Array 10-K 19 Aug 16 2016 FY Annual report Financial data

Document and Entity Information

Document and Entity Information - USD ($)	12 Months Ended
	Jun. 30, 2016	Aug. 15, 2016	Dec. 31, 2015
Document and Entity Information
Entity Registrant Name	ARRAY BIOPHARMA INC
Entity Central Index Key	1,100,412
Current Fiscal Year End Date	--06-30
Entity Filer Category	Accelerated Filer
Document Type	10-K
Document Period End Date	Jun. 30, 2016
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	FY
Amendment Flag	false
Entity Current Reporting Status	Yes
Entity Common Stock, Shares Outstanding		145,022,564
Entity Well-known Seasoned Issuer	No
Entity Voluntary Filers	No
Entity Public Float			$ 593,428,976

Balance Sheets

Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2016	Jun. 30, 2015
Current assets
Cash and cash equivalents	$ 56,598	$ 55,691
Marketable securities	53,344	122,635
Accounts receivable	39,302	6,307
Prepaid expenses and other current assets	6,057	6,414
Total current assets	155,301	191,047
Long-term assets
Marketable securities	596	496
Property and equipment, net	6,680	5,050
Other long-term assets	6,323	1,614
Total long-term assets	13,599	7,160
Total assets	168,900	198,207
Current liabilities
Accounts payable	10,147	4,570
Accrued outsourcing costs	19,140	17,402
Accrued compensation and benefits	8,633	7,507
Other accrued expenses	1,068	2,714
Deferred rent	590	1,285
Deferred revenue	12,856	8,946
Total current liabilities	52,434	42,424
Long-term liabilities
Deferred rent	4,184	3,314
Deferred revenue	35,961	2,040
Long-term debt, net	113,655	107,280
Other long-term liabilities	598	496
Total long-term liabilities	154,398	113,130
Total liabilities	206,832	155,554
Commitments and contingencies
Stockholders' equity (deficit)
Preferred stock, $0.001 par value; 10,000,000 shares authorized, no shares issued and outstanding	0	0
Common stock, $0.001 par value; 280,000,000 and 220,000,000 shares authorized as of June 30, 2016 and June 30, 2015, respectively, 143,690,104 and 142,107,025 shares issued and outstanding as of June 30, 2016 and June 30, 2015, respectively	144	142
Additional paid-in capital	763,324	751,073
Accumulated other comprehensive income	7	5
Accumulated deficit	(801,407)	(708,567)
Total stockholders' equity (deficit)	(37,932)	42,653
Total liabilities and stockholders' equity (deficit)	$ 168,900	$ 198,207

Balance Sheets (Parenthetical)

Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2016	Jun. 30, 2015
Statement of Financial Position [Abstract]
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, authorized (in shares)	10,000,000	10,000,000
Preferred stock, issued (in shares)	0	0
Preferred stock, outstanding (in shares)	0	0
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, authorized (in shares)	280,000,000	220,000,000
Common stock, issued (in shares)	143,690,104	142,107,025
Common stock, outstanding (in shares)	143,690,104	142,107,025

Statements of Operations and Co

Statements of Operations and Comprehensive Income (Loss) - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Revenue
License and milestone revenue	$ 3,876	$ 20,367	$ 25,111
Reimbursement revenue	107,330	7,020	0
Collaboration and other revenue	26,673	24,522	16,967
Total revenue	137,879	51,909	42,078
Operating expenses
Cost of partnered programs	23,166	44,392	45,965
Research and development for proprietary programs	160,655	54,442	49,824
General and administrative	36,267	31,433	21,907
Total operating expenses	220,088	130,267	117,696
Gain on the Binimetinib and Encorafenib Agreements, net	0	80,010	0
Gain on sale of CMC, net	0	1,641	0
Income (loss) from operations	(82,209)	3,293	(75,618)
Other income (expense)
Realized gain from marketable securities, net	0	16,255	0
Interest income	243	68	77
Interest expense	(10,874)	(10,247)	(9,716)
Total other income (expense), net	(10,631)	6,076	(9,639)
Net income (loss)	(92,840)	9,369	(85,257)
Change in unrealized gain on marketable securities	2	3	4
Comprehensive income (loss)	$ (92,838)	$ 9,372	$ (85,253)
Net earnings (loss) per share – basic (in dollars per share)	$ (0.65)	$ 0.07	$ (0.69)
Net earnings (loss) per share – diluted (in dollars per share)	$ (0.65)	$ 0.07	$ (0.69)
Weighted average shares outstanding – basic (in shares)	142,964	136,679	123,403
Weighted average shares outstanding – diluted (in shares)	142,964	141,692	123,403

