Ligand Pharmaceuticals (LGND) 10-K 1 Mar 18 2017 FY Annual report Financial data

Document and Entity Information

Document and Entity Information - USD ($) $ in Billions	12 Months Ended
	Dec. 31, 2017	Feb. 26, 2018	Jun. 30, 2017
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, 2017
Amendment Flag	false
Document Fiscal Year Focus	2,017
Document Fiscal Period Focus	FY
Current Fiscal Year End Date	--12-31
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		21,204,264
Entity Public Float			$ 2.2
Entity Voluntary Filers	No
Entity Well-Known Seasoned Issuer	Yes
Entity Current Reporting Status	Yes

CONSOLIDATED BALANCE SHEETS

CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 20,620	$ 18,752
Short-term investments	181,041	122,296
Accounts receivable, net	25,596	14,700
Note receivable from Viking	3,877	3,207
Inventory	4,373	1,923
Other current assets	1,514	2,175
Total current assets	237,021	163,053
Deferred income taxes	84,422	123,891
Investment in Viking	6,438	8,345
Intangible assets, net	228,584	204,705
Goodwill	85,959	72,207
Commercial license rights	19,526	25,821
Property and equipment, net	4,212	1,819
Other assets	4,859	1,744
Total assets	671,021	601,585
Current liabilities:
Accounts payable	2,259	2,734
Accrued liabilities	7,377	6,397
Current contingent liabilities	4,703	5,088
2019 convertible senior notes, net	224,529	212,910
Total current liabilities	238,868	227,129
Long-term contingent liabilities	9,258	2,916
Long-term deferred revenue, net	3,525
Other long-term liabilities	723	687
Total liabilities	252,374	230,732
Commitments and contingencies
Equity component of currently redeemable convertible notes (Note 6)	18,859	29,563
Stockholders’ equity:
Common stock, $0.001 par value; 33,333,333 shares authorized; 21,148,665 and 20,909,301 shares issued and outstanding at December 31, 2017 and 2016, respectively	21	21
Additional paid-in capital	798,205	769,653
Accumulated other comprehensive income	2,486	2,743
Accumulated deficit	(400,924)	(431,127)
Total stockholders’ equity	399,788	341,290
Total liabilities and stockholders’ equity	$ 671,021	$ 601,585

CONSOLIDATED BALANCE SHEETS (Pa

CONSOLIDATED BALANCE SHEETS (Parenthetical) - $ / shares	Dec. 31, 2017	Dec. 31, 2016
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)	21,148,665	20,909,301
Common stock, shares outstanding (shares)	21,148,665	20,909,301

CONSOLIDATED STATEMENTS OF OPER

CONSOLIDATED STATEMENTS OF OPERATIONS - USD ($) shares in Thousands, $ in Thousands		12 Months Ended
		Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Revenues:
Royalties		$ 88,685	$ 59,423	$ 38,194
Material sales		22,070	22,502	27,662
License fees, milestones and other revenues		30,347	27,048	6,058
Total revenues		141,102	108,973	71,914
Operating costs and expenses:
Cost of sales	[1]	5,366	5,571	5,807
Amortization of intangibles		12,120	10,643	2,375
Research and development		26,887	21,221	11,005
General and administrative		28,653	27,653	25,398
Total operating costs and expenses		73,026	65,088	44,585
Income from operations		68,076	43,885	27,329
Other (expense) income:
Interest expense, net		(11,400)	(12,178)	(11,802)
Increase in contingent liabilities		(2,580)	(3,334)	(5,013)
Gain on deconsolidation of Viking		0	0	28,190
Loss from Viking		(2,048)	(23,132)	(5,143)
Other income, net		5,183	2,719	1,768
Total other (expense) income, net		(10,845)	(35,925)	8,000
Income before income tax benefit (expense)		57,231	7,960	35,329
Income tax benefit (expense)		(44,675)	(10,327)	192,115
Income (loss) from operations		12,556	(2,367)	227,444
Discontinued operations:
Gain on sale of Oncology Product Line before income taxes		0	1,139	0
Income tax expense on discontinued operations		0	(408)	0
Income from discontinued operations			731	0
Net income (loss) including noncontrolling interests		12,556	(1,636)	227,444
Less: Net loss attributable to noncontrolling interests		0	0	(2,380)
Net income (loss)		$ 12,556	$ (1,636)	$ 229,824
Basic per share amounts:
Income (loss) from continuing operations (USD per share)	[2]	$ 0.60	$ (0.11)	$ 11.61
Income from discontinued operations (USD per share)	[2]		0.04	0
Net income (loss) - Basic (USD per share)	[2]	0.60	(0.08)	11.61
Diluted per share amounts:
Income (loss) from continuing operations (USD per share)	[2]	0.53	(0.11)	10.83
Income from discontinued operations (USD per share)	[2]		0.04	0
Net (loss) income - Diluted (USD per share)	[2]	$ 0.53	$ (0.08)	$ 10.83
Weighted-average shares outstanding - basic (shares)		21,032	20,831	19,790
Weighted-average shares outstanding - diluted (shares)		23,481	20,831	21,228
[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, 2017	Dec. 31, 2016	Dec. 31, 2015
Statement of Comprehensive Income [Abstract]
Net income (loss)	$ 12,556	$ (1,636)	$ 229,824
Unrealized net gain on available-for-sale securities, net of tax	143	93	1,933
Less:Reclassification of net realized gains included in net income, net of tax	(400)	(2,253)	(1,965)
Comprehensive income (loss)	$ 12,299	$ (3,796)	$ 229,792

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 (shares) at Dec. 31, 2014		19,575,150
Balance at beginning of period at Dec. 31, 2014	$ 24,408	$ 20	$ 680,660	$ 4,953	$ (659,315)	$ (1,910)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock under employee stock compensation plans, net (in shares)		379,982
Issuance of common stock under employee stock compensation plans, net	8,849		8,849
Shares issued in OMT acquisition	0
Reclassification of equity component of currently redeemable convertible notes	(39,628)		(39,628)
Stock-based compensation	$ 12,458		12,458
Repurchase of common stock (shares)	(6,120)	(6,120)
Repurchase of common stock	$ (489)		(489)
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 (shares) at Dec. 31, 2015		19,949,012
Balance at end of period at Dec. 31, 2015	237,282	$ 20	661,850	4,903	(429,491)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock under employee stock compensation plans, net (in shares)		210,626
Issuance of common stock under employee stock compensation plans, net	5,416		5,416
Shares issued in OMT acquisition (shares)		790,163
Shares issued in OMT acquisition	77,331	$ 1	77,330
Reclassification of equity component of currently redeemable convertible notes	10,065		10,065
Stock-based compensation	$ 18,893		18,893
Repurchase of common stock (shares)	(40,500)	(40,500)
Repurchase of common stock	$ (3,901)		(3,901)
Other comprehensive income	(2,160)			(2,160)
Net income	(1,636)				(1,636)
Net loss in noncontrolling interests	0
Balance at end of period (shares) at Dec. 31, 2016		20,909,301
Balance at end of period at Dec. 31, 2016	341,290	$ 21	769,653	2,743	(431,127)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income	5,079
Balance at beginning of period (shares) at Dec. 31, 2016		20,909,301
Balance at beginning of period at Dec. 31, 2016	341,290	$ 21	769,653	2,743	(431,127)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock under employee stock compensation plans, net (in shares)		253,364
Issuance of common stock under employee stock compensation plans, net	(5,558)		(5,558)
Shares issued in OMT acquisition	0
Reclassification of equity component of currently redeemable convertible notes	10,704		10,704
Stock-based compensation	$ 24,916		24,916
Repurchase of common stock (shares)	(14,000)	(14,000)
Repurchase of common stock	$ (1,966)		(1,966)
Other comprehensive income	(257)			(257)
Net income	12,556				12,556
Net loss in noncontrolling interests	0
Balance at end of period (shares) at Dec. 31, 2017		21,148,665
Balance at end of period at Dec. 31, 2017	399,788	$ 21	798,205	$ 2,486	(400,924)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Cumulative-effect adjustment from adoption of ASU 2016-09 | Accounting Standards Update 2016-09					17,900
Cumulative-effect adjustment from adoption of ASU 2016-09 | Accounting Standards Update 2016-09	$ 18,103		$ 456		$ 17,647

CONSOLIDATED STATEMENTS OF CASH

CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Operating activities
Net income (loss)	$ 12,556	$ (1,636)	$ 227,444
Less: gain from discontinued operations	0	731	0
Income (loss) from continuing operations	12,556	(2,367)	227,444
Adjustments to reconcile net income to net cash provided by operating activities:
Change in estimated fair value of contingent liabilities	2,580	3,334	5,013
Realized gain on sale of short-term investment	(831)	(2,352)	(2,603)
Depreciation and amortization	11,714	11,290	2,627
Gain on deconsolidation of Viking	0	0	(28,190)
Loss on equity investment in Viking	2,048	23,132	5,143
Change in fair value of the convertible debt receivable from Viking and warrants	(4,032)	(462)	765
Amortization of premium (discount) on investments, net	(81)	348	0
Amortization of debt discount and issuance fees	11,619	10,925	10,274
Stock-based compensation	24,915	18,893	12,458
Deferred income taxes	44,518	10,697	(192,132)
Other	0	183	107
Changes in operating assets and liabilities, net of acquisition:
Accounts receivable, net	(8,358)	(8,525)	6,489
Inventory	(843)	(244)	(401)
Other current assets	402	526	987
Accounts payable and accrued liabilities	(1,713)	(2,369)	(4,027)
Deferred revenue	(926)	(8)	(2,227)
Net cash provided by operating activities	93,568	63,001	41,727
Investing activities
Purchase of commercial license rights	0	(17,695)	(4,030)
Reduction of cash due to deconsolidation of Viking	0	0	(247)
Cash paid for acquisition, net of cash acquired	(26,653)	(92,502)	0
Payments to CVR holders and other contingency payments	(4,998)	(8,777)	(6,740)
Purchases of property and equipment	(2,156)	(1,850)	(93)
Purchases of short-term investments	(254,258)	(164,438)	(166,025)
Proceeds from sale of short-term investments	86,985	24,596	16,039
Proceeds from maturity of short-term investments	109,649	118,874	57,234
Proceeds from commercial license rights	7,054	0	0
Proceeds received from repayment of Viking note receivable	200	300	0
Net cash used in investing activities	(84,177)	(143,192)	(112,862)
Financing activities
Net proceeds from stock option exercises and ESPP	4,517	6,415	8,849
Taxes paid related to net share settlement of equity awards	(10,074)	(999)	0
Share repurchases	(1,966)	(3,901)	(489)
Net cash (used in) provided by financing activities	(7,523)	1,515	8,360
Net increase (decrease) in cash and cash equivalents	1,868	(78,676)	(62,775)
Cash and cash equivalents at beginning of year	18,752	97,428	160,203
Cash and cash equivalents at end of year	20,620	18,752	97,428
Supplemental disclosure of cash flow information
Interest paid	1,838	1,838	1,822
Taxes paid	157	38	28
Supplemental schedule of non-cash investing and financing activities
Stock issued for acquisition, net of issuance cost	0	(77,331)	0
Stock and warrant received for repayment of Viking notes receivable	0	1,200	0
Accrued inventory purchases	1,007	646	1,333
Unrealized gain on AFS investments	144	(1,109)	3,005
Viking Therapeutics, Inc.
Investing activities
Common stock and warrants in equity method investments	0	(700)	(9,000)
Purchase of Common Stock
Investing activities
Common stock and warrants in equity method investments	$ 0	$ (1,000)	$ 0

