17.76 106,242 17.76 $21.92 - $21.92 225,105 6.13 21.92 213,199 21.92 $32.00 - $53.34 72,330 6.02 36.18 62,747 34.73 $56.26 - $59.26 183,595 8.11 56.26 70,877 56.26 $63.58 - $68.62 26,382 7.50 67.20 21,976 67.50 $74.42 - $74.42 227,856 7.12 74.42 162,233 74.42 $85.79 - $138.53 298,204 9.03 93.19 62,726 89.71 $8.58 – $138.53 1,752,275 6.19 $ 42.12 1,298,561 $ 30.21
Stock option weighted average assumptions	The assumptions used for the specified reporting periods and the resulting estimates of weighted-average grant date fair value per share of options granted: Year Ended December 31, 2016 2015 2014 Risk-free interest rate 1.3%-1.9% 1.7%-2.0% 1.9% Expected volatility 48%-50% 50%-58% 62%-69% Expected term 6.6 to 6.7 years 6.5 years 6.0 years Forfeiture rate 5.00% 8.52% 8.6%-9.7%
Restricted stock activity	The following is a summary of the Company’s restricted stock activity and related information: Shares Weighted-Average Grant Date Fair Value Outstanding at December 31, 2015 130,749 $ 60.36 Granted 234,855 95.31 Vested (54,421 ) 66.79 Forfeited (2,483 ) 67.95 Outstanding at December 31, 2016 308,700 $ 86.61

Income Taxes (Tables)

Income Taxes (Tables)	12 Months Ended
	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Schedule of the components of income tax benefit	The components of the income tax expense (benefit) for continuing operations are as follows (in thousands): Year Ended December 31, 2016 2015 2014 Current expense (benefit): Federal $ 21 $ 11 $ 15 State 12 7 19 33 18 34 Deferred expense (benefit): Federal 10,534 (167,413 ) 406 State (240 ) (24,720 ) (30 ) $ 10,327 $ (192,115 ) $ 410
Schedule of deferred tax assets and liabilities	Significant components of the Company’s deferred tax assets and liabilities as of December 31, 2016 and 2015 are shown below. The Company assesses the positive and negative evidence to determine if sufficient future taxable income will be generated to use the existing deferred tax assets. The Company's evaluation of evidence resulted in management concluding that the majority of the Company's deferred tax assets will be realized. However, the Company maintains a valuation allowance to offset certain net deferred tax assets as management believes realization of such assets are uncertain as of December 31, 2016 , 2015 and 2014 . The valuation allowance increased $6.3 million in 2016, decreased $231.7 million in 2015 and decreased $7.2 million in 2014. December 31, 2016 2015 (in thousands) Deferred assets: Net operating loss carryforwards $ 150,226 $ 160,595 Research credit carryforwards 26,878 25,613 Fixed assets and intangibles 4,385 8,839 Accrued expenses 943 1,523 Contingent liabilities 578 707 Deferred revenue — 3 Present value of royalties 591 3,007 Deferred rent 45 68 Capital Loss Carryforward 4,432 — Viking Equity Method Investment 5,692 1,840 Other 19,312 15,441 213,082 217,636 Valuation allowance for deferred tax assets (15,349 ) (9,066 ) Net deferred tax assets $ 197,733 $ 208,570 Deferred tax liabilities: Retrophin fair value adjustment $ (52 ) $ (1,256 ) Convertible debt (1,196 ) (1,844 ) Identified intangibles (68,631 ) (12,770 ) Identified indefinite lived intangibles (3,963 ) (3,617 ) Total $ 123,891 $ 189,083
Schedule of effective income tax rate reconciliation	A reconciliation of income tax expense (benefit) from continuing operations to the amount computed by applying the statutory federal income tax rate to the net income (loss) from continuing operations is summarized as follows: Year Ended December 31, 2016 2015 2014 Amounts computed at statutory federal rate $ 2,786 $ 13,198 $ 3,843 State taxes net of federal benefit 175 386 697 Meals & entertainment 16 16 9 Imputed interest (1 ) (161 ) 53 Section 162(m) limitation 94 197 490 Contingent liabilities 1,225 1,684 1,748 Stock-based compensation 263 140 89 Expired NOLs — 232 88 Research and development credits (1,525 ) 304 (113 ) Change in uncertain tax positions 1,423 27,188 7 Rate change for changes in state law 25 (5,756 ) 119 APIC Excess Tax Benefit True Up (622 ) — — Increase in deferred tax assets from completion of 382 analysis (120 ) 3,329 43 Avinza true up — (2,107 ) — Change in valuation allowance 6,283 (231,370 ) (7,243 ) Other 305 605 580 $ 10,327 $ (192,115 ) $ 410
Schedule of unrecognized tax benefits	A reconciliation of the amount of unrecognized tax benefits at December 31, 2016 , 2015 and 2014 is as follows (in thousands): December 31, 2016 2015 2014 Balance at beginning of year $ 36,452 $ 8,524 $ 8,504 Additions based on tax positions related to the current year 70 154 40 Additions for tax positions of prior years 2,408 28,224 — Reductions for tax positions of prior years (160 ) (450 ) (20 ) Balance at end of year $ 38,770 $ 36,452 $ 8,524

Summary of Unaudited Quarterl28

Summary of Unaudited Quarterly Financial Information (Tables)	12 Months Ended
	Dec. 31, 2016
Quarterly Financial Information Disclosure [Abstract]
Schedule of Quarterly Financial Information	The following financial information reflects all normal recurring adjustments, which are, in the opinion of management, necessary for a fair statement of the results and cash flows of interim periods. Summarized quarterly data for fiscal years 2016 and 2015 are as follows (in thousands, except per share amounts): First Quarter Second Quarter Third Quarter Fourth Quarter 2016 Total revenues $ 29,648 $ 19,521 $ 21,619 $ 38,185 Total operating costs and expenses 14,552 15,552 16,153 18,831 Income tax (expense) benefit (3,694 ) 3,881 (160 ) (10,354 ) Income (loss) from continuing operations 5,877 (6,170 ) 1,051 (3,125 ) Income from discontinued operations 731 — — — Net income (loss) 6,608 (6,170 ) 1,051 (3,125 ) Basic per share amounts: Net income (loss) $ 0.32 $ (0.30 ) $ 0.05 $ 0.15 Diluted per share amounts: Net income (loss) 0.30 (0.30 ) 0.05 0.15 Weighted average shares—basic 20,708 20,832 20,887 20,898 Weighted average shares—diluted 22,284 20,832 22,997 20,898 2015 Total revenues $ 14,602 $ 18,418 $ 17,701 $ 21,193 Total operating costs and expenses 11,253 14,053 9,104 10,175 Income tax (expense) benefit (15 ) (265 ) 191,881 514 (Loss) income from continuing operations (89 ) 22,027 199,165 6,341 Net loss attributable to noncontrolling interests (843 ) (1,537 ) — — Net income 754 23,564 199,165 6,341 Basic per share amounts: Net income $ 0.04 $ 1.19 $ 10.01 $ 0.32 Diluted per share amounts: Net income $ 0.04 $ 1.11 $ 9.28 $ 0.29 Weighted average shares—basic 19,612 19,725 19,887 19,933 Weighted average shares—diluted 20,631 21,276 21,460 21,542