Statements of Stockholders' Equ

Statements of Stockholders' Equity (Deficit) - USD ($) shares in Thousands, $ in Thousands	Total	Preferred Stock [Member]	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Other Comprehensive Income [Member]	Accumulated Deficit [Member]
Balance (in shares) at Jun. 30, 2013		0	116,878
Balance at Jun. 30, 2013	$ (21,909)	$ 0	$ 117	$ 610,655	$ (2)	$ (632,679)
Increase (Decrease) in Stockholders' Equity
Shares issued for cash under employee share plans, net (in shares)			1,132
Shares issued for cash under employee share plans, net	3,693		$ 1	3,692
Employee share-based compensation expense	4,331			4,331
Issuance of common stock, net of offering costs (in shares)			13,807
Issuance of common stock, net of offering costs	73,448		$ 14	73,434
Offering costs for convertible senior notes, equity portion	(31)			(31)
Change in unrealized gain (loss) on marketable securities	4				4
Net income (loss)	(85,257)					(85,257)
Balance (in shares) at Jun. 30, 2014		0	131,817
Balance at Jun. 30, 2014	(25,721)	$ 0	$ 132	692,081	2	(717,936)
Increase (Decrease) in Stockholders' Equity
Shares issued for cash under employee share plans, net (in shares)			1,325
Shares issued for cash under employee share plans, net	4,398		$ 1	4,397
Employee share-based compensation expense	7,513			7,513
Non-employee share-based compensation expense	547			547
Issuance of common stock, net of offering costs (in shares)			8,965
Issuance of common stock, net of offering costs	46,544		$ 9	46,535
Change in unrealized gain (loss) on marketable securities	3				3
Net income (loss)	9,369					9,369
Balance (in shares) at Jun. 30, 2015		0	142,107
Balance at Jun. 30, 2015	42,653	$ 0	$ 142	751,073	5	(708,567)
Increase (Decrease) in Stockholders' Equity
Shares issued for cash under employee share plans, net (in shares)			782
Shares issued for cash under employee share plans, net	2,032		$ 1	2,031
Employee share-based compensation expense	7,283			7,283
Warrants exercised - cashless (in shares)			223
Warrants exercised for cash (in shares)			12
Warrants exercised for cash	46			46
Issuance of common stock, net of offering costs (in shares)			566
Issuance of common stock, net of offering costs	2,892		$ 1	2,891
Change in unrealized gain (loss) on marketable securities	2				2
Net income (loss)	(92,840)					(92,840)
Balance (in shares) at Jun. 30, 2016		0	143,690
Balance at Jun. 30, 2016	$ (37,932)	$ 0	$ 144	$ 763,324	$ 7	$ (801,407)

Statements of Cash Flows

Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Cash flows from operating activities
Net income (loss)	$ (92,840)	$ 9,369	$ (85,257)
Adjustments to reconcile net income (loss) to net cash used in operating activities:
Depreciation and amortization expense	1,529	3,702	4,506
Non-cash interest expense	6,375	5,799	5,258
Share-based compensation expense	7,283	7,809	4,331
Extinguishment of co-development liability, net	0	(21,610)	0
Realized gain from marketable securities, net	0	(16,255)	0
Gain on sale of CMC, net	0	(1,641)	0
Non-cash license revenue	0	0	(4,500)
Changes in operating assets and liabilities:
Accounts receivable	(32,995)	(7,592)	4,166
Prepaid expenses and other assets	(4,352)	(1,260)	(1,961)
Accounts payable and other accrued expenses	3,931	(1,113)	1,866
Accrued outsourcing costs	1,738	7,362	4,464
Accrued compensation and benefits	1,126	(702)	(1,272)
Co-development liability	0	12,169	5,165
Deferred rent	175	(3,236)	(3,645)
Deferred revenue	37,831	1,584	(4,807)
Other long-term liabilities	109	(178)	4
Net cash used in operating activities	(70,090)	(5,793)	(71,682)
Cash flows from investing activities
Purchases of property and equipment	(3,159)	(2,507)	(2,614)
Proceeds from sale of CMC	0	3,750	0
Purchases of marketable securities	(139,150)	(202,908)	(95,602)
Proceeds from sales and maturities of marketable securities	208,336	143,616	100,698
Net cash provided by (used in) investing activities	66,027	(58,049)	2,482
Cash flows from financing activities
Proceeds from the issuance of common stock	2,992	47,500	75,000
Proceeds from employee stock purchases and options exercised	2,032	4,398	3,693
Warrants exercised for cash	46	0	0
Payment of debt issuance costs	0	0	(86)
Payment of stock offering costs	(100)	(956)	(1,552)
Net cash provided by financing activities	4,970	50,942	77,055
Net increase (decrease) in cash and cash equivalents	907	(12,900)	7,855
Cash and cash equivalents at beginning of period	55,691	68,591	60,736
Cash and cash equivalents at end of period	56,598	55,691	68,591
Supplemental disclosure of cash flow information
Cash paid for interest	4,466	4,450	4,349
Change in unrealized gain on marketable securities	$ 2	$ 3	$ 4