Basis of Presentation and Summa

Basis of Presentation and Summary of Significant Accounting Policies	12 Months Ended
	Dec. 31, 2017
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 subsidiaries. All intercompany transactions and balances have been eliminated in consolidation. 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 (loss), 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 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 account 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, 2017 2016 2015 Partner A 46 % 41 % 27 % Partner B 19 % 14 % 23 % Partner C — — 18 % The Company obtains Captisol from two sites at a single supplier, Hovione. If this supplier were not able to supply the requested amounts of Captisol from each site, and if our safety stocks of material were depleted, the Company would be unable to continue to derive revenues from the sale of Captisol until it obtained material from 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 collectability 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, 2017 and 2016 . 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. Business Combinations The acquisition method of accounting for business combinations requires us to use significant estimates and assumptions, including fair value estimates, as of the business combination date and to refine those estimates as necessary during the measurement period (defined as the period, not to exceed one year, in which we may adjust the provisional amounts recognized for a business combination). Under the acquisition method of accounting we recognize separately from goodwill the identifiable assets acquired, the liabilities assumed, including contingent consideration and all contractual contingencies, generally at the acquisition date fair value. Contingent purchase consideration to be settled in cash are remeasured to estimated fair value at each reporting period with the change in fair value recorded in 'Increase in contingent liabilities'. Costs that we incur to complete the business combination such as investment banking, legal and other professional fees are not considered part of consideration and we charge them to general and administrative expense as they are incurred. We measure goodwill as of the acquisition date as the excess of consideration transferred, which we also measure at fair value, over the net of the acquisition date amounts of the identifiable assets acquired and liabilities assumed. In addition, IPR&D is capitalized and assessed for impairment annually. IPR&D is amortized upon product commercialization or upon out-licensing the underlying intellectual property where we no have active involvement in the licensee's development activities. IPR&D is amortized over the estimated life of the commercial product or licensing arrangement. Should the initial accounting for a business combination be incomplete by the end of a reporting period that falls within the measurement period, we report provisional amounts in our financial statements. During the measurement period, we adjust the provisional amounts recognized at the acquisition date to reflect new information obtained about facts and circumstances that existed as of the acquisition date that, if known, would have affected the measurement of the amounts recognized as of that date and we record those adjustments to our financial statements in the period of change, if any. Under the acquisition method of accounting for business combinations, if we identify changes to acquired deferred tax asset valuation allowances or liabilities related to uncertain tax positions during the measurement period and they relate to new information obtained about facts and circumstances that existed as of the acquisition date, those changes are considered a measurement period adjustment and we record the offset to goodwill. We record all other changes to deferred tax asset valuation allowances and liabilities related to uncertain tax positions in current period income tax expense. Contingent Liabilities In connection with the acquisition of Crystal in October 2017, we may be required to pay up to an additional $10.5 million in purchase consideration upon achievement of certain commercial and development milestones to the Crystal shareholders. See footnote 7, Balance Sheet Account Details. 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 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. Goodwill, Intangible Assets and Other Long-Lived 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, 2017, was due to the acquisition of Crystal. 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 the goodwill impairment review, we assess qualitative factors to determine whether it is more likely than not that the fair value of our reporting unit is less than the carrying amount, including goodwill. The qualitative factors include, but are not limited to, macroeconomic conditions, industry and market considerations, and the overall financial performance. If, after assessing the totality of these qualitative factors, we determine that it is not more likely than not that the fair value of our reporting unit is less than the carrying amount, then no additional assessment is deemed necessary. Otherwise, we proceed to perform the two-step test for goodwill impairment. The first step involves comparing the estimated fair value of the reporting unit with the carrying value, including goodwill. If the carrying amount of the reporting unit exceeds the fair value, the second step of the goodwill impairment test is performed to determine the amount of loss, which involves comparing the implied fair value of the goodwill to the carrying value of the goodwill. We 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. We performed the annual assessment for goodwill impairment in the fourth quarter of 2017, noting no impairment. Our identifiable intangible assets are typically comprised of acquired core technologies, licensed technologies, customer relationships and trade names. The cost of identifiable intangible assets with finite lives is generally amortized on a straight-line basis over the assets’ respective estimated useful lives. We regularly perform reviews to determine if any event has occurred that may indicate that intangible assets with finite useful lives and other long-lived assets are potentially impaired. If indicators of impairment exist, an impairment test is performed to assess the recoverability of the affected assets by determining whether the carrying amount of such assets exceeds the undiscounted expected future cash flows. If the affected assets are not recoverable, we estimate the fair value of the assets and record an impairment loss if the carrying value of the assets exceeds the fair value. Factors that may indicate potential impairment include a significant decline in our stock price and market capitalization compared to the net book value, significant changes in the ability of a particular asset to generate positive cash flows, and the pattern of utilization of a particular asset. Commercial license rights Commercial license rights consist of the following (in thousands): December 31, December 31, 2017 2016 Aziyo & CorMatrix $ 17,696 $ 17,696 Selexis 8,602 8,602 26,298 26,298 Less: accumulated amortization (6,772 ) (477 ) Total commercial rights, net $ 19,526 $ 25,821 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. In May 2017, the Company entered into a Royalty Agreement with Aziyo pursuant to which the Company will receive royalties from certain marketed products that Aziyo acquired from CorMatrix. Pursuant to the Royalty Agreement, the Company received $10 million in 2017 from Aziyo to buydown the royalty rates on the products CorMatrix sold to Aziyo. The Royalty Agreement closed on May 31, 2017, in connection with the closing of the asset sale from CorMatrix to Aziyo (the “CorMatrix Asset Sale”). Pursuant to the Royalty Agreement, the Company will receive a 5% royalty on the products Aziyo acquired in the CorMatrix Asset Sale, reduced from the original 20% royalty from CorMatrix pursuant to the previously disclosed Interest Purchase Agreement, dated May 3, 2016 (the “Original Interest Purchase Agreement”) between CorMatrix and the Company. In addition, Aziyo has agreed to pay the Company up to $10 million of additional milestones tied to cumulative net sales of the products Aziyo acquired in the CorMatrix Asset Sale and to extend the term on these royalties by one year. The Royalty Agreement will terminate on May 31, 2027. In addition, in May 2017, the Company entered into an amended and restated interest purchase agreement (the “Amended Interest Purchase Agreement”) with CorMatrix, which supersedes in its entirety the Original Interest Purchase Agreement. Other than removing the commercial products sold to Aziyo in the CorMatrix Sale, the terms of the Amended Interest Purchase Agreement remain unchanged with respect to the CorMatrix developmental pipeline products, including the royalty rate of 5% on such pipeline products. The Amended Interest Purchase Agreement will terminate 10 years from the date of the first commercial sale of such products. The Company accounts for the Aziyo commercial license right as a financial asset in accordance with ASC 310 and amortizes the commercial license right using the 'effective interest' method whereby the Company forecasts expected cash flows over the term of the arrangement to arrive at an annualized effective interest. The annual effective interest associated with the forecasted cash flows from the Royalty Agreement with Aziyo as of December 31, 2017 is 26% . Revenue is calculated by multiplying the carrying value of the commercial license right by the effective interest. The payments received in 2017 were accordingly allocated between revenue and the amortization of the commercial license rights. We elected a prospective approach to account for changes in estimated cash flows and selected a method for determining when an impairment would be recognized and how to measure that impairment. In circumstances where our new estimate of expected cash flows is greater than previously expected, we will update our yield prospectively. While it has not occurred to date, in circumstances where our new estimate of expected cash flows is less than previously expected and below our original estimated yield we will record impairment. Impairment will be recognized by reducing the financial asset to an amount that represents the present value of our most recent estimate of expected cash flows discounted by the original effective interest rate. In circumstances where our new estimate of expected cash flows is less than previously expected, but not below our original estimated yield, we will update our yield prospectively. The Company accounts for commercial license rights related to developmental pipeline products on a non-accrual basis. These developmental pipeline products are non-commercialized, non-approved products that require FDA or other regulatory approval, and thus have uncertain cash flows. The developmental pipeline products are on a non-accrual basis as the Company is not yet able to forecast future cash flows given their pre-commercial stages of development. The Company will prospectively update its yield model under the effective interest method once the underlying products are commercialized and the Company can reliably forecast expected cash flows. Income will be calculated by multiplying the carrying value of the commercial license right by the effective interest rate. In 2017, the Company identified and corrected an immaterial error related to 2016. The adjustment related to the recognition of the income associated with this financial asset. The Company determined the 'effective interest' method should have been used to recognize income associated with the financial asset and that the method utilized previously was incorrect. The error had the impact of understating Commercial License Rights, revenue and net income in 2016. Management evaluated the effect of the adjustment on previously issued consolidated financial statements in accordance with SAB No. 99 and SAB No. 108 and concluded that it was qualitatively and quantitatively immaterial to the historical periods. Management also concluded that correcting the error in 2017 did not have a material impact on the 2017 financial results. As a result, in accordance with SAB No. 108, we corrected our Consolidated Balance Sheets as of June 30, 2017. The error resulted in an understatement of 2016 revenue of $1.3 million and net income of $0.8 million , or $0.04 per diluted share and overstatement of 2017 revenue of $1.3 million and net income of $0.8 million , or $0.04 per diluted share. 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 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 . Convertible Debt In August 2014, the Company completed a $245.0 million offering of 2019 Convertible Senior Notes, which bear interest at 0.75% . The Company accounted for the 2019 Convertible Senior Notes by separating the liability and equity components of the instrument in a manner that reflects the Company's nonconvertible debt borrowing rate. As a result, the Company assigned a value to the debt component of the 2019 Convertible Senior Notes equal to the estimated fair value of similar debt instruments without the conversion feature, which resulted in the Company recording the debt instrument at a discount. The Company is amortizing the debt discount over the life of the 2019 Convertible Senior Notes as additional non-cash interest expense utilizing the effective interest method. 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, 2017, we had a working capital deficit of $1.8 million , which includes the 2019 Convertible Senior notes that are currently redeemable as of December 31, 2017 but excludes another $18.9 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 three 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 since December 31, 2013 and, accordingly, while there can be no assurance, we believe we have the ability to raise additional capital through an S-3 registration or via alternative financing arrangements such as convertible or straight debt. 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 amount

Investment in Viking

Investment in Viking	12 Months Ended
	Dec. 31, 2017
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 also 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 statements of operations. Viking is considered a related party as the Company maintains a seat on Viking's board of directors. In January 2016 and May 2017, the Company entered into two amendments respectively to the LSA with Viking to, among other things, (i) extend the maturity of the convertible loan to May 21, 2018 , (ii) reduce the interest rate from 5.0% to 2.5% , and (iii) 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, the amendments caused Viking to repay $1.5 million and $0.2 million of the Viking Note obligation to the Company in April 2016 and July 2017 , respectively as further discussed below. 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 an 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 warrants have an exercise price of $1.50 per share, are immediately exercisable and will expire on April 13, 2021. As part of this public offering, the Company purchased 560,000 shares of Viking 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 first amendment to the LSA, 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 ended on January 23, 2017 in accordance with the amended LSA. In July 2017, pursuant to the terms of the second amendment to the LSA, Viking paid $0.2 million of the convertible notes in cash, which reduced the accrued interest at the time. As of December 31, 2017, the aggregate fair value of the note receivable was $3.9 million . For the years ended December 31, 2017 and 2016 , a gain of of $3.2 million and $0.3 million on the fair market value of the warrants was included within other income, respectively. See further discussion in Note 4 Fair Value Measurement. 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 17.6% and 30.3% as of December 31, 2017 and 2016, respectively. As a result Viking's public stock offerings, the Company recorded a dilution gain of $2.7 million and a dilution loss of $10.7 million for the years ended December 31, 2017 and 2016, respectively. These amounts were recognized in Loss from Viking in the Company's consolidated statement of operations. 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 a 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. The following table presents summarized financial information of Viking (in thousands): Year ended December 31, (in thousands) 2017 2016 2015 Condensed Statement of Operations: Total revenue — — — Gross profit — — — Loss from operations $19,070 $13,847 $11,996 Net Loss $20,578 $14,732 $23,404 As of December 31, (in thousands) 2017 2016 Condensed Balance Sheet: Current assets $ 21,852 $ 13,975 Noncurrent assets 270 561 22,122 14,536 Current liabilities 8,657 6,477 Noncurrent liabilities — 16 Stockholders' equity 13,465 8,043

Business Combinations

Business Combinations	12 Months Ended
	Dec. 31, 2017
Business Combinations [Abstract]
Business Combinations	Business Combinations Acquisition of Crystal On October 6, 2017, the Company acquired all of the assets and liabilities of Crystal. Crystal is a biotechnology company focused in avian genetics and the generation of fully-human therapeutic engineering of animals for the generation of fully-human therapeutic antibodies through its OmniChicken® technology. Under the terms of the agreement, Ligand was to pay Crystal shareholders $27.2 million in cash including $2.2 million working capital adjustment, and up to an additional $10.5 million of cash consideration based on Crystal’s achievement of certain research and business milestones prior to December 31, 2019 . In addition, Crystal’s shareholders will receive 10% of revenues realized by Ligand above $15 million between the closing date and December 31, 2022 from existing collaboration agreements between Crystal and three of its collaborators, and Crystal’s shareholders will receive 20% of revenues above $1.5 million generated between the closing date and December 31, 2022 pursuant to a four th existing collaboration agreement with a large pharmaceutical company. As of December 31, 2017 , $0.3 million of the initial $27.2 million of cash consideration remained outstanding. The transaction was accounted for as a business combination. At the closing of the acquisition, the Company recorded a $8.4 million contingent liability for amounts potentially due to Crystal shareholders. The initial fair value of the liability was determined using a probability weighted income approach incorporating the estimated future cash flows from potential milestones and revenue sharing. These cash flows were then discounted to present value using discount rates based on the Company’s estimated corporate credit rating, and averaged to approximately 4.6% . Refer to Note 4 Fair Value Measurement for further discussion. The liability will be periodically assessed based on events and circumstances related to the underlying milestones, and any change in fair value will be recorded in the Company’s consolidated statements of operations. The carrying amount of the liability may fluctuate significantly and actual amounts paid may be materially different than the carrying amount of the liability. There was no change in the fair value of the contingent liabilities from the initial valuation date to December 31, 2017 . The aggregate acquisition consideration was determined to be $35.7 million , consisting of (in thousands): Cash paid to Crystal shareholders $ 26,877 Cash payable to Crystal Shareholders 336 Assumed liabilities 129 Fair value of contingent consideration 8,401 Total consideration $ 35,743 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 $ 224 Accounts receivable 2,513 Prepaid expenses and other assets 201 Property and equipment, net 589 Current liabilities assumed (354 ) Deferred revenue (4,624 ) Deferred tax liabilities, net (12,558 ) Intangible asset with finite life - core technology 36,000 Goodwill 13,752 Total consideration $ 35,743 The estimated fair values of assets acquired and liabilities assumed, including deferred tax assets and liabilities, purchased intangibles and deferred revenue, as well as the estimated fair value of contingent consideration described above are provisional. The accounting for these amounts falls within the measurement period and therefore we may adjust these provisional amounts to reflect new information obtained about facts and circumstances that existed as of the acquisition date. The fair value of the core technology, or OmniChicken 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 OmniChicken technology. These projected cash flows were discounted to present value using a discount rate of 10.8% . 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 $13.8 million and was recorded as goodwill, which is not deductible for tax purposes and is primarily attributable to Crystal’s potential revenue growth from combining the Crystal and Ligand businesses and workforce, as well as the benefits of access to different markets and customers. Acquisition of OMT 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. The transaction was accounted for as a business combination and 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, 2017
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, 2017 and 2016 (in thousands): Fair Value Measurements at Reporting Date Using December 31, 2017 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) $ 181,041 $ 1,896 $ 179,145 $ — Note receivable Viking (2) 3,877 — — 3,877 Investment in warrants (3) 3,846 3,846 — — Total assets $ 188,764 $ 5,742 $ 179,145 $ 3,877 Liabilities: Current contingent liabilities - Crystal (7) $ 4,618 $ — $ — $ 4,618 Current contingent liabilities - Cydex (4) 86 — — 86 Long-term contingent liabilities - Metabasis (5) 3,971 — 3,971 — Long-term contingent liabilities - Crystal (7) 3,783 — — 3,783 Long-term contingent liabilities - CyDex (4) 1,503 — — 1,503 Liability for amounts owed to a former licensor (6) 284 284 — — Total liabilities $ 14,245 $ 284 $ 3,971 $ 9,990 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 $ 3,738 $ 119,242 $ 3,207 Liabilities: Current contingent liabilities - CyDex (4) $ 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 a former licensor (6) 371 371 — — Total liabilities $ 3,388 $ 371 $ 1,413 $ 1,604 (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, 2017 approximates the book value since the contractual maturity date was within five months from the end of 2017, and there is no plan to extend the maturity date. The fair value at December 31, 2016 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 . Changes in these assumptions may materially affect the fair value estimate. For the years ended December 31, 2017 , December 31, 2016 , and December 31, 2015 , the Company reported an increase in the fair value of 0.9 million , a decrease in the fair value $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, is 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 CyDex contingent liabilities was 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 developmental and regulatory milestones. Changes in these assumptions can materially affect the fair value. The following table represents significant unobservable inputs used in determining the fair value of contingent liabilities assumed in the acquisition of CyDex: December 31, 2017 2016 Revenue volatility 25% 25% Average of probability of commercialization 12.5% 12.5% Market price of risk 2.9% 3.2% (5) The liability for CVRs for Metabasis is determined using quoted market prices in a market that is not active for the underlying CVR. (6) The liability for amounts owed to a former licensor is determined using quoted market prices in active markets for the underlying investment received from a partner, a portion of which is owed to a former licensor. (7) The fair value of Crystal contingent liabilities was determined using a probability weighted income approach. Most of the contingent payments are based on development or regulatory milestones as defined in the merger agreement with Crystal. The fair value is subjective and is affected by changes in inputs to the valuation model including management’s estimates regarding the timing and probability of achievement of certain developmental and regulatory milestones. At December 31, 2017 , most of the development and regulatory milestones were estimated to be highly probable of being achieved between 2018 and 2020 . Changes in these estimates may materially affect the fair value. A reconciliation of the level 3 financial instruments as of December 31, 2017 is as follows (in thousands): Assets: Fair value of level 3 financial instruments as of December 31, 2016 $ 3,207 Viking note receivable fair market value adjustment 870 Cash payment received as partial repayment of note receivable (200 ) Fair value of level 3 financial instrument assets as of December 31, 2017 $ 3,877 Liabilities Fair value of level 3 financial instruments as of December 31, 2016 $ 1,604 Fair value of Crystal contingent consideration 8,401 Payments to CVR holders and other contingency payments (25 ) Fair value adjustments to contingent liabilities 10 Fair value of level 3 financial instruments as of December 31, 2017 $ 9,990 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 $446.4 million as of December 31, 2017 . 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 $25.6 million as of December 31, 2017 .