Summary of Significant Accoun29

Summary of Significant Accounting Policies (Details 6) - Customer Concentration Risk - Revenue	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Partner A
Revenue, Major Customer
Total revenues	41.00%	27.00%	37.00%
Partner B
Revenue, Major Customer
Total revenues	14.00%	23.00%	31.00%
Partner C
Revenue, Major Customer
Total revenues	0.00%	18.00%	10.00%

Summary of Significant Accoun30

Summary of Significant Accounting Policies (Details Textual)	12 Months Ended
	Dec. 31, 2016USD ($)	Dec. 31, 2015USD ($)	Dec. 31, 2014USD ($)	Jan. 31, 2010right
Basis of Presentation [Line Items]
Working capital deficit	$ 64,100,000
Mezzanine equity excluded from working capital deficit	$ 30,000,000
Days after threshold consecutive trading days to complete payment of principal	3 days
Number of consecutive trading days	50 days
Maturity period of cash and cash equivalents, maximum	3 months
Write-downs related to obsolete inventory	$ 0	$ 0
Goodwill impairment	0
Royalty revenue	59,423,000	38,194,000	$ 29,994,000
Accounts receivable, net	$ 14,700,000	6,170,000
Restocking fee (percent)	20.00%
Share-based Compensation [Abstract]
Expected dividend rate (percent)	0.00%
Gain on disposition of product line	$ 1,100,000
Provision for taxes on gain	$ 408,000	$ 0	$ 0
Stock Options | 2002 Stock Incentive Plan
Share-based Compensation [Abstract]
Award expiration period	10 years
Stock Options | Vest 1/8 on the six month anniversary of the date of grant | 2002 Stock Incentive Plan
Share-based Compensation [Abstract]
Award vesting period	6 months
Award vesting right percentage	12.50%
Stock Options | Vest 1/48 each month for forty-two months | 2002 Stock Incentive Plan
Share-based Compensation [Abstract]
Award vesting period	42 months
Award vesting right percentage	2.08%
Director
Basis of Presentation [Line Items]
Mr. Aryeh's ownership percentage in CorMatrix (percent, less than)	1.00%
Director | 2002 Stock Incentive Plan
Share-based Compensation [Abstract]
Award vesting period	1 year
Minimum
Basis of Presentation [Line Items]
Property and equipment, useful life	3 years
Sales/revenues from partners reporting period	30 days
Maximum
Basis of Presentation [Line Items]
Property and equipment, useful life	10 years
Sales/revenues from partners reporting period	60 days
Metabasis Therapeutics
Basis of Presentation [Line Items]
Number of contingent value rights | right				4
IPR&D
Basis of Presentation [Line Items]
Impairment charge	$ 0
CorMatrix
Basis of Presentation [Line Items]
Royalty revenue	1,500,000
Accounts receivable, net	$ 200,000

Summary of Significant Accoun31

Summary of Significant Accounting Policies (Details) - shares shares in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Weighted average shares outstanding (shares):	20,898	20,887	20,832	20,708	19,933	19,887	19,725	19,612	20,831	19,790	20,419
Dilutive potential common shares:
Restricted stock (shares)									0	56	36
Stock options (shares)									0	882	978
2019 Convertible Senior Notes (shares)									0	499	0
Shares used to compute diluted income per share (shares)	20,898	22,997	20,832	22,284	21,542	21,460	21,276	20,631	20,831	21,228	21,433
Potentially dilutive shares excluded from calculation due to anti-dilutive effect (shares)									3,544	3,333	5,104

Investment in Viking (Details T

Investment in Viking (Details Textual) $ / shares in Units, $ in Thousands	Apr. 13, 2016USD ($)shares	Apr. 30, 2016USD ($)$ / sharesshares	Jan. 31, 2016USD ($)	May 31, 2015USD ($)$ / sharesshares	Apr. 30, 2015	May 31, 2014USD ($)program	Dec. 31, 2016USD ($)	Dec. 31, 2015USD ($)	Dec. 31, 2014USD ($)	May 31, 2015$ / shares	Aug. 31, 2014$ / sharesshares
Variable Interest Entity [Line Items]
Warrants to purchase number of shares (shares) | shares											3,264,643
Exercise price per share of warrants (in USD per share) | $ / shares											$ 125.08
Proceeds received from repayment of Viking note receivable							$ 300	$ 0	$ 0
Note receivable from Viking							$ 3,207	$ 4,782
Viking
Variable Interest Entity [Line Items]
Number of programs licensed | program						5
Loss recorded (percent)										100.00%
Debt | Viking
Variable Interest Entity [Line Items]
Convertible loan facility extended						$ 2,500
Repayment in equity (percent)					200.00%
Common Stock
Variable Interest Entity [Line Items]
Aggregate value of shares received in Viking IPO				$ 29,200
Shares of Viking stock purchased (shares) | shares				1,100,000
Purchase of Viking common stock				$ 9,000
Equity Method Investee
Variable Interest Entity [Line Items]
Shares sold in Viking IPO (shares) | shares		7,500,000
Initial offering price per share (in usd per share) | $ / shares		$ 1.25
Shares of Viking stock purchased (shares) | shares		560,000
Purchase of Viking common stock		$ 700
Interest rate on note due from Viking (percent)			2.50%					5.00%
Extension of lock-up period			1 year
Amount of loan to be repaid upon consummation of first capital financing transaction			$ 1,500
Amount of loan to be repaid in cash upon consummation of first capital financing transaction			$ 300
Warrants to purchase number of shares (shares) | shares		7,500,000
Exercise price per share of warrants (in USD per share) | $ / shares		$ 1.50
Warrants purchased (shares) | shares		560,000
Proceeds received from repayment of Viking note receivable	$ 300
Shares received pursuant to MLA amendment (shares) | shares	960,000
Warrants received, licensing agreement (shares) | shares	960,000
Value of consideration received for repayment of convertible notes	$ 1,200
Aggregate ownership, percent		32.70%					30.30%
Decrease in equity method investment		$ (10,700)
Other than temporary impairment of investment in Viking							$ 7,400
Equity Method Investee | IPO | Common Stock
Variable Interest Entity [Line Items]
Shares sold in Viking IPO (shares) | shares				3,700,000
Aggregate offering price				$ 29,200
Initial offering price per share (in usd per share) | $ / shares				$ 8						$ 8