Lease Obligations

Lease Obligations	12 Months Ended
	Dec. 31, 2017
Leases [Abstract]
Lease Obligations	Lease Obligations The Company leases office facilities in California and Kansas. These leases expire between 2018 and 2023 . Total rent expense, net under all office leases for 2017 , 2016 and 2015 was $0.3 million , $0.3 million and $0.4 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, 2017 (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 $ 131 $ 275 $ 291 $ 50 $ 747 Office and research facility-La Jolla, CA June 2019 737 373 — — 1,110 Bioscience and Technology Business Center-Lawrence, KS December 2020 57 113 — — 170 Office - Emeryville, CA August 2021 253 528 186 — 967 Research Facility - Emeryville, CA August 2021 197 412 142 — $ 751 Total operating lease obligations $ 1,375 $ 1,701 $ 619 $ 50 $ 3,745 Sublease payments expected to be received: Office and research facility-La Jolla, CA June 2019 641 361 — — 1,002 Net operating lease obligations $ 734 $ 1,340 $ 619 $ 50 $ 2,743

Financing Arrangements

Financing Arrangements	12 Months Ended
	Dec. 31, 2017
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 2017 and 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, 2017 and 2016. As a result, the related unamortized discount of $18.9 million and $29.6 million , at December 31, 2017 and 2016, respectively, 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, 2017 , the “if-converted value” exceeded the principal amount of the 2019 Convertible Senior Notes by $202.0 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 $1.6 million and $2.5 million as of December 31, 2017 and 2016 , 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, 2017 , 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, 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, 2017. 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, 2017 December 31, 2016 2019 Convertible Senior Notes Principal amount outstanding $ 245,000 $ 245,000 Unamortized discount (20,471 ) (32,090 ) Total current portion of notes payable $ 224,529 $ 212,910 As of December 31, 2017 , there were no events of default or violation of any covenants under the Company's financing obligations.

Balance Sheet Account Details

Balance Sheet Account Details	12 Months Ended
	Dec. 31, 2017
Other Balance Sheet Details [Abstract]
Balance Sheet Account Details	Balance Sheet Account Details Short-term Investments The following table summarizes the various investment categories at December 31, 2017 and 2016 (in thousands): Cost Gross unrealized gains Gross unrealized losses Estimated fair value December 31, 2017 Short-term investments Bank deposits $ 80,095 $ 6 $ (42 ) $ 80,059 Corporate bonds 55,335 — (96 ) 55,239 Corporate equity securities 207 1,689 — 1,896 Commercial paper 27,933 — (20 ) 27,913 Agency bonds 4,991 — (1 ) 4,990 U.S. Government bonds 8,939 — (10 ) 8,929 Municipal bonds 2,028 — (13 ) 2,015 $ 179,528 $ 1,695 $ (182 ) $ 181,041 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 Other current assets consist of the following (in thousands): December 31, 2017 2016 Prepaid expenses $ 1,017 $ 1,864 Other receivables 497 311 $ 1,514 $ 2,175 Property and equipment is stated at cost and consists of the following (in thousands): December 31, 2017 2016 Lab and office equipment $ 3,460 $ 1,067 Leasehold improvements 1,917 1,754 Computer equipment and software 697 569 6,074 3,390 Less accumulated depreciation and amortization (1,862 ) (1,571 ) $ 4,212 $ 1,819 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 $ 0.4 million , $0.2 million , and $0.2 million was recognized for the years ended December 31, 2017 , 2016 , and 2015 , respectively and is included in operating expenses. Goodwill and identifiable intangible assets consist of the following (in thousands): December 31, 2017 2016 Indefinite lived intangible assets IPR&D $ 7,923 $ 12,246 Goodwill 85,959 72,207 Definite lived intangible assets Complete technology 222,900 182,577 Less: Accumulated amortization (23,301 ) (12,792 ) Trade name 2,642 2,642 Less: Accumulated amortization (916 ) (784 ) Customer relationships 29,600 29,600 Less: Accumulated amortization (10,264 ) (8,784 ) Total goodwill and other identifiable intangible assets, net $ 314,543 $ 276,912 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 $11.3 million , $10.6 million , and $2.4 million was recognized for the years ended December 31, 2017 and 2016 , and 2015 . Estimated amortization expense for the years ending December 31, 2018 through 2022 is $12.8 million per year. For each of the years ended December 31, 2017 , 2016 , and 2015 , there was no impairment of intangible assets with finite lives. Accrued liabilities consist of the following (in thousands): December 31, 2017 2016 Compensation $ 4,085 $ 2,603 Legal 430 829 Amounts owed to former licensees 396 899 Royalties owed to third parties 954 942 Deferred revenue 173 — Other 1,339 1,124 $ 7,377 $ 6,397 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 paid 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, 2015 Payments Fair Value Adjustment December 31, 2016 Payments Fair Value Adjustment Additions December 31, 2017 Cydex $ 9.5 $ (6.2 ) $ 3.3 $ 6.6 (5.0 ) $ — $ — $ 1.6 Metabasis 4.0 (2.6 ) 0.1 1.5 — 2.5 — 4.0 Crystal — — — — — — 8.4 8.4 Total $ 13.5 $ (8.8 ) $ 3.4 $ 8.1 $ (5.0 ) $ 2.5 $ 8.4 $ 14.0 Other long-term liabilities consist of the following (in thousands): December 31, 2017 2016 Deferred rent $ 321 $ 357 Deposits 43 43 Other 359 287 $ 723 $ 687

Stockholders' Equity

Stockholders' Equity	12 Months Ended
	Dec. 31, 2017
Equity [Abstract]
Stockholders' Equity	Stockholders’ Equity Share-based Compensation Expense The following table summarizes stock-based compensation expense (in thousands): December 31, 2017 2016 2015 Stock-based compensation expense as a component of: Research and development expenses $ 14,235 $ 8,836 $ 4,080 General and administrative expenses 10,680 10,057 8,378 $ 24,915 $ 18,893 $ 12,458 Stock Plans 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, 2017 , there were 0.8 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, 2016 1,754,275 $ 42.12 6.19 $ 104,247 Granted 273,353 112.58 Exercised (148,252 ) 31.58 Forfeited (3,044 ) 79.74 Balance at December 31, 2017 1,876,332 53.17 5.77 157,340 Exercisable at December 31, 2017 1,431,245 40.08 4.95 138,616 Options vested and expected to vest as of December 31, 2017 1,876,332 $ 53.17 5.77 $ 157,340 The weighted-average grant-date fair value of all stock options granted during 2017 , 2016 and 2015 was $53.17 , $46.53 and $35.39 per share, respectively. The total intrinsic value of all options exercised during 2017 , 2016 and 2015 was approximately $13.3 million , $12.0 million and $20.7 million , respectively. Cash received from options exercised, net of fees paid, in 2017 , 2016 and 2015 was $4.7 million , $6.2 million and $8.7 million , respectively. Following is a further breakdown of the options outstanding as of December 31, 2017 : Range of exercise prices Options outstanding Weighted average remaining life in years Weighted average exercise price Options exercisable Weighted average exercise price $8.58 - $10.05 208,032 2.88 $ 9.97 208,032 $ 9.97 $10.12 - $12.81 71,850 3.95 11.44 71,850 11.44 $14.47 - $14.47 285,879 4.11 14.47 271,879 14.47 $16.14 - $17.88 72,777 1.16 16.32 72,777 16.32 $21.92 - $21.92 207,004 5.13 21.92 207,004 21.92 $32.00 - $56.26 226,287 6.72 50.50 160,301 48.49 $63.58 - $68.62 25,757 6.50 67.17 23,726 67.34 $74.42 - $74.42 216,118 6.11 74.42 206,828 74.42 $85.79 - $97.92 238,675 6.99 88.93 138,712 90.54 $100.38 - $141.61 323,953 9.12 112.75 70,136 106.78 $8.58 – $141.61 1,876,332 5.77 $ 53.17 — 1,431,245 $ 40.08 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, 2017 2016 2015 Risk-free interest rate 2.0%-2.2% 1.3%-1.9% 1.7%-2.0% Expected volatility 43%-47% 48%-50% 50%-58% Expected term 6.5 to 6.8 years 6.6 to 6.7 years 6.5 years As of December 31, 2017 , there was $19.4 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 2.52 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, 2016 308,700 $ 86.61 Granted 73,799 99.53 Vested (187,864 ) 84.50 Forfeited (61,341 ) 97.78 Outstanding at December 31, 2017 133,294 $ 91.60 As of December 31, 2017 , unrecognized compensation cost related to non-vested stock awards amounted to $6.5 million . That cost is expected to be recognized over a weighted average period of 1.34 years. Employee Stock Purchase Plan As of December 31, 2017, 67,394 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 3,061 , 1,961 and 3,374 shares issued under the ESPP in 2017, 2016 and 2015, respectively. Share Repurchases During the years ended December 31, 2017 , 2016 and 2015 the Company repurchased 14,000 shares for $2.0 million , 40,500 shares for $3.9 million , 6,120 shares for $0.5 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 $193.6 million of its common stock remained as of December 31, 2017.

Litigation

Litigation	12 Months Ended
	Dec. 31, 2017
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. 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 was voluntarily dismissed without prejudice on May 15, 2017. In November 2017, CyDex, our wholly owned subsidiary, received a paragraph IV certification from Teva Pharmaceuticals USA, Inc., Teva Pharmaceutical Industries Ltd. and Actavis, LLC (collectively “Teva”) alleging that certain of our patents related to Captisol were invalid, unenforceable and/or will not be infringed by Teva’s ANDA related to Spectrum Pharmaceuticals’ NDA for Evomela. On December 20, 2017, CyDex filed a complaint against Teva in the U.S. District Court for the District of Delaware, asserting that Teva’s ANDA would infringe our patents.

Income Taxes

Income Taxes	12 Months Ended
	Dec. 31, 2017
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The Tax Act was enacted on December 22, 2017 and includes a number of changes to existing tax laws that impact the Company, most notably it reduces the US federal corporate tax rate from 35% to 21% , effective January 1, 2018. At December 31, 2017, we have made a reasonable estimate of the effects on our existing deferred tax balances. In other cases, we have not been able to make a reasonable estimate and continue to account for those items based on our existing accounting under ASC 740, Income Taxes, and the provisions of the tax laws that were in effect immediately prior to enactment. For the items for which we were able to determine a reasonable estimate, we recognized a provisional amount of $32.4 million , which is included as a component of income tax expense from continuing operations. In conjunction with the tax law changes, the SEC staff issued Staff Accounting Bulletin No. 118 ("SAB 118") to address the application of U.S. GAAP in situations when a registrant does not have the necessary information available, prepared, or analyzed (including computations) in reasonable detail to complete the accounting for certain income tax effects of the Tax Act. The ultimate impact may differ from these provisional amounts, possibly materially, due to, among other things, additional analysis, changes in interpretations and assumptions the Company has made, additional regulatory guidance that may be issued, and actions the Company may take as a result of the Tax Act. The components of the income tax expense (benefit) for continuing operations are as follows (in thousands): Year Ended December 31, 2017 2016 2015 Current expense (benefit): Federal $ — $ 21 $ 11 State 111 12 7 Foreign 261 — — 372 33 18 Deferred expense (benefit): Federal 44,075 10,534 (167,413 ) State 228 (240 ) (24,720 ) Foreign — — — $ 44,675 $ 10,327 $ (192,115 ) 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, 2017 2016 2015 Tax at federal statutory rate $ 20,031 $ 2,786 $ 13,198 State, net of federal benefit 622 175 386 Contingent liabilities 903 1,225 1,684 Stock-based compensation (4,019 ) 263 140 Research and development credits (2,821 ) (1,525 ) 304 Change in uncertain tax positions 1,308 1,423 27,188 Rate change for changes in federal or state law 32,429 25 (5,756 ) Change in valuation allowance (4,169 ) 6,283 (231,370 ) Other 391 (328 ) 2,111 $ 44,675 $ 10,327 $ (192,115 ) We remeasured certain deferred tax assets and liabilities based on the rates at which they are expected to reverse in the future, which is generally 21% . However, we are still analyzing certain aspects of the Tax Act and refining our calculations, which could potentially affect the measurement of these balances or potentially give rise to new deferred tax amounts. The provisional amount recorded related to the remeasurement of our deferred tax balance was $32.4 million . Significant components of the Company’s deferred tax assets and liabilities as of December 31, 2017 and 2016 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, 2017 , 2016 and 2015 . The valuation allowance decreased $8.4 million in 2017, increased $6.3 million in 2016 and decreased $231.7 million in 2015. December 31, 2017 2016 (in thousands) Deferred assets: Net operating loss carryforwards $ 90,272 $ 150,226 Research credit carryforwards 30,677 26,878 Fixed assets and intangibles 1,984 4,385 Accrued expenses 845 943 Contingent liabilities 354 578 Deferred revenue 17 — Present value of royalties — 591 Deferred rent 28 45 Capital Loss Carryforward 1,609 4,432 Viking Equity Method Investment 5,137 5,692 Other 12,117 19,312 143,040 213,082 Valuation allowance for deferred tax assets (6,987 ) (15,349 ) Net deferred tax assets $ 136,053 $ 197,733 Deferred tax liabilities: Retrophin fair value adjustment $ (243 ) $ (52 ) Convertible debt (737 ) (1,196 ) Identified intangibles (48,237 ) (68,631 ) Identified indefinite lived intangibles (2,414 ) (3,963 ) Total $ 84,422 $ 123,891 As of December 31, 2017 , the Company had federal and state net operating loss carryforwards set to expire through 2036 of $387.9 million and $126.5 million of state net operating loss carryforwards. The Company also has $23.8 million of federal research and development credit carryforwards, which expire through 2036 . The Company has $20.7 million of California research and development credit carryforwards that have no expiration date. Pursuant to Section 382 and 383 of the Internal Revenue Code, utilization of the Company’s net operating losses and credits may be subject to annual limitations in the event of any significant future changes in its ownership structure. These annual limitations may result in the expiration of net operating losses and credits prior to utilization. The deferred tax assets as of December 31, 2017 are net of any previous limitations due to Section 382 and 383. 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, 2017 , 2016 and 2015 is as follows (in thousands): December 31, 2017 2016 2015 Balance at beginning of year $ 38,770 $ 36,452 $ 8,524 Additions based on tax positions related to the current year 1,067 70 154 Additions for tax positions of prior years 109 2,408 28,224 Reductions for tax positions of prior years (10,583 ) (160 ) (450 ) Balance at end of year $ 29,363 $ 38,770 $ 36,452 Included in the balance of unrecognized tax benefits at December 31, 2017 is $26.8 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, 2017 and December 31, 2016 , 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 the present. The state income tax returns generally remain open for the 2012 tax year through the present. Net operating loss and research credit carryforwards arising prior to these years are also open to examination if and when utilized.