Business Combinations (Details)

Business Combinations (Details) $ in Thousands	Jan. 08, 2016USD ($)programplatform	Dec. 31, 2016USD ($)	Dec. 31, 2015USD ($)
Business Acquisition [Line Items]
Finite-lived intangible asset, useful life		20 years
Goodwill		$ 72,207	$ 12,238
OMT, Inc.
Business Acquisition [Line Items]
Number of transgenic animal platforms | platform	3
Number of partnered programs added | program	16
Consideration transferred	$ 173,400
Goodwill	$ 59,969
Core Technology | OMT, Inc.
Business Acquisition [Line Items]
Projected cash flow discount rate (percent)	15.50%
Finite-lived intangible asset, useful life	20 years

Business Combinations - Conside

Business Combinations - Consideration Transferred (Details) - OMT, Inc. $ / shares in Units, shares in Thousands, $ in Thousands	Jan. 08, 2016USD ($)$ / sharesshares
Business Acquisition [Line Items]
Cash consideration	$ 96,006
Actual number of shares issued (shares) | shares	790
Multiplied by: Ligand closing share price on January 8, 2016 (in USD per share) | $ / shares	$ 98
Total share consideration	$ 77,373
Total consideration	$ 173,379

Business Combinations - Assets

Business Combinations - Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Jan. 08, 2016	Dec. 31, 2015
Business Acquisition [Line Items]
Goodwill	$ 72,207		$ 12,238
OMT, Inc.
Business Acquisition [Line Items]
Cash and cash equivalents		$ 3,504
Accounts receivable		5
Income tax receivable		136
Prepaid expenses and other current assets		1
Deferred tax liabilities, net		(55,708)
Intangible asset with finite life - core technology		167,000
Liabilities assumed		(1,528)
Goodwill		59,969
Total consideration		$ 173,379

Business Combinations - Pro For

Business Combinations - Pro Forma Information (Details) - OMT, Inc. - USD ($) $ / shares in Units, $ in Thousands	Jan. 07, 2016	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2016	Dec. 31, 2015
Business Acquisition [Line Items]
Revenue		$ 38,185	$ 24,571	$ 111,449	$ 80,365
Net (loss) income		$ (3,126)	$ 5,888	$ 632	$ 222,788
Basic (loss) income per share (in USD per share):		$ (0.15)	$ 0.30	$ 0.03	$ 11.26
Diluted (loss) income per share (in USD per share):		$ (0.15)	$ 0.27	$ 0.03	$ 10.50
Pro forma adjustment for share-based compensation expense			$ 300		$ 900
Pro forma adjustment for additional amortization of intangible assets			$ 2,100		6,300
Pro forma adjustment for platform license fee paid					$ 3,000
Pro forma adjustment for revenue of OMT, Inc. prior to acquisition date	$ 2,500

Fair Value Measurement (Details

Fair Value Measurement (Details) - USD ($) $ in Thousands		12 Months Ended
		Dec. 31, 2016		Dec. 31, 2015
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Convertible Notes Receivable, Fair Value, Period Increase (Decrease)		$ (200)		$ (800)
Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value		126,187		100,572
Liabilities, fair value		3,388		14,241
Recurring | Current portion of contingent liabilities - CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[1]	101		7,812
Recurring | Current contingent liabilities-Metabasis
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[2]			2,602
Recurring | Long-term portion of contingent liabilities - Metabasis
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[2]	1,413		1,355
Recurring | Long-term portion of contingent liabilities - CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[1]	1,503		1,678
Recurring | Liability for restricted investments owed to former licensees
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[3]	371		794
Recurring | Cash Equivalents
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[4]			3,015
Recurring | Short-term investments
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[5]	122,296		92,775
Recurring | Notes Receivable
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[6]	$ 3,207		$ 4,782
Revenue volatility (percent)		75.00%		65.00%
Recurring | Investment in warrants
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[7]	$ 684
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value		3,054		$ 6,786
Liabilities, fair value		371		794
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Current portion of contingent liabilities - CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[1]	0		0
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Current contingent liabilities-Metabasis
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[2]			0
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Long-term portion of contingent liabilities - Metabasis
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[2]	0		0
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Long-term portion of contingent liabilities - CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[1]	0		0
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Liability for restricted investments owed to former licensees
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[3]	371		794
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Cash Equivalents
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[4]			0
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Short-term investments
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[5]	3,054		6,786
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Notes Receivable
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[6]	0		0
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Investment in warrants
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[7]	684
Recurring | Significant Other Observable Inputs (Level 2)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value		119,242		89,004
Liabilities, fair value		1,413		3,957
Recurring | Significant Other Observable Inputs (Level 2) | Current portion of contingent liabilities - CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[1]	0		0
Recurring | Significant Other Observable Inputs (Level 2) | Current contingent liabilities-Metabasis
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[2]			2,602
Recurring | Significant Other Observable Inputs (Level 2) | Long-term portion of contingent liabilities - Metabasis
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[2]	1,413		1,355
Recurring | Significant Other Observable Inputs (Level 2) | Long-term portion of contingent liabilities - CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[1]	0		0
Recurring | Significant Other Observable Inputs (Level 2) | Liability for restricted investments owed to former licensees
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[3]	0		0
Recurring | Significant Other Observable Inputs (Level 2) | Cash Equivalents
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[4]			3,015
Recurring | Significant Other Observable Inputs (Level 2) | Short-term investments
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[5]	119,242		85,989
Recurring | Significant Other Observable Inputs (Level 2) | Notes Receivable
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[6]	0		0
Recurring | Significant Other Observable Inputs (Level 2) | Investment in warrants
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[7]	0
Recurring | Significant Unobservable Inputs (Level 3)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value		3,207		4,782
Liabilities, fair value		1,604		9,490
Recurring | Significant Unobservable Inputs (Level 3) | Current portion of contingent liabilities - CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[1]	101		7,812
Recurring | Significant Unobservable Inputs (Level 3) | Current contingent liabilities-Metabasis
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[2]			0
Recurring | Significant Unobservable Inputs (Level 3) | Long-term portion of contingent liabilities - Metabasis
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[2]	0		0
Recurring | Significant Unobservable Inputs (Level 3) | Long-term portion of contingent liabilities - CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[1]	1,503		1,678
Recurring | Significant Unobservable Inputs (Level 3) | Liability for restricted investments owed to former licensees
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	[3]	0		0
Recurring | Significant Unobservable Inputs (Level 3) | Short-term investments
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[5]	0		0
Recurring | Significant Unobservable Inputs (Level 3) | Notes Receivable
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value		3,207	[6]	$ 4,782
Recurring | Significant Unobservable Inputs (Level 3) | Investment in warrants
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	[7]	$ 0
[1]	The fair value of the liabilities for CyDex contingent liabilities were determined based on the income approach using a Monte Carlo analysis. The fair value is subjective and is affected by changes in inputs to the valuation model including management’s assumptions regarding revenue volatility, probability of commercialization of products, estimates of timing and probability of achievement of certain revenue thresholds and developmental and regulatory milestones which may be achieved and affect amounts owed to former license holders and CVR holders. Changes in these assumptions can materially affect the fair value estimate.
[2]	The liability for CVRs for Metabasis are determined using quoted market prices in a market that is not active for the underlying CVR.
[3]	The liability for amounts owed to former licensees are determined using quoted market prices in active markets for the underlying investment received from a partner, a portion of which is owed to former licensees.
[4]	Highly liquid investments with maturities less than 90 days from the purchase date are recorded as cash equivalents that are classified as 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.
[5]	Investments in equity securities, are classified as level 1 as the fair value is determined using quoted market prices in active markets for the same securities. Short-term investments in marketable securities with maturities greater than 90 days are classified as 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.
[6]	The fair value of the convertible note receivable from Viking at December 31, 2015 was determined using a probability weighted option pricing model. The fair value is subjective and is affected by certain significant input to the valuation model such as the estimated volatility of the common stock, which was estimated to be 75% at December 31, 2016 and 65% at December 31, 2015. Changes in these assumptions may materially affect the fair value estimate. For the year ended December 31, 2016 and December 31, 2015, the Company reported a decrease in the fair value of the Viking convertible notes of $0.2 million and$0.8 million respectively in "Other, net" of the consolidated statement of operations.
[7]	Investment in warrants, which the Company received as a result of Viking’s partial repayment of the Viking note receivable and the Company’s 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.