Summary of Unaudited Quarterly

Summary of Unaudited Quarterly Financial Information	12 Months Ended
	Dec. 31, 2017
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 2017 and 2016 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 ) 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 2017 Total revenues $ 29,267 $ 27,995 $ 33,375 $ 50,465 Total operating costs and expenses 19,051 14,980 16,882 22,113 Income tax (expense) benefit (1,114 ) (2,242 ) (3,645 ) (37,674 ) Net Income (loss) 5,079 6,058 8,426 (7,007 ) Basic per share amounts: Net income $ 0.24 $ 0.29 $ 0.40 $ (0.33 ) Diluted per share amounts: Net income $ 0.22 $ 0.26 $ 0.36 $ (0.33 ) Weighted average shares—basic 20,938 21,013 21,071 21,109 Weighted average shares—diluted 23,019 23,216 23,551 21,109

Basis of Presentation and Sum19

Basis of Presentation and Summary of Significant Accounting Policies (Policies)	12 Months Ended
	Dec. 31, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
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.
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 (loss), stockholders' equity and operating cash flows as previously reported.
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
Concentrations of Business 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 & 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 collectability 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	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.
Business Combinations	Business Combinations The acquisition method of accounting for business combinations requires us to use significant estimates and assumptions, including fair value estimates, as of the business combination date and to refine those estimates as necessary during the measurement period (defined as the period, not to exceed one year, in which we may adjust the provisional amounts recognized for a business combination). Under the acquisition method of accounting we recognize separately from goodwill the identifiable assets acquired, the liabilities assumed, including contingent consideration and all contractual contingencies, generally at the acquisition date fair value. Contingent purchase consideration to be settled in cash are remeasured to estimated fair value at each reporting period with the change in fair value recorded in 'Increase in contingent liabilities'. Costs that we incur to complete the business combination such as investment banking, legal and other professional fees are not considered part of consideration and we charge them to general and administrative expense as they are incurred. We measure goodwill as of the acquisition date as the excess of consideration transferred, which we also measure at fair value, over the net of the acquisition date amounts of the identifiable assets acquired and liabilities assumed. In addition, IPR&D is capitalized and assessed for impairment annually. IPR&D is amortized upon product commercialization or upon out-licensing the underlying intellectual property where we no have active involvement in the licensee's development activities. IPR&D is amortized over the estimated life of the commercial product or licensing arrangement. Should the initial accounting for a business combination be incomplete by the end of a reporting period that falls within the measurement period, we report provisional amounts in our financial statements. During the measurement period, we adjust the provisional amounts recognized at the acquisition date to reflect new information obtained about facts and circumstances that existed as of the acquisition date that, if known, would have affected the measurement of the amounts recognized as of that date and we record those adjustments to our financial statements in the period of change, if any. Under the acquisition method of accounting for business combinations, if we identify changes to acquired deferred tax asset valuation allowances or liabilities related to uncertain tax positions during the measurement period and they relate to new information obtained about facts and circumstances that existed as of the acquisition date, those changes are considered a measurement period adjustment and we record the offset to goodwill. We record all other changes to deferred tax asset valuation allowances and liabilities related to uncertain tax positions in current period income tax expense.
Goodwill, Intangible Assets and Other Long-Lived Assets	Goodwill, Intangible Assets and Other Long-Lived 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, 2017, was due to the acquisition of Crystal. 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 the goodwill impairment review, we assess qualitative factors to determine whether it is more likely than not that the fair value of our reporting unit is less than the carrying amount, including goodwill. The qualitative factors include, but are not limited to, macroeconomic conditions, industry and market considerations, and the overall financial performance. If, after assessing the totality of these qualitative factors, we determine that it is not more likely than not that the fair value of our reporting unit is less than the carrying amount, then no additional assessment is deemed necessary. Otherwise, we proceed to perform the two-step test for goodwill impairment. The first step involves comparing the estimated fair value of the reporting unit with the carrying value, including goodwill. If the carrying amount of the reporting unit exceeds the fair value, the second step of the goodwill impairment test is performed to determine the amount of loss, which involves comparing the implied fair value of the goodwill to the carrying value of the goodwill. We 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. We performed the annual assessment for goodwill impairment in the fourth quarter of 2017, noting no impairment. Our identifiable intangible assets are typically comprised of acquired core technologies, licensed technologies, customer relationships and trade names. The cost of identifiable intangible assets with finite lives is generally amortized on a straight-line basis over the assets’ respective estimated useful lives. We regularly perform reviews to determine if any event has occurred that may indicate that intangible assets with finite useful lives and other long-lived assets are potentially impaired. If indicators of impairment exist, an impairment test is performed to assess the recoverability of the affected assets by determining whether the carrying amount of such assets exceeds the undiscounted expected future cash flows. If the affected assets are not recoverable, we estimate the fair value of the assets and record an impairment loss if the carrying value of the assets exceeds the fair value. Factors that may indicate potential impairment include a significant decline in our stock price and market capitalization compared to the net book value, significant changes in the ability of a particular asset to generate positive cash flows, and the pattern of utilization of a particular asset.
Commercial license rights	Commercial license rights Commercial license rights consist of the following (in thousands): December 31, December 31, 2017 2016 Aziyo & CorMatrix $ 17,696 $ 17,696 Selexis 8,602 8,602 26,298 26,298 Less: accumulated amortization (6,772 ) (477 ) Total commercial rights, net $ 19,526 $ 25,821 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. In May 2017, the Company entered into a Royalty Agreement with Aziyo pursuant to which the Company will receive royalties from certain marketed products that Aziyo acquired from CorMatrix. Pursuant to the Royalty Agreement, the Company received $10 million in 2017 from Aziyo to buydown the royalty rates on the products CorMatrix sold to Aziyo. The Royalty Agreement closed on May 31, 2017, in connection with the closing of the asset sale from CorMatrix to Aziyo (the “CorMatrix Asset Sale”). Pursuant to the Royalty Agreement, the Company will receive a 5% royalty on the products Aziyo acquired in the CorMatrix Asset Sale, reduced from the original 20% royalty from CorMatrix pursuant to the previously disclosed Interest Purchase Agreement, dated May 3, 2016 (the “Original Interest Purchase Agreement”) between CorMatrix and the Company. In addition, Aziyo has agreed to pay the Company up to $10 million of additional milestones tied to cumulative net sales of the products Aziyo acquired in the CorMatrix Asset Sale and to extend the term on these royalties by one year. The Royalty Agreement will terminate on May 31, 2027. In addition, in May 2017, the Company entered into an amended and restated interest purchase agreement (the “Amended Interest Purchase Agreement”) with CorMatrix, which supersedes in its entirety the Original Interest Purchase Agreement. Other than removing the commercial products sold to Aziyo in the CorMatrix Sale, the terms of the Amended Interest Purchase Agreement remain unchanged with respect to the CorMatrix developmental pipeline products, including the royalty rate of 5% on such pipeline products. The Amended Interest Purchase Agreement will terminate 10 years from the date of the first commercial sale of such products. The Company accounts for the Aziyo commercial license right as a financial asset in accordance with ASC 310 and amortizes the commercial license right using the 'effective interest' method whereby the Company forecasts expected cash flows over the term of the arrangement to arrive at an annualized effective interest. The annual effective interest associated with the forecasted cash flows from the Royalty Agreement with Aziyo as of December 31, 2017 is 26% . Revenue is calculated by multiplying the carrying value of the commercial license right by the effective interest. The payments received in 2017 were accordingly allocated between revenue and the amortization of the commercial license rights. We elected a prospective approach to account for changes in estimated cash flows and selected a method for determining when an impairment would be recognized and how to measure that impairment. In circumstances where our new estimate of expected cash flows is greater than previously expected, we will update our yield prospectively. While it has not occurred to date, in circumstances where our new estimate of expected cash flows is less than previously expected and below our original estimated yield we will record impairment. Impairment will be recognized by reducing the financial asset to an amount that represents the present value of our most recent estimate of expected cash flows discounted by the original effective interest rate. In circumstances where our new estimate of expected cash flows is less than previously expected, but not below our original estimated yield, we will update our yield prospectively. The Company accounts for commercial license rights related to developmental pipeline products on a non-accrual basis. These developmental pipeline products are non-commercialized, non-approved products that require FDA or other regulatory approval, and thus have uncertain cash flows. The developmental pipeline products are on a non-accrual basis as the Company is not yet able to forecast future cash flows given their pre-commercial stages of development. The Company will prospectively update its yield model under the effective interest method once the underlying products are commercialized and the Company can reliably forecast expected cash flows. Income will be calculated by multiplying the carrying value of the commercial license right by the effective interest rate. In 2017, the Company identified and corrected an immaterial error related to 2016. The adjustment related to the recognition of the income associated with this financial asset. The Company determined the 'effective interest' method should have been used to recognize income associated with the financial asset and that the method utilized previously was incorrect. The error had the impact of understating Commercial License Rights, revenue and net income in 2016. Management evaluated the effect of the adjustment on previously issued consolidated financial statements in accordance with SAB No. 99 and SAB No. 108 and concluded that it was qualitatively and quantitatively immaterial to the historical periods. Management also concluded that correcting the error in 2017 did not have a material impact on the 2017 financial results. As a result, in accordance with SAB No. 108, we corrected our Consolidated Balance Sheets as of June 30, 2017. The error resulted in an understatement of 2016 revenue of $1.3 million and net income of $0.8 million , or $0.04 per diluted share and overstatement of 2017 revenue of $1.3 million and net income of $0.8 million , or $0.04 per diluted share.
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 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.
Discontinued Operations	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.
Convertible Debt	The Company accounted for the 2019 Convertible Senior Notes by separating the liability and equity components of the instrument in a manner that reflects the Company's nonconvertible debt borrowing rate. As a result, the Company assigned a value to the debt component of the 2019 Convertible Senior Notes equal to the estimated fair value of similar debt instruments without the conversion feature, which resulted in the Company recording the debt instrument at a discount. The Company is amortizing the debt discount over the life of the 2019 Convertible Senior Notes as additional non-cash interest expense utilizing the effective interest method.
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).
Recently Issued Accounting Pronouncements	Accounting Standards Recently Adopted Stock Compensation - In March 2016, the FASB issued ASU 2016-09, Compensation - Stock Compensation ("Topic 718"), which aims to simplify the accounting for share-based payment transactions, including accounting for income taxes, classification on the statement of cash flows, accounting for forfeitures, and classification of awards as either liabilities or equity. This ASU was effective for us beginning in the first quarter of 2017. This new standard increases the volatility of net income by requiring excess tax benefits from share-based payment arrangements to be classified as discrete items within the provision for income taxes, rather than recognizing excess tax benefits in additional paid-in capital. Upon adoption in the first quarter of 2017, the Company recorded $17.9 million , to retained earnings, primarily related to unrealized tax benefits associated with share-based compensation. During the year ended December 31, 2017, excess tax benefits of $4.7 million were reflected as a component of the provision for income taxes. Also, as a result of the adoption of this new standard, the Company made an accounting policy election to recognize forfeitures as they occur and will no longer estimate expected forfeitures. In addition, excess income tax benefits from share-based compensation arrangements are classified as cash flows from operations, rather than cash flows from financing activities. We elected to apply the cash flows classification guidance prospectively and have not adjusted prior periods. Accounting Standards Not Yet Adopted Revenue Recognition - In May 2014, the FASB issued new guidance related to revenue recognition, ASU 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. 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. In addition, ASU 2014-09 adds a new Subtopic to the Codification, ASC 340-40, Other Assets and Deferred Costs: Contracts with Customers, to provide guidance on costs related to obtaining a contract with a customer and costs incurred in fulfilling a contract with a customer that are not in the scope of another ASC Topic. We have substantially completed our assessment of the new standards and are finalizing the new required disclosures. The standard will have a material impact on our consolidated financial statements by accelerating the timing of recognition for revenues related to royalties, and potentially certain contingent milestone based payments. We will adopt ASC 606 effective January 1, 2018, by recognizing the cumulative effect of initially applying the new standard as a decrease to the opening balance of accumulated deficit. Based on our analysis of open contracts as of December 31, 2017, we expect this amount to be approximately $33 million . Financial Instruments - In January 2016, the FASB issued ASU 2016-01, Financial Instruments - Overall ("Subtopic 825-10"), which requires equity investments (other than those accounted for under the equity method or those that result in consolidation) to be measured at fair value, with changes in fair value recognized in net income. ASU 2016-01 will be effective for us beginning in the first quarter of 2018. We anticipate that the adoption of ASU 2016- 01 may increase the volatility of other income and expense. In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses: Measurement of Credit Losses on Financial Instruments, which amends the impairment model by requiring entities to use a forward-looking approach based on expected losses to estimate credit losses on certain types of financial instruments, including trade receivables and available for sale debt securities. The ASU is effective for us beginning in the first quarter of 2020, with early adoption permitted. We are currently evaluating the impact of ASU 2016-13 on the consolidated financial statements. Statement of Cash Flows - 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. Business Combinations - In January 2017 the FASB issued ASU 2017-01, Business Combinations (Topic 805): Clarifying the Definition of a Business. This new standard clarifies the definition of a business in order to allow for the evaluation of whether transactions should be accounted for as acquisitions or disposals of assets or businesses. The standard is effective for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years, which means that it will be effective for us in the first quarter of 2018. We are currently evaluating the impact of our pending adoption of ASU 2017-01 on our consolidated financial statements. Goodwill Impairment - In January 2017 the FASB issued ASU 2017-04, Intangibles—Goodwill and Other (Topic 350), Simplifying the Test for Goodwill Impairment. This new standard eliminates Step 2 from the goodwill impairment test. Instead, an entity should compare the fair value of a reporting unit with its carrying amount and recognize an impairment charge for the amount by which the carrying amount exceeds the reporting unit's fair value, not to exceed the total amount of goodwill allocated to the reporting unit. The standard is effective for fiscal years beginning after December 15, 2019, including interim periods within those fiscal years, which means that it will be effective for us in the first quarter of 2020. Early adoption is permitted. We are currently evaluating the impact of our pending adoption of ASU 2017-04 on our consolidated financial statements. 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.

Basis of Presentation and Sum20

Basis of Presentation and Summary of Significant Accounting Policies (Tables)	12 Months Ended
	Dec. 31, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Schedule of Major Customers	A relatively small number of partners account 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, 2017 2016 2015 Partner A 46 % 41 % 27 % Partner B 19 % 14 % 23 % Partner C — — 18 %
Schedule of Commercial License Rights	Commercial license rights consist of the following (in thousands): December 31, December 31, 2017 2016 Aziyo & CorMatrix $ 17,696 $ 17,696 Selexis 8,602 8,602 26,298 26,298 Less: accumulated amortization (6,772 ) (477 ) Total commercial rights, net $ 19,526 $ 25,821
Schedule 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, 2017 2016 2015 Weighted average shares outstanding: 21,032 20,831 19,790 Dilutive potential common shares: Restricted stock 141 — 56 Stock options 1,000 — 882 Warrants 94 — — 2019 Convertible Senior Notes 1,214 — 499 Shares used to compute diluted income per share 23,481 20,831 21,228 Potentially dilutive shares excluded from calculation due to anti-dilutive effect 335 3,544 3,333

Investment in Viking (Tables)

Investment in Viking (Tables)	12 Months Ended
	Dec. 31, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Schedule of Financial Information of Viking	The following table presents summarized financial information of Viking (in thousands): Year ended December 31, (in thousands) 2017 2016 2015 Condensed Statement of Operations: Total revenue — — — Gross profit — — — Loss from operations $19,070 $13,847 $11,996 Net Loss $20,578 $14,732 $23,404 As of December 31, (in thousands) 2017 2016 Condensed Balance Sheet: Current assets $ 21,852 $ 13,975 Noncurrent assets 270 561 22,122 14,536 Current liabilities 8,657 6,477 Noncurrent liabilities — 16 Stockholders' equity 13,465 8,043

Business Combinations (Tables)

Business Combinations (Tables)	12 Months Ended
	Dec. 31, 2017
Business Combinations [Abstract]
Schedule of Business Acquisitions	The aggregate acquisition consideration was determined to be $35.7 million , consisting of (in thousands): Cash paid to Crystal shareholders $ 26,877 Cash payable to Crystal Shareholders 336 Assumed liabilities 129 Fair value of contingent consideration 8,401 Total consideration $ 35,743 The transaction was accounted for as a business combination and 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 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 $ 224 Accounts receivable 2,513 Prepaid expenses and other assets 201 Property and equipment, net 589 Current liabilities assumed (354 ) Deferred revenue (4,624 ) Deferred tax liabilities, net (12,558 ) Intangible asset with finite life - core technology 36,000 Goodwill 13,752 Total consideration $ 35,743
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, 2017
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, 2017 and 2016 (in thousands): Fair Value Measurements at Reporting Date Using December 31, 2017 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) $ 181,041 $ 1,896 $ 179,145 $ — Note receivable Viking (2) 3,877 — — 3,877 Investment in warrants (3) 3,846 3,846 — — Total assets $ 188,764 $ 5,742 $ 179,145 $ 3,877 Liabilities: Current contingent liabilities - Crystal (7) $ 4,618 $ — $ — $ 4,618 Current contingent liabilities - Cydex (4) 86 — — 86 Long-term contingent liabilities - Metabasis (5) 3,971 — 3,971 — Long-term contingent liabilities - Crystal (7) 3,783 — — 3,783 Long-term contingent liabilities - CyDex (4) 1,503 — — 1,503 Liability for amounts owed to a former licensor (6) 284 284 — — Total liabilities $ 14,245 $ 284 $ 3,971 $ 9,990 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 $ 3,738 $ 119,242 $ 3,207 Liabilities: Current contingent liabilities - CyDex (4) $ 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 a former licensor (6) 371 371 — — Total liabilities $ 3,388 $ 371 $ 1,413 $ 1,604 (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, 2017 approximates the book value since the contractual maturity date was within five months from the end of 2017, and there is no plan to extend the maturity date. The fair value at December 31, 2016 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 . Changes in these assumptions may materially affect the fair value estimate. For the years ended December 31, 2017 , December 31, 2016 , and December 31, 2015 , the Company reported an increase in the fair value of 0.9 million , a decrease in the fair value $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, is 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 CyDex contingent liabilities was 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 developmental and regulatory milestones. Changes in these assumptions can materially affect the fair value.
Schedule of 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, 2017 2016 Revenue volatility 25% 25% Average of probability of commercialization 12.5% 12.5% Market price of risk 2.9% 3.2% (5) The liability for CVRs for Metabasis is determined using quoted market prices in a market that is not active for the underlying CVR. (6) The liability for amounts owed to a former licensor is determined using quoted market prices in active markets for the underlying investment received from a partner, a portion of which is owed to a former licensor. (7) The fair value of Crystal contingent liabilities was determined using a probability weighted income approach. Most of the contingent payments are based on development or regulatory milestones as defined in the merger agreement with Crystal. The fair value is subjective and is affected by changes in inputs to the valuation model including management’s estimates regarding the timing and probability of achievement of certain developmental and regulatory milestones. At December 31, 2017 , most of the development and regulatory milestones were estimated to be highly probable of being achieved between 2018 and 2020 . Changes in these estimates may materially affect the fair value.
Schedule of Reconciliation of Level 3 Financial Instruments	A reconciliation of the level 3 financial instruments as of December 31, 2017 is as follows (in thousands): Assets: Fair value of level 3 financial instruments as of December 31, 2016 $ 3,207 Viking note receivable fair market value adjustment 870 Cash payment received as partial repayment of note receivable (200 ) Fair value of level 3 financial instrument assets as of December 31, 2017 $ 3,877 Liabilities Fair value of level 3 financial instruments as of December 31, 2016 $ 1,604 Fair value of Crystal contingent consideration 8,401 Payments to CVR holders and other contingency payments (25 ) Fair value adjustments to contingent liabilities 10 Fair value of level 3 financial instruments as of December 31, 2017 $ 9,990

Lease Obligations (Tables)

Lease Obligations (Tables)	12 Months Ended
	Dec. 31, 2017
Leases [Abstract]
Schedule of Payments Expected to be 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, 2017 (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 $ 131 $ 275 $ 291 $ 50 $ 747 Office and research facility-La Jolla, CA June 2019 737 373 — — 1,110 Bioscience and Technology Business Center-Lawrence, KS December 2020 57 113 — — 170 Office - Emeryville, CA August 2021 253 528 186 — 967 Research Facility - Emeryville, CA August 2021 197 412 142 — $ 751 Total operating lease obligations $ 1,375 $ 1,701 $ 619 $ 50 $ 3,745 Sublease payments expected to be received: Office and research facility-La Jolla, CA June 2019 641 361 — — 1,002 Net operating lease obligations $ 734 $ 1,340 $ 619 $ 50 $ 2,743

Financing Arrangements (Tables)

Financing Arrangements (Tables)	12 Months Ended
	Dec. 31, 2017
Debt Disclosure [Abstract]
Schedule 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, 2017 December 31, 2016 2019 Convertible Senior Notes Principal amount outstanding $ 245,000 $ 245,000 Unamortized discount (20,471 ) (32,090 ) Total current portion of notes payable $ 224,529 $ 212,910

Balance Sheet Account Details (

Balance Sheet Account Details (Tables)	12 Months Ended
	Dec. 31, 2017
Other Balance Sheet Details [Abstract]
Schedule of Investment Categories	The following table summarizes the various investment categories at December 31, 2017 and 2016 (in thousands): Cost Gross unrealized gains Gross unrealized losses Estimated fair value December 31, 2017 Short-term investments Bank deposits $ 80,095 $ 6 $ (42 ) $ 80,059 Corporate bonds 55,335 — (96 ) 55,239 Corporate equity securities 207 1,689 — 1,896 Commercial paper 27,933 — (20 ) 27,913 Agency bonds 4,991 — (1 ) 4,990 U.S. Government bonds 8,939 — (10 ) 8,929 Municipal bonds 2,028 — (13 ) 2,015 $ 179,528 $ 1,695 $ (182 ) $ 181,041 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
Schedule of Other Current Assets	Other current assets consist of the following (in thousands): December 31, 2017 2016 Prepaid expenses $ 1,017 $ 1,864 Other receivables 497 311 $ 1,514 $ 2,175
Schedule of Property and Equipment	Property and equipment is stated at cost and consists of the following (in thousands): December 31, 2017 2016 Lab and office equipment $ 3,460 $ 1,067 Leasehold improvements 1,917 1,754 Computer equipment and software 697 569 6,074 3,390 Less accumulated depreciation and amortization (1,862 ) (1,571 ) $ 4,212 $ 1,819
Schedule of Goodwill and Other Identifiable Intangible Assets	Goodwill and identifiable intangible assets consist of the following (in thousands): December 31, 2017 2016 Indefinite lived intangible assets IPR&D $ 7,923 $ 12,246 Goodwill 85,959 72,207 Definite lived intangible assets Complete technology 222,900 182,577 Less: Accumulated amortization (23,301 ) (12,792 ) Trade name 2,642 2,642 Less: Accumulated amortization (916 ) (784 ) Customer relationships 29,600 29,600 Less: Accumulated amortization (10,264 ) (8,784 ) Total goodwill and other identifiable intangible assets, net $ 314,543 $ 276,912
Schedule of Accrued Liabilities	Accrued liabilities consist of the following (in thousands): December 31, 2017 2016 Compensation $ 4,085 $ 2,603 Legal 430 829 Amounts owed to former licensees 396 899 Royalties owed to third parties 954 942 Deferred revenue 173 — Other 1,339 1,124 $ 7,377 $ 6,397
Schedule of Contingent Liabilities	Contingent liabilities consist of the following (in millions): December 31, 2015 Payments Fair Value Adjustment December 31, 2016 Payments Fair Value Adjustment Additions December 31, 2017 Cydex $ 9.5 $ (6.2 ) $ 3.3 $ 6.6 (5.0 ) $ — $ — $ 1.6 Metabasis 4.0 (2.6 ) 0.1 1.5 — 2.5 — 4.0 Crystal — — — — — — 8.4 8.4 Total $ 13.5 $ (8.8 ) $ 3.4 $ 8.1 $ (5.0 ) $ 2.5 $ 8.4 $ 14.0
Schedule of Other Long-Term Liabilities	Other long-term liabilities consist of the following (in thousands): December 31, 2017 2016 Deferred rent $ 321 $ 357 Deposits 43 43 Other 359 287 $ 723 $ 687

Stockholders' Equity (Tables)

Stockholders' Equity (Tables)	12 Months Ended
	Dec. 31, 2017
Equity [Abstract]
Schedule of Accounting for Share-Based Compensation	The following table summarizes stock-based compensation expense (in thousands): December 31, 2017 2016 2015 Stock-based compensation expense as a component of: Research and development expenses $ 14,235 $ 8,836 $ 4,080 General and administrative expenses 10,680 10,057 8,378 $ 24,915 $ 18,893 $ 12,458
Schedule of 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, 2016 1,754,275 $ 42.12 6.19 $ 104,247 Granted 273,353 112.58 Exercised (148,252 ) 31.58 Forfeited (3,044 ) 79.74 Balance at December 31, 2017 1,876,332 53.17 5.77 157,340 Exercisable at December 31, 2017 1,431,245 40.08 4.95 138,616 Options vested and expected to vest as of December 31, 2017 1,876,332 $ 53.17 5.77 $ 157,340
Schedule of Stock Option Plan Activity by Exercise Price Range	Following is a further breakdown of the options outstanding as of December 31, 2017 : Range of exercise prices Options outstanding Weighted average remaining life in years Weighted average exercise price Options exercisable Weighted average exercise price $8.58 - $10.05 208,032 2.88 $ 9.97 208,032 $ 9.97 $10.12 - $12.81 71,850 3.95 11.44 71,850 11.44 $14.47 - $14.47 285,879 4.11 14.47 271,879 14.47 $16.14 - $17.88 72,777 1.16 16.32 72,777 16.32 $21.92 - $21.92 207,004 5.13 21.92 207,004 21.92 $32.00 - $56.26 226,287 6.72 50.50 160,301 48.49 $63.58 - $68.62 25,757 6.50 67.17 23,726 67.34 $74.42 - $74.42 216,118 6.11 74.42 206,828 74.42 $85.79 - $97.92 238,675 6.99 88.93 138,712 90.54 $100.38 - $141.61 323,953 9.12 112.75 70,136 106.78 $8.58 – $141.61 1,876,332 5.77 $ 53.17 — 1,431,245 $ 40.08
Schedule of 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, 2017 2016 2015 Risk-free interest rate 2.0%-2.2% 1.3%-1.9% 1.7%-2.0% Expected volatility 43%-47% 48%-50% 50%-58% Expected term 6.5 to 6.8 years 6.6 to 6.7 years 6.5 years
Schedule of 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, 2016 308,700 $ 86.61 Granted 73,799 99.53 Vested (187,864 ) 84.50 Forfeited (61,341 ) 97.78 Outstanding at December 31, 2017 133,294 $ 91.60

Income Taxes (Tables)