Fair Value Measurement (Detai38

Fair Value Measurement (Details 1) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Fair Value Disclosures [Abstract]
Change in fair value of Viking convertible notes	$ 0.2	$ 0.8

Fair Value Measurement (Detai39

Fair Value Measurement (Details 2) - USD ($) $ in Thousands		12 Months Ended
		Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Assets:
Fair value of level 3 financial instruments as of December 31, 2015		$ 4,782
Fair market value of stock received as partial repayment of note receivable		(215)
Cash payment received as partial repayment of note receivable		(300)
Viking note receivable fair market value adjustment		(1,060)
Fair value of level 3 financial instrument assets as of December 31, 2016		3,207	$ 4,782
Liabilities
Fair value of level 3 financial instruments as of December 31, 2015		9,490
Other	[1]	4,987
Fair value of level 3 financial instruments as of December 31, 2016		1,604	9,490
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Payments to CVR holders and other contingency payments		(8,777)	(6,740)	$ (3,493)
Fair value adjustments to contingent liabilities		3,400	5,000
Viking Therapeutics, Inc.
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Equity Method Investment, Quoted Market Value		7,500
2019 Convertible Senior Notes | Senior Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of convertible debt		331,700
CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Payments to CVR holders and other contingency payments		(6,158)	(5,848)
Fair value adjustments to contingent liabilities		$ 3,259	$ 3,800
[1]	Balance represents Cydex CVR obligation, which was determined based on actual amount owed to Cydex CVR holders as the Cydex CVR agreement ended at December 31, 2016.

Fair Value Measurements - Unobs

Fair Value Measurements - Unobservable Inputs (Details) - USD ($) $ in Thousands		12 Months Ended
		Dec. 31, 2016	Dec. 31, 2015
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Amount owed to Cydex CVR holders		$ 2,916	$ 3,033
CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Revenue Threshold for Revenue Sharing			15,000
Range of annual revenue subject to revenue sharing	[1]		$ 22,500
Revenue volatility (percent)		25.00%	25.00%
Average of probability of commercialization (percent)		12.50%	73.00%
Sales beta (decimal)			0.40
Credit rating (non-numeric)		BB	BB
Equity risk premiun (percent)		6.00%	6.00%
Market price of risk (percent)		3.20%
Amount owed to Cydex CVR holders		$ 5,000
[1]	For the December 31, 2015 valuation date, revenue subject to revenue sharing represent management’s estimate of the range of total annual revenue subject to revenue sharing (i.e. annual revenues in excess of $15 million) through December 31, 2016, which is the term of the CVR agreement. For the December 31, 2016 valuation date, the Cydex CVR was determined based on the actual $5.0 million amount owed to Cydex CVR holders as the Cydex CVR agreement ended at December 31, 2016. This amount was subsequently paid in February 2017.

Lease Obligations (Details)

Lease Obligations (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2016USD ($)
Payments expected to received from sublease agreements
Operating lease obligation, Less than 1 year	$ 900
Operating lease obligation, 1-2 years	1,378
Operating leases obligation, 3-4 years	283
Operating lease obligation, Thereafter	197
Operating lease obligation, Total	2,758
Operating lease obligation, Less than 1 year, net	244
Operating lease obligation, 1-2 years, net	376
Operating lease obligation, 3-4 years, net	283
Operating lease obligation, Thereafter, net	197
Operating lease obligation, net, Total	$ 1,100
Corporate Headquarters - San Diego, CA | CALIFORNIA
Payments expected to received from sublease agreements
Lease Termination Date	Apr. 30, 2023
Operating lease obligation, Less than 1 year	$ 128
Operating lease obligation, 1-2 years	267
Operating leases obligation, 3-4 years	283
Operating lease obligation, Thereafter	197
Operating lease obligation, Total	$ 875
Office and Research Facility - La Jolla, CA | CALIFORNIA
Payments expected to received from sublease agreements
Lease Termination Date	Jun. 30, 2019
Operating lease obligation, Less than 1 year	$ 718
Operating lease obligation, 1-2 years	1,111
Operating leases obligation, 3-4 years	0
Operating lease obligation, Thereafter	0
Operating lease obligation, Total	1,829
Sublease payments expected to be received, Less than 1 year	656
Sublease payments expected to be received, 1-2 years	1,002
Sublease payments expected to be received, 3-4 years	0
Sublease payments expected to be received, Thereafter	0
Sublease payments expected to be received, Total	$ 1,658
Bioscience and Technology Business Center - Lawrence, KS | KANSAS
Payments expected to received from sublease agreements
Lease Termination Date	Dec. 1, 2017
Operating lease obligation, Less than 1 year	$ 54
Operating lease obligation, Total	$ 54

Lease Obligations (Details Text

Lease Obligations (Details Textual) - USD ($) $ in Thousands	1 Months Ended	12 Months Ended
	May 31, 2016	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Operating Leased Assets [Line Items]
Lease expiration year, Maximum		2,023
Rent expense		$ 300	$ 400	$ 700
Lease exit and termination costs		1,032	1,020	1,084
Rent expense, net of sublease income		1,700	3,300
Adjustment for accretion and changes in lease assumptions		700	900	$ 1,100
Corporate Headquarters - San Diego, CA | CALIFORNIA
Operating Leased Assets [Line Items]
Rent expense	$ 100
Initial term of lease	7 years
Annual escalation of operating lease (percent)	3.00%
Renewal term of lease	5 years
Contract Termination
Operating Leased Assets [Line Items]
Lease exit and termination costs		$ 0	$ 900

Financing Arrangements (Details

Financing Arrangements (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Notes Payable, Current and Noncurrent [Abstract]
Total current portion of notes payable	$ 212,910	$ 201,985
2019 Convertible Senior Notes
Notes Payable, Current and Noncurrent [Abstract]
Principal amount outstanding	245,000	245,000
Unamortized discount	$ (32,090)	$ (43,015)

Financing Arrangements (Detai44

Financing Arrangements (Details Textual)	1 Months Ended	12 Months Ended
	Aug. 31, 2014USD ($)d$ / sharesshares	Dec. 31, 2016USD ($)	Dec. 31, 2015USD ($)	Dec. 31, 2014USD ($)
Debt Instrument [Line Items]
Number of consecutive trading days		50 days
Carrying value of equity component		$ 29,563,000	$ 39,628,000
Equity component of convertible debt issuance, net of issuance costs		10,065,000	(39,628,000)	$ 51,271,000
Warrants to purchase number of shares (shares) | shares	3,264,643
Exercise price per share of convertible bond hedges | $ / shares	$ 75.05
Payments for convertible bond hedges		0	0	48,143,000
Exercise price per share of warrants (in USD per share) | $ / shares	$ 125.08
Sale of warrants	$ 11,600,000			$ 11,638,000
2019 Convertible Senior Notes
Debt Instrument [Line Items]
Principal amount outstanding		245,000,000	245,000,000
Senior Notes
Debt Instrument [Line Items]
Payments for convertible bond hedges	48,100,000
Senior Notes | 2019 Convertible Senior Notes
Debt Instrument [Line Items]
Principal amount outstanding	245,000,000
Net proceeds from debt issuance	$ 239,300,000
Convertible debt conversion ratio	0.0133251
Debt conversion price per share | $ / shares	$ 75.05
Interest on debt instrument (percent)	0.75%
Carrying value of equity component		51,300,000
Proceeds from issuance of debt	$ 245,000,000
Discount rate (percent)	5.83%
Convertible debt, noncurrent	$ 192,500,000
If-converted value of debt in excess of principal		86,700,000
Debt issuance cost	5,700,000
Equity component of convertible debt issuance, net of issuance costs	1,200,000
Unamortized debt issuance costs	$ 4,500,000
Debt issuance costs, net		$ 2,500,000	$ 3,400,000
Term of debt (duration)	5 years
Senior Notes | 2019 Convertible Senior Notes | Debt Instrument, Redemption, Period One
Debt Instrument [Line Items]
Number of trading days | d	20
Number of consecutive trading days	30 days
Stock price trigger threshold (percent)	130.00%
Senior Notes | 2019 Convertible Senior Notes | Debt Instrument, Redemption, Period Two
Debt Instrument [Line Items]
Number of trading days | d	5
Number of consecutive trading days	10 days
Debt threshold trigger price (percent)	98.00%

Other Balance Sheet Details - I

Other Balance Sheet Details - Investment categories (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Short-term investments
Schedule of Available-for-sale Securities [Line Items]
Cost	$ 120,758	$ 97,891
Gross unrealized gains	1,564	4,944
Gross unrealized losses	(26)	(44)
Estimated fair value	122,296	102,791
Bank Deposits
Schedule of Available-for-sale Securities [Line Items]
Cost	40,715	43,043
Gross unrealized gains	19	0
Gross unrealized losses	0	(4)
Estimated fair value	40,734	43,039
Corporate Bonds
Schedule of Available-for-sale Securities [Line Items]
Cost	11,031	41,238
Gross unrealized gains	0	0
Gross unrealized losses	(5)	(35)
Estimated fair value	11,026	41,203
Corporate Equity Securities
Schedule of Available-for-sale Securities [Line Items]
Cost	1,512	1,843
Gross unrealized gains	1,542	4,944
Gross unrealized losses	0	0
Estimated fair value	3,054	6,787
Commercial Paper
Schedule of Available-for-sale Securities [Line Items]
Cost	33,074	1,747
Gross unrealized gains	2	0
Gross unrealized losses	(9)	0
Estimated fair value	33,067	1,747
Agency bonds
Schedule of Available-for-sale Securities [Line Items]
Cost	7,294
Gross unrealized gains	1
Gross unrealized losses	0
Estimated fair value	7,295
U.S. Government bonds
Schedule of Available-for-sale Securities [Line Items]
Cost	7,508
Gross unrealized gains	0
Gross unrealized losses	(1)
Estimated fair value	7,507
Asset-backed Securities
Schedule of Available-for-sale Securities [Line Items]
Cost		10,020
Gross unrealized gains		0
Gross unrealized losses		(5)
Estimated fair value		$ 10,015
Municipal bonds
Schedule of Available-for-sale Securities [Line Items]
Cost	19,624
Gross unrealized gains	0
Gross unrealized losses	(11)
Estimated fair value	$ 19,613

Other Balance Sheet Details (De

Other Balance Sheet Details (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Other Balance Sheet Details [Abstract]
Prepaid expenses	$ 1,864	$ 1,177
Other receivables	311	731
Other current assets	$ 2,175	$ 1,908