Income Taxes (Tables)	12 Months Ended
	Dec. 31, 2017
Income Tax Disclosure [Abstract]
Schedule of 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, 2017 2016 2015 Current expense (benefit): Federal $ — $ 21 $ 11 State 111 12 7 Foreign 261 — — 372 33 18 Deferred expense (benefit): Federal 44,075 10,534 (167,413 ) State 228 (240 ) (24,720 ) Foreign — — — $ 44,675 $ 10,327 $ (192,115 )
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, 2017 2016 2015 Tax at federal statutory rate $ 20,031 $ 2,786 $ 13,198 State, net of federal benefit 622 175 386 Contingent liabilities 903 1,225 1,684 Stock-based compensation (4,019 ) 263 140 Research and development credits (2,821 ) (1,525 ) 304 Change in uncertain tax positions 1,308 1,423 27,188 Rate change for changes in federal or state law 32,429 25 (5,756 ) Change in valuation allowance (4,169 ) 6,283 (231,370 ) Other 391 (328 ) 2,111 $ 44,675 $ 10,327 $ (192,115 )
Schedule of Deferred Tax Assets and Liabilities	Significant components of the Company’s deferred tax assets and liabilities as of December 31, 2017 and 2016 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, 2017 , 2016 and 2015 . The valuation allowance decreased $8.4 million in 2017, increased $6.3 million in 2016 and decreased $231.7 million in 2015. December 31, 2017 2016 (in thousands) Deferred assets: Net operating loss carryforwards $ 90,272 $ 150,226 Research credit carryforwards 30,677 26,878 Fixed assets and intangibles 1,984 4,385 Accrued expenses 845 943 Contingent liabilities 354 578 Deferred revenue 17 — Present value of royalties — 591 Deferred rent 28 45 Capital Loss Carryforward 1,609 4,432 Viking Equity Method Investment 5,137 5,692 Other 12,117 19,312 143,040 213,082 Valuation allowance for deferred tax assets (6,987 ) (15,349 ) Net deferred tax assets $ 136,053 $ 197,733 Deferred tax liabilities: Retrophin fair value adjustment $ (243 ) $ (52 ) Convertible debt (737 ) (1,196 ) Identified intangibles (48,237 ) (68,631 ) Identified indefinite lived intangibles (2,414 ) (3,963 ) Total $ 84,422 $ 123,891
Schedule of Unrecognized Tax Benefits	A reconciliation of the amount of unrecognized tax benefits at December 31, 2017 , 2016 and 2015 is as follows (in thousands): December 31, 2017 2016 2015 Balance at beginning of year $ 38,770 $ 36,452 $ 8,524 Additions based on tax positions related to the current year 1,067 70 154 Additions for tax positions of prior years 109 2,408 28,224 Reductions for tax positions of prior years (10,583 ) (160 ) (450 ) Balance at end of year $ 29,363 $ 38,770 $ 36,452

Summary of Unaudited Quarterl29

Summary of Unaudited Quarterly Financial Information (Tables)	12 Months Ended
	Dec. 31, 2017
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 2017 and 2016 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 ) 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 2017 Total revenues $ 29,267 $ 27,995 $ 33,375 $ 50,465 Total operating costs and expenses 19,051 14,980 16,882 22,113 Income tax (expense) benefit (1,114 ) (2,242 ) (3,645 ) (37,674 ) Net Income (loss) 5,079 6,058 8,426 (7,007 ) Basic per share amounts: Net income $ 0.24 $ 0.29 $ 0.40 $ (0.33 ) Diluted per share amounts: Net income $ 0.22 $ 0.26 $ 0.36 $ (0.33 ) Weighted average shares—basic 20,938 21,013 21,071 21,109 Weighted average shares—diluted 23,019 23,216 23,551 21,109

Basis of Presentation and Sum30

Basis of Presentation and Summary of Significant Accounting Policies - Narrative (Details)		3 Months Ended								12 Months Ended
		Dec. 31, 2017USD ($)$ / shares	Sep. 30, 2017USD ($)$ / shares	Jun. 30, 2017USD ($)$ / shares	Mar. 31, 2017USD ($)$ / shares	Dec. 31, 2016USD ($)$ / shares	Sep. 30, 2016USD ($)$ / shares	Jun. 30, 2016USD ($)$ / shares	Mar. 31, 2016USD ($)$ / shares	Dec. 31, 2017USD ($)d$ / shares		Dec. 31, 2016USD ($)$ / shares		Dec. 31, 2015USD ($)$ / shares		Oct. 06, 2017USD ($)	May 03, 2016	Aug. 31, 2014USD ($)	Jan. 31, 2010right
Basis of Presentation [Line Items]
Maturity period of cash and cash equivalents, maximum										3 months
Write-downs related to obsolete inventory										$ 0		$ 0
Revenue		$ 50,465,000	$ 33,375,000	$ 27,995,000	$ 29,267,000	$ 38,185,000	$ 21,619,000	$ 19,521,000	$ 29,648,000	141,102,000		108,973,000		$ 71,914,000
Net income (loss)		$ (7,007,000)	$ 8,426,000	$ 6,058,000	$ 5,079,000	$ (3,125,000)	$ 1,051,000	$ (6,170,000)	$ 6,608,000	$ 12,556,000		$ (1,636,000)		$ 229,824,000
Earnings per share - diluted (USD per share) | $ / shares		$ (0.33)	$ 0.36	$ 0.26	$ 0.22	$ 0.15	$ 0.05	$ (0.30)	$ 0.30	$ 0.53	[1]	$ (0.08)	[1]	$ 10.83	[1]
Restocking fee (as a percent)										20.00%
Share-based Compensation
Expected dividend rate (as a percent)										0.00%
Gain on disposition of product line												$ 1,100,000
Provision for taxes on gain from discontinued operations										$ 0		408,000		$ 0
Equity component of currently redeemable convertible notes (Note 6)		$ 18,859,000				$ 29,563,000				18,859,000		29,563,000
Excess tax benefit of share-based compensation										4,700,000
Retained earnings (accumulated deficit)		$ (400,924,000)				(431,127,000)				$ (400,924,000)		(431,127,000)
Stock Options | 2002 Stock Incentive Plan
Share-based Compensation
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
Award vesting period										6 months
Award vesting right (as a percent)										12.50%
Stock Options | Vest 1/48 each month for forty-two months | 2002 Stock Incentive Plan
Share-based Compensation
Award vesting period										42 months
Award vesting right (as a percent)										2.08%
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
Crystal
Basis of Presentation [Line Items]
Value of share consideration																$ 10,500,000
Metabasis Therapeutics
Basis of Presentation [Line Items]
Number of contingent value rights | right																			4
Royalty Agreements
Basis of Presentation [Line Items]
Product royalty (as a percent)																	20.00%
Aziyo | Royalty Agreements
Basis of Presentation [Line Items]
Proceeds from royalties received										$ 10,000,000
Product royalty (as a percent)		5.00%								5.00%
Additional royalties receivable under sales-based milestones		$ 10,000,000								$ 10,000,000
Effective interest rate of forecasted cash flows (as a percent)										26.00%
CorMatrix | Royalty Agreements
Basis of Presentation [Line Items]
Product royalty (as a percent)		5.00%								5.00%
Expiration period of royalty agreement										10 years
2019 Convertible Senior Notes
Share-based Compensation
Principal amount outstanding		$ 245,000,000				$ 245,000,000				$ 245,000,000		245,000,000
2019 Convertible Senior Notes | Senior Notes
Share-based Compensation
Principal amount outstanding																		$ 245,000,000
Interest on debt instrument (as a percent)																		0.75%
Working capital deficit		1,800,000								1,800,000
Equity component of currently redeemable convertible notes (Note 6)		51,300,000								$ 51,300,000
Threshold business days for repayment of principal										3 days
Number of consecutive trading days | d										50
Accounting Standards Update 2016-09
Share-based Compensation
Cumulative-effect adjustment from adoption of ASU 2016-09		18,103,000								$ 18,103,000
Retained Earnings
Basis of Presentation [Line Items]
Net income (loss)										12,556,000		(1,636,000)		$ 229,824,000
Retained Earnings | Accounting Standards Update 2016-09
Share-based Compensation
Cumulative-effect adjustment from adoption of ASU 2016-09		17,647,000			$ 17,900,000					17,647,000
Difference between Revenue Guidance in Effect before and after Topic 606 | Accounting Standards Update 2014-09
Share-based Compensation
Retained earnings (accumulated deficit)		$ 33,000,000								33,000,000
Immaterial Error related to Contracts | Restatement Adjustment
Basis of Presentation [Line Items]
Revenue										1,300,000		(1,300,000)
Net income (loss)										$ 800,000		$ (800,000)
Earnings per share - diluted (USD per share) | $ / shares	[1]									$ 0.04		$ (0.04)
[1]	The sum of net income per share amounts may not equal the total due to rounding

Basis of Presentation and Sum31

Basis of Presentation and Summary of Significant Accounting Policies - Revenue from Significant Partners (Details) - Customer Concentration Risk - Revenue	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Partner A
Revenue, Major Customer
Total revenues (as a percent)	46.00%	41.00%	27.00%
Partner B
Revenue, Major Customer
Total revenues (as a percent)	19.00%	14.00%	23.00%
Partner C
Revenue, Major Customer
Total revenues (as a percent)	0.00%	0.00%	18.00%

Basis of Presentation and Sum32

Basis of Presentation and Summary of Significant Accounting Policies - Commercial License Rights (Details) - Licensing Agreements - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	$ 26,298	$ 26,298
Less: accumulated amortization	(6,772)	(477)
Total commercial rights, net	19,526	25,821
Aziyo & CorMatrix
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	17,696	17,696
Selexis
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	$ 8,602	$ 8,602

Basis of Presentation and Sum33

Basis of Presentation and Summary of Significant Accounting Policies - Calculation of Earnings per Share (Details) - shares shares in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Weighted-average shares outstanding - basic (shares)	21,109	21,071	21,013	20,938	20,898	20,887	20,832	20,708	21,032	20,831	19,790
Dilutive potential common shares:
Restricted stock (shares)									141	0	56
Stock options (shares)									1,000	0	882
Warrants (shares)									94	0	0
2019 Convertible Senior Notes (shares)									1,214	0	499
Shares used to compute diluted income per share (shares)	21,109	23,551	23,216	23,019	20,898	22,997	20,832	22,284	23,481	20,831	21,228
Potentially dilutive shares excluded from calculation due to anti-dilutive effect (shares)									335	3,544	3,333

Investment in Viking - Narrativ

Investment in Viking - Narrative (Details) $ / shares in Units, $ in Thousands	Apr. 13, 2016USD ($)shares	Apr. 30, 2016USD ($)$ / sharesshares	May 31, 2015USD ($)$ / sharesshares	May 31, 2014USD ($)program	Dec. 31, 2016USD ($)	Dec. 31, 2017USD ($)	Dec. 31, 2016USD ($)	Dec. 31, 2015USD ($)	May 31, 2015$ / shares	Jul. 31, 2017USD ($)	May 31, 2017	Jan. 31, 2016USD ($)	Aug. 31, 2014$ / sharesshares
Variable Interest Entity [Line Items]
Warrants to purchase shares (shares) | shares													3,264,643
Exercise price of warrants (USD per share) | $ / shares													$ 125.08
Proceeds received from repayment of Viking note receivable						$ 200	$ 300	$ 0
Note receivable from Viking					$ 3,207	$ 3,877	$ 3,207
Viking
Variable Interest Entity [Line Items]
Number of programs licensed | program				5
Loss recorded (as a percent)									100.00%
Debt | Viking
Variable Interest Entity [Line Items]
Convertible loan facility extended				$ 2,500
Repayment in equity (as a percent)		200.00%
Equity Method Investee
Variable Interest Entity [Line Items]
Shares sold in Viking IPO (shares) | shares		7,500,000
Initial offering price (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 (as a 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										$ 200
Warrants to purchase shares (shares) | shares		7,500,000
Exercise price of warrants (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 (as a percent)		32.70%			30.30%	17.60%	30.30%
Increase (decrease) in equity method investment					$ (10,700)	$ 2,700
Other than temporary impairment of investment in Viking							$ 7,400
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
Common Stock | Equity Method Investee | IPO
Variable Interest Entity [Line Items]
Shares sold in Viking IPO (shares) | shares			3,700,000
Aggregate offering price			$ 29,200
Initial offering price (USD per share) | $ / shares			$ 8						$ 8
Warrants
Variable Interest Entity [Line Items]
Gain on changes in fair value						$ 3,200	$ 300

Investment in Viking - Financia

Investment in Viking - Financial Information of Viking (Details) - Viking - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Condensed Statement of Operations:
Total revenue	$ 0	$ 0	$ 0
Gross profit	0	0	0
Loss from operations	19,070	13,847	11,996
Net Loss	20,578	14,732	$ 23,404
Condensed Balance Sheet:
Current assets	21,852	13,975
Noncurrent assets	270	561
Total assets	22,122	14,536
Current liabilities	8,657	6,477
Noncurrent liabilities	0	16
Stockholders' equity	$ 13,465	$ 8,043

Business Combinations - Narrati

Business Combinations - Narrative (Details)	Oct. 06, 2017USD ($)collaboration_agreement	Jan. 08, 2016USD ($)	Dec. 31, 2017USD ($)	Dec. 31, 2016USD ($)
Business Acquisition [Line Items]
Revenue royalty payable on all Cydex-related revenue (as a percent)				20.00%
Cydex-related revenue amount that triggers royalty payments				$ 15,000,000
Finite-lived intangible asset, useful life			20 years
Goodwill			$ 85,959,000	$ 72,207,000
Crystal
Business Acquisition [Line Items]
Gross payments to acquire business	$ 27,200,000
Working capital adjustment	2,200,000
Total share consideration	10,500,000
Cash payable to Crystal Shareholders	336,000
Fair value of contingent consideration	8,401,000
Total consideration	35,743,000
Goodwill	$ 13,752,000
OMT, Inc.
Business Acquisition [Line Items]
Gross payments to acquire business		$ 96,006,000
Total share consideration		77,373,000
Total consideration		173,379,000
Goodwill		59,969,000
Consideration transferred		$ 173,400,000
Core Technology | Crystal
Business Acquisition [Line Items]
Average cash flow discount rate (as a percent)	4.60%
Projected cash flow discount rate (as a percent)	10.80%
Core Technology | OMT, Inc.
Business Acquisition [Line Items]
Projected cash flow discount rate (as a percent)		15.50%
Finite-lived intangible asset, useful life		20 years
Threshold of Revenues above $15 million with Three Collaboration Agreements | Crystal
Business Acquisition [Line Items]
Revenue royalty payable on all Cydex-related revenue (as a percent)	10.00%
Cydex-related revenue amount that triggers royalty payments	$ 15,000,000
Threshold of Revenues above $1.5 million with Four Collaboration Agreements | Crystal
Business Acquisition [Line Items]
Revenue royalty payable on all Cydex-related revenue (as a percent)	20.00%
Cydex-related revenue amount that triggers royalty payments	$ 1,500,000
Number of collaboration agreements | collaboration_agreement	4