Other Balance Sheet Details - P

Other Balance Sheet Details - Property and Equipment (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Property, Plant and Equipment [Line Items]
Property and equipment , gross	$ 3,390	$ 3,153
Less accumulated depreciation and amortization	(1,571)	(2,781)
Property and equipment, net	1,819	372
Depreciation	200	200	$ 300
Lab and office equipment
Property, Plant and Equipment [Line Items]
Property and equipment , gross	1,067	2,248
Leasehold improvements
Property, Plant and Equipment [Line Items]
Property and equipment , gross	1,754	273
Computer equipment and software
Property, Plant and Equipment [Line Items]
Property and equipment , gross	$ 569	$ 632
Minimum
Property, Plant and Equipment [Line Items]
Property and equipment, useful life	3 years
Maximum
Property, Plant and Equipment [Line Items]
Property and equipment, useful life	10 years

Other Balance Sheet Details - G

Other Balance Sheet Details - Goodwill and Other Intangible Assets (Details) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Finite-Lived Intangible Assets [Line Items]
Goodwill	$ 72,207,000	$ 12,238,000
Total goodwill and other identifiable intangible assets, net	$ 276,912,000	60,585,000
Finite-lived intangible asset, useful life	20 years
Amortization expense	$ 10,600,000	2,400,000	$ 2,400,000
Amortization expense, 2017	10,600,000
Amortization expense, 2018	10,600,000
Amortization expense, 2019	10,600,000
Amortization expense, 2020	10,600,000
Amortization expense, 2021	10,600,000
Impairment of intangible assets with finite lives	0
Customer relationships
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	29,600,000	29,600,000
Less: Accumulated amortization	(8,784,000)	(7,304,000)
Trade name
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	2,642,000	2,642,000
Less: Accumulated amortization	(784,000)	(652,000)
Complete technology
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	182,577,000	15,267,000
Less: Accumulated amortization	(12,792,000)	(3,762,000)
Licensing agreements
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	26,298,000	8,602,000
Less: Accumulated amortization	(477,000)	(48,000)
Total goodwill and other identifiable intangible assets, net	25,821,000	8,554,000
Acquired in-process research and development
Finite-Lived Intangible Assets [Line Items]
IPR&D	12,246,000	12,556,000
CorMatrix | Licensing agreements
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	17,696,000	0
Selexis | Licensing agreements
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	$ 8,602,000	$ 8,602,000

Other Balance Sheet Details (49

Other Balance Sheet Details (Details 1) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Other Balance Sheet Details [Abstract]
Compensation	$ 2,603	$ 1,711
Legal	829	726
Amounts owed to former licensees	899	915
Royalties owed to third parties	942	823
Other	1,124	1,230
Accrued liabilities	$ 6,397	$ 5,405

Other Balance Sheet Details - C

Other Balance Sheet Details - Contingent Liabilities (Details) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Business Acquisition [Line Items]
Revenue royalty payable on all Cydex-related revenue (percent)	20.00%
Cydex-related revenue amount that triggers royalty payments	$ 15,000,000
Additional revenue royalty payable when higher threshold of Cydex-related revenue met (percent)	10.00%
Cydex-related revenue amount that triggers additional royalty payments	$ 35,000,000
Contingent Liability [Roll Forward]
Commercial rights, beginning	13,500,000	$ 15,200,000
Payments	(8,777,000)	(6,740,000)	$ (3,493,000)
Fair Value Adjustment	3,400,000	5,000,000
Commercial rights, ending	8,100,000	13,500,000	15,200,000
CyDex
Contingent Liability [Roll Forward]
Commercial rights, beginning	9,500,000	11,497,000
Payments	(6,158,000)	(5,848,000)
Fair Value Adjustment	3,259,000	3,800,000
Commercial rights, ending	6,600,000	9,500,000	11,497,000
Metabasis
Contingent Liability [Roll Forward]
Commercial rights, beginning	4,000,000	3,652,000
Payments	(2,618,000)	(865,000)
Fair Value Adjustment	74,000	1,172,000
Commercial rights, ending	$ 1,500,000	$ 4,000,000	$ 3,652,000

Other Balance Sheet Details (51

Other Balance Sheet Details (Details 2) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Other Balance Sheet Details [Abstract]
Deferred rent	$ 357	$ 0
Deposits	43	268
Other	287	29
Other long-term liabilities	$ 687	$ 297

Stockholders' Equity (Details)

Stockholders' Equity (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Shares [Rollforward]
Balance at Beginning of Period (shares)	1,683,341
Granted (shares)	263,489
Exercised (shares)	(164,440)
Forfeited (shares)	(28,115)
Balance at End of Period (shares)	1,754,275	1,683,341
Exercisable at December 31, 2016 (shares)	1,298,561
Options vested and expected to vest as of December 31, 2016 (shares)	1,752,275
Weighted Average Exercise Price [Roll Forward]
Balance at Beginning of Period (in usd per share)	$ 34.19
Granted (in usd per share)	92.09
Exercised (in usd per share)	38.08
Forfeited (in usd per share)	60.17
Balance at End of Period (in usd per share)	42.12	$ 34.19
Exercisable at December 31, 2016 (in usd per share)	30.21
Options vested and expected to vest as of December 31, 2016 (in usd per share)	$ 42.12
Weighted Average Remaining Contractual Term in Years	6 years 2 months 9 days	6 years 5 months 23 days
Exercisable, Weighted Average Remaining Contractual Term in Years	5 years 5 months 9 days
Options vested and expected to vest, Weighted Average Remaining Contractual Term in Years	6 years 2 months 9 days
Aggregate Intrinsic Value	$ 104,247	$ 124,800
Exercisable, Aggregate Intrinsic Value	92,723
Options vested and expected to vest, Aggregate Intrinsic Value	$ 104,247

Stockholders' Equity (Details 1

Stockholders' Equity (Details 1)	12 Months Ended
	Dec. 31, 2016$ / sharesshares
$8.58 – $138.53
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	$ 8.58
Range of exercise prices (per share), upper	$ 138.53
Options outstanding (shares) | shares	1,752,275
Weighted average remaining life in years	6 years 2 months 9 days
Weighted average exercise price (per share)	$ 42.12
Options exercisable (shares) | shares	1,298,561
Weighted average exercise price (per share)	$ 30.21
$8.58 - $12.53
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	8.58
Range of exercise prices (per share), upper	$ 12.53
Options outstanding (shares) | shares	247,574
Weighted average remaining life in years	3 years 11 months 9 days
Weighted average exercise price (per share)	$ 9.98
Options exercisable (shares) | shares	247,574
Weighted average exercise price (per share)	$ 9.98
$10.12 - $12.81
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	10.12
Range of exercise prices (per share), upper	$ 12.81
Options outstanding (shares) | shares	76,100
Weighted average remaining life in years	4 years 11 months 1 day
Weighted average exercise price (per share)	$ 11.38
Options exercisable (shares) | shares	76,100
Weighted average exercise price (per share)	$ 11.38
$14.47 - $14.47
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	14.47
Range of exercise prices (per share), upper	$ 14.47
Options outstanding (shares) | shares	288,887
Weighted average remaining life in years	5 years 1 month 10 days
Weighted average exercise price (per share)	$ 14.47
Options exercisable (shares) | shares	274,887
Weighted average exercise price (per share)	$ 14.47
$16.14 - $21.00
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	16.14
Range of exercise prices (per share), upper	$ 21
Options outstanding (shares) | shares	106,242
Weighted average remaining life in years	1 year 10 months 6 days
Weighted average exercise price (per share)	$ 17.76
Options exercisable (shares) | shares	106,242
Weighted average exercise price (per share)	$ 17.76
$21.92 - $21.92
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	21.92
Range of exercise prices (per share), upper	$ 21.92
Options outstanding (shares) | shares	225,105
Weighted average remaining life in years	6 years 1 month 17 days
Weighted average exercise price (per share)	$ 21.92
Options exercisable (shares) | shares	213,199
Weighted average exercise price (per share)	$ 21.92
$32.00 - $53.34
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	32
Range of exercise prices (per share), upper	$ 53.34
Options outstanding (shares) | shares	72,330
Weighted average remaining life in years	6 years 7 days
Weighted average exercise price (per share)	$ 36.18
Options exercisable (shares) | shares	62,747
Weighted average exercise price (per share)	$ 34.73
$56.26 - $59.26
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	56.26
Range of exercise prices (per share), upper	$ 59.26
Options outstanding (shares) | shares	183,595
Weighted average remaining life in years	8 years 1 month 10 days
Weighted average exercise price (per share)	$ 56.26
Options exercisable (shares) | shares	70,877
Weighted average exercise price (per share)	$ 56.26
$63.58 - $68.62
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	63.58
Range of exercise prices (per share), upper	$ 68.62
Options outstanding (shares) | shares	26,382
Weighted average remaining life in years	7 years 6 months
Weighted average exercise price (per share)	$ 67.20
Options exercisable (shares) | shares	21,976
Weighted average exercise price (per share)	$ 67.50
$74.42 - $74.42
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	74.42
Range of exercise prices (per share), upper	$ 74.42
Options outstanding (shares) | shares	227,856
Weighted average remaining life in years	7 years 1 month 13 days
Weighted average exercise price (per share)	$ 74.42
Options exercisable (shares) | shares	162,233
Weighted average exercise price (per share)	$ 74.42
$85.79 - $138.53
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	85.79
Range of exercise prices (per share), upper	$ 138.59
Options outstanding (shares) | shares	298,204
Weighted average remaining life in years	9 years 11 days
Weighted average exercise price (per share)	$ 93.19
Options exercisable (shares) | shares	62,726
Weighted average exercise price (per share)	$ 89.71

Stockholders' Equity (Details 2

Stockholders' Equity (Details 2) - Restricted Stock	12 Months Ended
	Dec. 31, 2016$ / sharesshares
Shares [Rollforward]
Nonvested at Beginning of Period (shares) | shares	130,749
Granted (shares) | shares	234,855
Vested (shares) | shares	(54,421)
Forfeited (shares) | shares	(2,483)
Nonvested at End of Period (shares) | shares	308,700
Weighted-Average Grant Date Fair Value [Roll Forward]
Nonvested at Beginning of Period (in usd per share) | $ / shares	$ 60.36
Granted (in usd per share) | $ / shares	95.31
Vested (in usd per share) | $ / shares	66.79
Forfeited (in usd per share) | $ / shares	67.95
Nonvested at End of Period (in usd per share) | $ / shares	$ 86.61

Stockholders' Equity (Details T

Stockholders' Equity (Details Textual) - USD ($)	May 31, 2012	May 29, 2009	May 31, 2016	Sep. 30, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Corporate Share Repurchase [Abstract]
Shares repurchased in period (shares)					40,500	6,120	1,253,425
Shares repurchased in period, value					$ 3,901,000	$ 489,000	$ 67,955,000
Stock repurchase program, authorized amount				$ 200,000,000
Stock repurchase program, period in force				3 years
Stock repurchase program, remaining authorized repurchase amount					$ 195,600,000
Stock Options
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted-average grant date fair value per share of stock options (in USD per share)					$ 46.53	$ 35.39	$ 46.20
Intrinsic value of options exercised					$ 12,000,000	$ 20,700,000	$ 15,300,000
Unrecognized compensation cost					$ 17,500,000
Weighted-average period in which cost is expected to be recognized					2 years 2 months 20 days
Cash received from options exercised					$ 6,200,000	$ 8,700,000	$ 4,400,000
Restricted Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted-average period in which cost is expected to be recognized					1 year 1 month 20 days
Unrecognized compensation cost, restricted stock					$ 13,800,000
2002 Stock Incentive Plan | Stock Options
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Increase the number of shares under the 2002 Stock Incentive Plan (shares)	1,800,000	1,300,000	900,000
Shares available for future option grants (shares)					1,000,000
Amended ESPP
Employee Stock Purchase Plan [Abstract]
Shares allowed to purchase in employee stock purchase plan (shares)					1,250
Percentage lesser of fair market value taken as purchase price of share					85.00%
Common stock issued under amended ESSP (shares)					1,961	3,374	3,774

Stockholders' Equity - Share-ba

Stockholders' Equity - Share-base Compensation (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based compensation expense	$ 18,893	$ 12,458	$ 11,270
Research and development expenses
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based compensation expense	8,836	4,080	3,595
General and administrative expenses
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based compensation expense	$ 10,057	$ 8,378	$ 7,675

Stockholders' Equity - Assumpti

Stockholders' Equity - Assumptions (Details)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate (percent)			1.90%
Expected term		6 years 6 months	6 years
Forfeiture rate (percent)	5.00%	8.52%
Minimum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate (percent)	1.30%	1.70%
Expected volatility (percent)	48.00%	50.00%	62.00%
Expected term	6 years 7 months 6 days
Forfeiture rate (percent)			8.60%
Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate (percent)	1.90%	2.00%
Expected volatility (percent)	50.00%	58.00%	69.00%
Expected term	6 years 8 months 12 days
Forfeiture rate (percent)			9.70%