Business Combinations - Conside

Business Combinations - Consideration Transferred (Details) - USD ($) $ / shares in Units, shares in Thousands	Oct. 06, 2017	Jan. 08, 2016
Crystal
Business Acquisition [Line Items]
Cash paid to Crystal shareholders	$ 26,877,000
Cash payable to Crystal Shareholders	336,000
Assumed liabilities	129,000
Fair value of contingent consideration	8,401,000
Cash consideration	27,200,000
Total share consideration	10,500,000
Total consideration	$ 35,743,000
OMT, Inc.
Business Acquisition [Line Items]
Assumed liabilities		$ 1,528,000
Cash consideration		$ 96,006,000
Actual number of shares issued (shares)		790
Multiplied by: Ligand closing share price on January 8, 2016 (USD per share)		$ 98
Total share consideration		$ 77,373,000
Total consideration		$ 173,379,000

Business Combinations - Assets

Business Combinations - Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Oct. 06, 2017	Dec. 31, 2016	Jan. 08, 2016
Business Acquisition [Line Items]
Goodwill	$ 85,959		$ 72,207
Crystal
Business Acquisition [Line Items]
Cash and cash equivalents		$ 224
Accounts receivable		2,513
Prepaid expenses and other current assets		201
Property and equipment, net		589
Current liabilities assumed		(354)
Deferred revenue		(4,624)
Deferred tax liabilities, net		(12,558)
Intangible asset with finite life - core technology		36,000
Liabilities assumed		(129)
Goodwill		13,752
Total consideration		$ 35,743
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 related to OMT Acquisition (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 (USD per share)		$ (0.15)	$ 0.30	$ 0.03	$ 11.26
Diluted (loss) income per share (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 - Assets

Fair Value Measurement - Assets and Liabilities Measured at Fair Value on Recurring Basis (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Notes receivable fair market value adjustment	$ 870
Increase (decrease) in notes receivable fair value		$ (200)	$ (800)
Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	188,764	126,187
Liabilities, fair value	14,245	3,388
Recurring | Current portion of contingent liabilities - Crystal
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	4,618
Recurring | Current portion of contingent liabilities - CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	86	101
Recurring | Long-term portion of contingent liabilities - Metabasis
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	3,971	1,413
Recurring | Long-term portion of contingent liabilities - Crystal
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	3,783
Recurring | Long-term portion of contingent liabilities - CyDex
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	1,503	1,503
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	284	371
Recurring | Short-term investments
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	181,041	122,296
Recurring | Notes receivable Viking
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	3,877	$ 3,207
Revenue volatility (as a percent)		75.00%
Recurring | Investment in warrants
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	3,846	$ 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	5,742	3,738
Liabilities, fair value	284	371
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Current portion of contingent liabilities - Crystal
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	0
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	0	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	0	0
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Long-term portion of contingent liabilities - Crystal
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	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	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	284	371
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	1,896	3,054
Recurring | Quoted Prices in Active Markets for Identical Assets (Level 1) | Notes receivable Viking
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	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	3,846	684
Recurring | Significant Other Observable Inputs (Level 2)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	179,145	119,242
Liabilities, fair value	3,971	1,413
Recurring | Significant Other Observable Inputs (Level 2) | Current portion of contingent liabilities - Crystal
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	0
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	0	0
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	3,971	1,413
Recurring | Significant Other Observable Inputs (Level 2) | Long-term portion of contingent liabilities - Crystal
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	0
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	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	0	0
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	179,145	119,242
Recurring | Significant Other Observable Inputs (Level 2) | Notes receivable Viking
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	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	0	0
Recurring | Significant Unobservable Inputs (Level 3)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	3,877	3,207
Liabilities, fair value	9,990	1,604
Recurring | Significant Unobservable Inputs (Level 3) | Current portion of contingent liabilities - Crystal
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	4,618
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	86	101
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	0	0
Recurring | Significant Unobservable Inputs (Level 3) | Long-term portion of contingent liabilities - Crystal
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Liabilities, fair value	3,783
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	1,503	1,503
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	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	0	0
Recurring | Significant Unobservable Inputs (Level 3) | Notes receivable Viking
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Assets, fair value	3,877	3,207
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	$ 0	$ 0

Fair Value Measurement - Unobse

Fair Value Measurement - Unobservable Inputs (Details) - CyDex	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Revenue volatility (as a percent)	25.00%	25.00%
Average of probability of commercialization (as a percent)	12.50%	12.50%
Market price of risk (as a percent)	2.90%	3.20%

Fair Value Measurement - Reconc

Fair Value Measurement - Reconciliation of Level 3 Financial Instruments (Details) - USD ($) $ in Thousands	Oct. 06, 2017	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Assets:
Fair value of level 3 financial instruments as of December 31, 2016		$ 3,207
Viking note receivable fair market value adjustment		(870)
Cash payment received as partial repayment of note receivable		(200)
Fair value of level 3 financial instrument assets as of December 31, 2017		3,877	$ 3,207
Liabilities
Fair value of level 3 financial instruments as of December 31, 2016		1,604
Payments to CVR holders and other contingency payments		(4,998)	(8,777)	$ (6,740)
Fair value adjustments to contingent liabilities		2,500	3,400
Fair value of level 3 financial instruments as of December 31, 2017		9,990	1,604
Viking Therapeutics, Inc.
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Quoted market value of equity method investment		25,600
2019 Convertible Senior Notes | Senior Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of convertible debt		446,400
Crystal
Liabilities
Fair value of Crystal contingent consideration	$ 8,401
Payments to CVR holders and other contingency payments		0	0
Fair value adjustments to contingent liabilities		0	$ 0
Cydex
Liabilities
Payments to CVR holders and other contingency payments		(25)
Cydex and Crystal
Liabilities
Fair value adjustments to contingent liabilities		$ 10

Lease Obligations - Operating L

Lease Obligations - Operating Lease Obligations and Payments (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2017USD ($)
Payments expected to received from sublease agreements
Operating lease obligation, Less than 1 year	$ 1,375
Operating lease obligation, 1-2 years	1,701
Operating leases obligation, 3-4 years	619
Operating lease obligation, Thereafter	50
Operating lease obligation, Total	3,745
Operating lease obligation, Less than 1 year, net	734
Operating lease obligation, 1-2 years, net	1,340
Operating lease obligation, 3-4 years, net	619
Operating lease obligation, Thereafter, net	50
Operating lease obligation, net, Total	$ 2,743
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	$ 131
Operating lease obligation, 1-2 years	275
Operating leases obligation, 3-4 years	291
Operating lease obligation, Thereafter	50
Operating lease obligation, Total	$ 747
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	$ 737
Operating lease obligation, 1-2 years	373
Operating leases obligation, 3-4 years	0
Operating lease obligation, Thereafter	0
Operating lease obligation, Total	1,110
Sublease payments expected to be received, Less than 1 year	641
Sublease payments expected to be received, 1-2 years	361
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	$ 1,002
Bioscience and Technology Business Center-Lawrence, KS | Kansas
Payments expected to received from sublease agreements
Lease Termination Date	Dec. 1, 2020
Operating lease obligation, Less than 1 year	$ 57
Operating lease obligation, 1-2 years	113
Operating lease obligation, Total	$ 170
Office - Emeryville, CA | California
Payments expected to received from sublease agreements
Lease Termination Date	Aug. 1, 2021
Operating lease obligation, Less than 1 year	$ 253
Operating lease obligation, 1-2 years	528
Operating leases obligation, 3-4 years	186
Operating lease obligation, Total	$ 967
Research Facility - Emeryville, CA | California
Payments expected to received from sublease agreements
Lease Termination Date	Aug. 1, 2021
Operating lease obligation, Less than 1 year	$ 197
Operating lease obligation, 1-2 years	412
Operating leases obligation, 3-4 years	142
Operating lease obligation, Total	$ 751

Lease Obligations - Narrative (

Lease Obligations - Narrative (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Leases [Abstract]
Maximum lease expiration year	2,023
Rent expense	$ 0.3	$ 0.3	$ 0.4

Financing Arrangements - Narrat

Financing Arrangements - Narrative (Details)	1 Months Ended	12 Months Ended
	Aug. 31, 2014USD ($)d$ / sharesshares	Dec. 31, 2017USD ($)d	Dec. 31, 2016USD ($)	Dec. 31, 2015USD ($)
Debt Instrument [Line Items]
Carrying value of equity component		$ 18,859,000	$ 29,563,000
Reclassification of equity component of currently redeemable convertible notes		10,704,000	10,065,000	$ (39,628,000)
Warrants to purchase shares (shares) | shares	3,264,643
Exercise price of convertible bond hedges (USD per share) | $ / shares	$ 75.05
Exercise price of warrants (USD per share) | $ / shares	$ 125.08
Sale of warrants	$ 11,600,000
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 (as a percent)	0.75%
Number of consecutive trading days | d		50
Carrying value of equity component		$ 51,300,000
Proceeds from issuance of debt	$ 245,000,000
Discount rate (as a percent)	5.83%
Convertible debt, noncurrent	$ 192,500,000
If-converted value of debt in excess of principal		202,000,000
Debt issuance cost	5,700,000
Reclassification of equity component of currently redeemable convertible notes	1,200,000
Unamortized debt issuance costs	$ 4,500,000
Debt issuance costs, net		1,600,000	$ 2,500,000
Term of debt	5 years
Working capital deficit		$ 1,800,000
Threshold business days for repayment of principal		3 days
Senior Notes | 2019 Convertible Senior Notes | Redemption Period One
Debt Instrument [Line Items]
Number of trading days | d	20
Number of consecutive trading days | d	30
Stock price trigger threshold (as a percent)	130.00%
Senior Notes | 2019 Convertible Senior Notes | Redemption Period Two
Debt Instrument [Line Items]
Number of trading days | d	5
Number of consecutive trading days | d	10
Debt threshold trigger price (as a percent)	98.00%

Financing Arrangements - Liabil

Financing Arrangements - Liability Components of Financing Arrangements (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
2019 Convertible Senior Notes
Total current portion of notes payable	$ 224,529	$ 212,910
2019 Convertible Senior Notes
2019 Convertible Senior Notes
Principal amount outstanding	245,000	245,000
Unamortized discount	$ (20,471)	$ (32,090)

Balance Sheet Account Details -

Balance Sheet Account Details - Investment Categories (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Short-term investments
Schedule of Available-for-sale Securities [Line Items]
Cost	$ 179,528	$ 120,758
Gross unrealized gains	1,695	1,564
Gross unrealized losses	(182)	(26)
Estimated fair value	181,041	122,296
Bank deposits
Schedule of Available-for-sale Securities [Line Items]
Cost	80,095	40,715
Gross unrealized gains	6	19
Gross unrealized losses	(42)	0
Estimated fair value	80,059	40,734
Corporate bonds
Schedule of Available-for-sale Securities [Line Items]
Cost	55,335	11,031
Gross unrealized gains	0	0
Gross unrealized losses	(96)	(5)
Estimated fair value	55,239	11,026
Corporate equity securities
Schedule of Available-for-sale Securities [Line Items]
Cost	207	1,512
Gross unrealized gains	1,689	1,542
Gross unrealized losses	0	0
Estimated fair value	1,896	3,054
Commercial paper
Schedule of Available-for-sale Securities [Line Items]
Cost	27,933	33,074
Gross unrealized gains	0	2
Gross unrealized losses	(20)	(9)
Estimated fair value	27,913	33,067
Agency bonds
Schedule of Available-for-sale Securities [Line Items]
Cost	4,991	7,294
Gross unrealized gains	0	1
Gross unrealized losses	(1)	0
Estimated fair value	4,990	7,295
U.S. Government bonds
Schedule of Available-for-sale Securities [Line Items]
Cost	8,939	7,508
Gross unrealized gains	0	0
Gross unrealized losses	(10)	(1)
Estimated fair value	8,929	7,507
Municipal bonds
Schedule of Available-for-sale Securities [Line Items]
Cost	2,028	19,624
Gross unrealized gains	0	0
Gross unrealized losses	(13)	(11)
Estimated fair value	$ 2,015	$ 19,613

Balance Sheet Account Details48

Balance Sheet Account Details - Other Current Assets (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Other Balance Sheet Details [Abstract]
Prepaid expenses	$ 1,017	$ 1,864
Other receivables	497	311
Other current assets	$ 1,514	$ 2,175

Balance Sheet Account Details49

Balance Sheet Account Details - Property and Equipment (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Property, Plant and Equipment [Line Items]
Property and equipment , gross	$ 6,074	$ 3,390
Less accumulated depreciation and amortization	(1,862)	(1,571)
Property and equipment, net	4,212	1,819
Depreciation expense	400	200	$ 200
Lab and office equipment
Property, Plant and Equipment [Line Items]
Property and equipment , gross	3,460	1,067
Leasehold improvements
Property, Plant and Equipment [Line Items]
Property and equipment , gross	1,917	1,754
Computer equipment and software
Property, Plant and Equipment [Line Items]
Property and equipment , gross	$ 697	$ 569
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

Balance Sheet Account Details50

Balance Sheet Account Details - Goodwill and Other Intangible Assets (Details) - USD ($)	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Finite-Lived Intangible Assets [Line Items]
Goodwill	$ 85,959,000	$ 72,207,000
Total goodwill and other identifiable intangible assets, net	$ 314,543,000	276,912,000
Finite-lived intangible asset, useful life	20 years
Amortization expense	$ 11,300,000	10,600,000	$ 2,400,000
Amortization expense, 2018	12,800,000
Amortization expense, 2019	12,800,000
Amortization expense, 2020	12,800,000
Amortization expense, 2021	12,800,000
Impairment of intangible assets with finite lives	0	0	$ 0
Complete technology
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	222,900,000	182,577,000
Less: Accumulated amortization	(23,301,000)	(12,792,000)
Trade name
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	2,642,000	2,642,000
Less: Accumulated amortization	(916,000)	(784,000)
Customer relationships
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	29,600,000	29,600,000
Less: Accumulated amortization	(10,264,000)	(8,784,000)
Licensing Agreements
Finite-Lived Intangible Assets [Line Items]
Definite lived intangible assets	26,298,000	26,298,000
Less: Accumulated amortization	(6,772,000)	(477,000)
IPR&D
Finite-Lived Intangible Assets [Line Items]
IPR&D	$ 7,923,000	$ 12,246,000

Balance Sheet Account Details51

Balance Sheet Account Details - Accrued Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Other Balance Sheet Details [Abstract]
Compensation	$ 4,085	$ 2,603
Legal	430	829
Amounts owed to former licensees	396	899
Royalties owed to third parties	954	942
Deferred revenue	173	0
Other	1,339	1,124
Accrued liabilities	$ 7,377	$ 6,397