Income Taxes (Details)

Income Taxes (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Current expense (benefit):
Federal									$ 21	$ 11	$ 15
State									12	7	19
Total Current Income Tax Benefit									33	18	34
Deferred expense (benefit):
Federal									10,534	(167,413)	406
State									(240)	(24,720)	(30)
Income tax expense from continuing operations	$ 10,354	$ 160	$ (3,881)	$ 3,694	$ (514)	$ (191,881)	$ 265	$ 15	$ 10,327	$ (192,115)	$ 410

Income Taxes (Details 2)

Income Taxes (Details 2) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Tax Expense (Benefit), Continuing Operations, Income Tax Reconciliation [Abstract]
Amounts computed at statutory federal rate									$ 2,786	$ 13,198	$ 3,843
State taxes net of federal benefit									175	386	697
Meals & entertainment									16	16	9
Imputed interest									(1)	(161)	53
Section 162(m) limitation									94	197	490
Contingent liabilities									1,225	1,684	1,748
Stock-based compensation									263	140	89
Expired NOLs									0	232	88
Research and development credits									(1,525)	304	(113)
Change in uncertain tax positions									1,423	27,188	7
Rate change for changes in state law									25	(5,756)	119
APIC Excess Tax Benefit True Up									(622)	0	0
Increase in deferred tax assets from completion of 382 analysis									(120)	3,329	43
Avinza true up									0	(2,107)	0
Change in valuation allowance									6,283	(231,370)	(7,243)
Other									305	605	580
Income tax expense from continuing operations	$ 10,354	$ 160	$ (3,881)	$ 3,694	$ (514)	$ (191,881)	$ 265	$ 15	$ 10,327	$ (192,115)	$ 410

Income Taxes (Details 1)

Income Taxes (Details 1) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Deferred assets:
Net operating loss carryforwards	$ 150,226	$ 160,595
Research credit carryforwards	26,878	25,613
Fixed assets and intangibles	4,385	8,839
Accrued expenses	943	1,523
Contingent liabilities	578	707
Deferred revenue	0	3
Present value of royalties	591	3,007
Deferred rent	45	68
Capital Loss Carryforward	4,432	0
Viking Equity Method Investment	5,692	1,840
Other	19,312	15,441
Deferred tax assets	213,082	217,636
Valuation allowance for deferred tax assets	(15,349)	(9,066)
Net deferred tax assets	197,733	208,570
Deferred tax liabilities:
Retrophin fair value adjustment	(52)	(1,256)
Convertible debt	(1,196)	(1,844)
Identified intangibles	(68,631)	(12,770)
Identified indefinite lived intangibles	(3,963)	(3,617)
Total	$ 123,891	$ 189,083

Income Taxes (Details 3)

Income Taxes (Details 3) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Reconciliation of Unrecognized Tax Benefits, Excluding Amounts Pertaining to Examined Tax Returns [Roll Forward]
Balance at beginning of period	$ 36,452	$ 8,524	$ 8,504
Additions based on tax positions related to the current year	70	154	40
Additions for tax positions of prior years	2,408	28,224	0
Reductions for tax positions of prior years	(160)	(450)	(20)
Balance at end of period	$ 38,770	$ 36,452	$ 8,524

Income Taxes (Details Textual)

Income Taxes (Details Textual) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Operating Loss Carryforwards [Line Items]
Valuation allowance, change in amount	$ 6.3	$ (231.7)	$ (7.2)
Unrecognized tax benefits that would impact effective tax rate	35.5
Realization Of Excess Tax Benefits From Share Based Compensation
Operating Loss Carryforwards [Line Items]
Deferred tax assets not recognized related to share-based compensation	13.7	$ 11.5
Research Tax Credit Carryforward
Operating Loss Carryforwards [Line Items]
Tax credit carryforward	21.9
California and New Jersey Research Tax Credit Carryforward
Operating Loss Carryforwards [Line Items]
Tax credit carryforward	19.4
Internal Revenue Service (IRS)
Operating Loss Carryforwards [Line Items]
Operating loss carryforward	446.3
State and Local Jurisdiction
Operating Loss Carryforwards [Line Items]
Operating loss carryforward	$ 140.5

Summary of Unaudited Quarterl63

Summary of Unaudited Quarterly Financial Information (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016		Dec. 31, 2015		Dec. 31, 2014
Quarterly Financial Information Disclosure [Abstract]
Total revenues	$ 38,185	$ 21,619	$ 19,521	$ 29,648	$ 21,193	$ 17,701	$ 18,418	$ 14,602	$ 108,973		$ 71,914		$ 64,538
Total operating costs and expenses	18,831	16,153	15,552	14,552	10,175	9,104	14,053	11,253	65,088		44,585		44,912
Income tax (expense) benefit	(10,354)	(160)	3,881	(3,694)	514	191,881	(265)	(15)	(10,327)		192,115		(410)
(Loss) income from continuing operations	(3,125)	1,051	(6,170)	5,877	6,341	199,165	22,027	(89)
Income from discontinued operations				731					731		0		0
Less: Net loss attributable to noncontrolling interests					0	0	(1,537)	(843)	0		(2,380)		(1,132)
Net income	$ (3,125)	$ 1,051	$ (6,170)	$ 6,608	$ 6,341	$ 199,165	$ 23,564	$ 754	$ (1,636)		$ 229,824		$ 12,024
Basic per share amounts(1):
Net income (loss) (in usd per share)	$ 0.15	$ 0.05	$ (0.30)	$ 0.32	$ 0.32	$ 10.01	$ 1.19	$ 0.04	$ (0.08)	[1]	$ 11.61	[1]	$ 0.59	[1]
Diluted per share amounts(1):
Net income (loss) (in usd per share)	$ 0.15	$ 0.05	$ (0.30)	$ 0.30	$ 0.29	$ 9.28	$ 1.11	$ 0.04	$ (0.08)	[1]	$ 10.83	[1]	$ 0.56	[1]
Weighted average shares—basic (shares)	20,898	20,887	20,832	20,708	19,933	19,887	19,725	19,612	20,831		19,790		20,419
Weighted average shares—diluted (shares)	20,898	22,997	20,832	22,284	21,542	21,460	21,276	20,631	20,831		21,228		21,433
[1]	The sum of net income per share amounts may not equal the total due to rounding