Balance Sheet Account Details52

Balance Sheet Account Details - Contingent Liabilities (Details) - USD ($)	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Business Acquisition [Line Items]
Revenue royalty payable on all Cydex-related revenue (as a 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 at beginning of period	$ 8,100,000	13,500,000
Payments	(4,998,000)	(8,777,000)	$ (6,740,000)
Fair Value Adjustment	2,500,000	3,400,000
Additions	8,400,000
Commercial rights at end of period	14,000,000	8,100,000	13,500,000
Cydex
Contingent Liability [Roll Forward]
Commercial rights at beginning of period	6,600,000	9,500,000
Payments	(5,000,000)	(6,200,000)
Fair Value Adjustment	0	3,300,000
Additions	0
Commercial rights at end of period	1,600,000	6,600,000	9,500,000
Metabasis
Contingent Liability [Roll Forward]
Commercial rights at beginning of period	1,500,000	4,000,000
Payments	0	(2,600,000)
Fair Value Adjustment	2,500,000	100,000
Additions	0
Commercial rights at end of period	4,000,000	1,500,000	4,000,000
Crystal
Contingent Liability [Roll Forward]
Commercial rights at beginning of period	0	0
Payments	0	0
Fair Value Adjustment	0	0
Additions	8,400,000
Commercial rights at end of period	$ 8,400,000	$ 0	$ 0

Balance Sheet Account Details53

Balance Sheet Account Details - Other Long-Term Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Other Balance Sheet Details [Abstract]
Deferred rent	$ 321	$ 357
Deposits	43	43
Other	359	287
Other long-term liabilities	$ 723	$ 687

Stockholders' Equity - Narrativ

Stockholders' Equity - Narrative (Details) - USD ($)	May 31, 2012	May 31, 2016	Sep. 30, 2015	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Corporate Share Repurchase
Shares repurchased in period (shares)				14,000	40,500	6,120
Shares repurchased in period, value				$ 1,966,000	$ 3,901,000	$ 489,000
Stock repurchase program, authorized amount			$ 200,000,000
Stock repurchase program, period in force			3 years
Stock repurchase program, remaining authorized repurchase amount				$ 193,600,000
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)				$ 53.17	$ 46.53	$ 35.39
Intrinsic value of options exercised				$ 13,300,000	$ 12,000,000	$ 20,700,000
Cash received from options exercised				4,700,000	$ 6,200,000	$ 8,700,000
Unrecognized compensation cost				$ 19,400,000
Weighted-average period in which cost is expected to be recognized				2 years 5 months 37 days
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 3 months 33 days
Unrecognized compensation cost, restricted stock				$ 6,500,000
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	900,000
Shares available for future option grants (shares)				800,000
Amended ESPP
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future option grants (shares)				67,394
Employee Stock Purchase Plan
Shares allowed to purchase in employee stock purchase plan per employee (shares)				1,250
Common stock issued under amended ESSP (shares)				3,061	1,961	3,374

Stockholders' Equity - Share-Ba

Stockholders' Equity - Share-Based Compensation (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based compensation expense	$ 24,915	$ 18,893	$ 12,458
Research and development expenses
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based compensation expense	14,235	8,836	4,080
General and administrative expenses
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based compensation expense	$ 10,680	$ 10,057	$ 8,378

Stockholders' Equity - Stock Op

Stockholders' Equity - Stock Option Plan Activity (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016
Shares [Rollforward]
Balance at Beginning of Period (shares)	1,754,275
Granted (shares)	273,353
Exercised (shares)	(148,252)
Forfeited (shares)	(3,044)
Balance at End of Period (shares)	1,876,332	1,754,275
Exercisable at December 31, 2016 (shares)	1,431,245
Options vested and expected to vest as of December 31, 2016 (shares)	1,876,332
Weighted Average Exercise Price [Roll Forward]
Balance at Beginning of Period (in usd per share)	$ 42.12
Granted (in usd per share)	112.58
Exercised (in usd per share)	31.58
Forfeited (in usd per share)	79.74
Balance at End of Period (in usd per share)	53.17	$ 42.12
Exercisable at December 31, 2016 (in usd per share)	40.08
Options vested and expected to vest as of December 31, 2016 (in usd per share)	$ 53.17
Weighted Average Remaining Contractual Term in Years	5 years 8 months 37 days	6 years 1 month 38 days
Exercisable, Weighted Average Remaining Contractual Term in Years	4 years 11 months 12 days
Options vested and expected to vest, Weighted Average Remaining Contractual Term in Years	5 years 8 months 37 days
Aggregate Intrinsic Value	$ 157,340	$ 104,247
Exercisable, Aggregate Intrinsic Value	138,616
Options vested and expected to vest, Aggregate Intrinsic Value	$ 157,340

Stockholders' Equity - Breakdow

Stockholders' Equity - Breakdown of Options Outstanding (Details)	12 Months Ended
	Dec. 31, 2017$ / sharesshares
$8.58 – $141.61
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	$ 141.61
Options outstanding (shares) | shares	1,876,332
Weighted average remaining life in years	5 years 8 months 37 days
Weighted average exercise price (per share)	$ 53.17
Options exercisable (shares) | shares	1,431,245
Weighted average exercise price (per share)	$ 40.08
$8.58 - $10.05
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	$ 10.05
Options outstanding (shares) | shares	208,032
Weighted average remaining life in years	2 years 10 months 18 days
Weighted average exercise price (per share)	$ 9.97
Options exercisable (shares) | shares	208,032
Weighted average exercise price (per share)	$ 9.97
$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	71,850
Weighted average remaining life in years	3 years 11 months 12 days
Weighted average exercise price (per share)	$ 11.44
Options exercisable (shares) | shares	71,850
Weighted average exercise price (per share)	$ 11.44
$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	285,879
Weighted average remaining life in years	4 years 1 month 10 days
Weighted average exercise price (per share)	$ 14.47
Options exercisable (shares) | shares	271,879
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	72,777
Weighted average remaining life in years	1 year 1 month 28 days
Weighted average exercise price (per share)	$ 16.32
Options exercisable (shares) | shares	72,777
Weighted average exercise price (per share)	$ 16.32
$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	207,004
Weighted average remaining life in years	5 years 1 month 18 days
Weighted average exercise price (per share)	$ 21.92
Options exercisable (shares) | shares	207,004
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	226,287
Weighted average remaining life in years	6 years 8 months 19 days
Weighted average exercise price (per share)	$ 50.50
Options exercisable (shares) | shares	160,301
Weighted average exercise price (per share)	$ 48.49
$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	25,757
Weighted average remaining life in years	6 years 5 months 31 days
Weighted average exercise price (per share)	$ 67.17
Options exercisable (shares) | shares	23,726
Weighted average exercise price (per share)	$ 67.34
$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	216,118
Weighted average remaining life in years	6 years 1 month 10 days
Weighted average exercise price (per share)	$ 74.42
Options exercisable (shares) | shares	206,828
Weighted average exercise price (per share)	$ 74.42
$85.79 - $97.92
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	$ 97.92
Options outstanding (shares) | shares	238,675
Weighted average remaining life in years	6 years 11 months 27 days
Weighted average exercise price (per share)	$ 88.93
Options exercisable (shares) | shares	138,712
Weighted average exercise price (per share)	$ 90.54
$100.38 - $141.61
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Range of exercise prices (per share), lower	100.38
Range of exercise prices (per share), upper	$ 141.61
Options outstanding (shares) | shares	323,953
Weighted average remaining life in years	9 years 1 month 12 days
Weighted average exercise price (per share)	$ 112.75
Options exercisable (shares) | shares	70,136
Weighted average exercise price (per share)	$ 106.78

Stockholders' Equity - Assumpti

Stockholders' Equity - Assumptions (Details)	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected term			6 years 6 months
Minimum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate (percent)	2.00%	1.30%	1.70%
Expected volatility (percent)	43.00%	48.00%	50.00%
Expected term	6 years 6 months	6 years 7 months 6 days
Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate (percent)	2.20%	1.90%	2.00%
Expected volatility (percent)	47.00%	50.00%	58.00%
Expected term	6 years 9 months 18 days	6 years 8 months 12 days

Stockholders' Equity - Restrict

Stockholders' Equity - Restricted Stock Activity (Details) - Restricted Stock	12 Months Ended
	Dec. 31, 2017$ / sharesshares
Shares [Rollforward]
Outstanding at Beginning of Period (shares) | shares	308,700
Granted (shares) | shares	73,799
Vested (shares) | shares	(187,864)
Forfeited (shares) | shares	(61,341)
Outstanding at End of Period (shares) | shares	133,294
Weighted-Average Grant Date Fair Value [Roll Forward]
Outstanding at Beginning of Period (in usd per share) | $ / shares	$ 86.61
Granted (in usd per share) | $ / shares	99.53
Vested (in usd per share) | $ / shares	84.50
Forfeited (in usd per share) | $ / shares	97.78
Outstanding at End of Period (in usd per share) | $ / shares	$ 91.60

Income Taxes - Narrative (Detai

Income Taxes - Narrative (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Operating Loss Carryforwards [Line Items]
Rate change for changes in tax law	$ 32,429	$ 25	$ (5,756)
Valuation allowance, change in amount	(8,400)	$ 6,300	$ (231,700)
Unrecognized tax benefits that would impact effective tax rate	26,800
Research Tax Credit Carryforward
Operating Loss Carryforwards [Line Items]
Tax credit carryforward	23,800
California and New Jersey Research Tax Credit Carryforward
Operating Loss Carryforwards [Line Items]
Tax credit carryforward	20,700
Internal Revenue Service (IRS)
Operating Loss Carryforwards [Line Items]
Operating loss carryforward	387,900
State and Local Jurisdiction
Operating Loss Carryforwards [Line Items]
Operating loss carryforward	$ 126,500

Income Taxes - Components of In

Income Taxes - Components of Income Tax Expense (Benefit) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Current expense (benefit):
Federal									$ 0	$ 21	$ 11
State									111	12	7
Foreign									261
Total Current Income Tax Benefit									372	33	18
Deferred expense (benefit):
Federal									44,075	10,534	(167,413)
State									228	(240)	(24,720)
Foreign									0	0	0
Income tax expense from continuing operations	$ 37,674	$ 3,645	$ 2,242	$ 1,114	$ 10,354	$ 160	$ (3,881)	$ 3,694	$ 44,675	$ 10,327	$ (192,115)

Income Taxes - Reconciliation o

Income Taxes - Reconciliation of Income Tax Expense (Benefit) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Income Tax Expense (Benefit), Continuing Operations, Income Tax Reconciliation [Abstract]
Amounts computed at statutory federal rate									$ 20,031	$ 2,786	$ 13,198
State taxes net of federal benefit									622	175	386
Contingent liabilities									903	1,225	1,684
Stock-based compensation									(4,019)	263	140
Research and development credits									(2,821)	(1,525)	304
Change in uncertain tax positions									1,308	1,423	27,188
Rate change for changes in state law									32,429	25	(5,756)
Change in valuation allowance									(4,169)	6,283	(231,370)
Other									391	(328)	2,111
Income tax expense from continuing operations	$ 37,674	$ 3,645	$ 2,242	$ 1,114	$ 10,354	$ 160	$ (3,881)	$ 3,694	$ 44,675	$ 10,327	$ (192,115)

Income Taxes - Deferred Taxes (

Income Taxes - Deferred Taxes (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Deferred assets:
Net operating loss carryforwards	$ 90,272	$ 150,226
Research credit carryforwards	30,677	26,878
Fixed assets and intangibles	1,984	4,385
Accrued expenses	845	943
Contingent liabilities	354	578
Deferred revenue	17	0
Present value of royalties	0	591
Deferred rent	28	45
Capital Loss Carryforward	1,609	4,432
Viking Equity Method Investment	5,137	5,692
Other	12,117	19,312
Deferred tax assets	143,040	213,082
Valuation allowance for deferred tax assets	(6,987)	(15,349)
Net deferred tax assets	136,053	197,733
Deferred tax liabilities:
Retrophin fair value adjustment	(243)	(52)
Convertible debt	(737)	(1,196)
Identified intangibles	(48,237)	(68,631)
Identified indefinite lived intangibles	(2,414)	(3,963)
Total	$ 84,422	$ 123,891

Income Taxes - Reconciliation64

Income Taxes - Reconciliation of Unrecognized Tax Benefits (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Reconciliation of Unrecognized Tax Benefits, Excluding Amounts Pertaining to Examined Tax Returns [Roll Forward]
Balance at beginning of period	$ 38,770	$ 36,452	$ 8,524
Additions based on tax positions related to the current year	1,067	70	154
Additions for tax positions of prior years	109	2,408	28,224
Reductions for tax positions of prior years	(10,583)	(160)	(450)
Balance at end of period	$ 29,363	$ 38,770	$ 36,452

Summary of Unaudited Quarterl65

Summary of Unaudited Quarterly Financial Information - Summary (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2017		Dec. 31, 2016		Dec. 31, 2015
Quarterly Financial Information Disclosure [Abstract]
Total revenues	$ 50,465	$ 33,375	$ 27,995	$ 29,267	$ 38,185	$ 21,619	$ 19,521	$ 29,648	$ 141,102		$ 108,973		$ 71,914
Total operating costs and expenses	22,113	16,882	14,980	19,051	18,831	16,153	15,552	14,552	73,026		65,088		44,585
Income tax (expense) benefit	(37,674)	(3,645)	(2,242)	(1,114)	(10,354)	(160)	3,881	(3,694)	(44,675)		(10,327)		192,115
Net Income (loss)	$ (7,007)	$ 8,426	$ 6,058	$ 5,079	$ (3,125)	$ 1,051	$ (6,170)	$ 6,608	$ 12,556		$ (1,636)		$ 229,824
Basic per share amounts:
Net income (loss) - Basic (USD per share)	$ (0.33)	$ 0.40	$ 0.29	$ 0.24	$ 0.15	$ 0.05	$ (0.30)	$ 0.32	$ 0.60	[1]	$ (0.08)	[1]	$ 11.61	[1]
Diluted per share amounts:
Net income (loss) - Diluted (USD per share)	$ (0.33)	$ 0.36	$ 0.26	$ 0.22	$ 0.15	$ 0.05	$ (0.30)	$ 0.30	$ 0.53	[1]	$ (0.08)	[1]	$ 10.83	[1]
Weighted average shares—basic (shares)	21,109	21,071	21,013	20,938	20,898	20,887	20,832	20,708	21,032		20,831		19,790
Weighted average shares—diluted (shares)	21,109	23,551	23,216	23,019	20,898	22,997	20,832	22,284	23,481		20,831		21,228
[1]	The sum of net income per share amounts may not equal the total due to rounding