OVERVIEW, BASIS OF PRESENTATION

OVERVIEW, BASIS OF PRESENTATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES	12 Months Ended
	Jun. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
OVERVIEW, BASIS OF PRESENTATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES	OVERVIEW, BASIS OF PRESENTATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES Organization Array BioPharma Inc. (also referred to as "Array,","we", "us", "our" or "the Company"), incorporated in Delaware on February 6, 1998, is a biopharmaceutical company focused on the discovery, development and commercialization of targeted small molecule drugs to treat patients afflicted with cancer. Basis of Presentation The accompanying financial statements have been prepared in accordance with U.S. generally accepted accounting principles (“U.S. GAAP”) and include all adjustments necessary for the fair presentation of our financial position, results of operations and cash flows for the periods presented. Our management performed an evaluation of our activities through the date of filing of this Annual Report on Form 10-K and concluded that there are no subsequent events. Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires the Company's management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue and expenses, and related disclosure of contingent assets and liabilities. Management bases its estimates on the Company's historical experience and on various other assumptions that it believes are reasonable under the circumstances. These estimates are the basis for the Company's judgments about the carrying values of assets and liabilities, which in turn may impact its reported revenue and expenses. The Company's actual results could differ significantly from these estimates under different assumptions or conditions. The Company believes the financial statements are most significantly impacted by the following accounting estimates and judgments: (i) identifying deliverables under collaboration, license and other agreements involving multiple elements and determining whether such deliverables are separable from other aspects of the contractual relationship; (ii) estimating the selling price of deliverables for the purpose of allocating arrangement consideration for revenue recognition; (iii) estimating the periods over which the allocated consideration for deliverables is recognized; (iv) estimating accrued outsourcing costs for clinical trials and preclinical testing; and (v) estimating the fair value of non-marketable equity received from licensing or other transactions. Reclassifications Certain prior period amounts in the Company's financial statements have been reclassified to conform to the current period presentation. The $39.4 million balance attributable to outstanding warrants, which was presented historically as a separate item in stockholders' equity (deficit) on the Company's balance sheet, has been combined with additional paid-in capital for all periods presented in these financial statements. Liquidity With the exception of fiscal year 2015, the Company has incurred operating losses and has an accumulated deficit as a result of ongoing research and development spending since inception. As of June 30, 2016 , we had an accumulated deficit of $801.4 million . We had a net loss of $92.8 million for the fiscal year ended June 30, 2016 . We have historically funded our operations from up-front fees and license and milestone payments received under our drug collaboration and other agreements, the sale of equity securities, and debt provided by convertible debt and other credit facilities. We believe that our cash, cash equivalents, receivables and marketable securities as of June 30, 2016 will enable us to continue to fund operations in the normal course of business for at least the next 12 months. Until we can generate sufficient levels of cash from current operations, which we do not expect to achieve in the foreseeable future, and because sufficient funds may not be available to us when needed from existing collaborations, we expect that we will be required to continue to fund our operations in part through the sale of debt or equity securities, through licensing select programs or partial economic rights that include up-front, royalty and/or milestone payments. Our ability to successfully raise sufficient funds through the sale of debt or equity securities or from debt financing from lenders when needed is subject to many risks and uncertainties and, even if we are successful, future equity issuances would result in dilution to our existing stockholders. We also may not successfully consummate new collaboration and other agreements that provide for up-front fees or milestone payments, or we may not earn milestone payments under such agreements when anticipated, or at all. Our ability to realize milestone or royalty payments under existing agreements and to enter into new arrangements that generate additional revenue through up-front fees and milestone or royalty payments is subject to a number of risks, many of which are beyond our control. In addition, our assessment of our future need for funding and our ability to continue to fund our operations is a forward-looking statement that is based on assumptions that may prove to be wrong and that involve substantial risks and uncertainties. Our actual future capital requirements could also vary as a result of a number of factors. If we are unable to generate enough revenue from our existing or new collaboration and other agreements when needed or to secure additional sources of funding, it may be necessary to significantly reduce the current rate of spending through further reductions in staff and delaying, scaling back, or stopping certain research and development programs, including more costly Phase 2 and Phase 3 clinical trials on our wholly-owned programs as these programs progress into later stage development. Insufficient liquidity may also require us to relinquish greater rights to product candidates at an earlier stage of development or on less favorable terms to us and our stockholders than we would otherwise choose in order to obtain up-front license fees needed to fund operations. These events could prevent us from successfully executing our operating plan and, in the future, could raise substantial doubt about our ability to continue as a going concern. Further, as discussed in Note 7 – Long-term Debt , if at any time our balance of total cash, cash equivalents and marketable securities at Comerica Bank and approved outside accounts falls below $22.0 million , we must maintain a balance of cash, cash equivalents and marketable securities at Comerica at least equivalent to the entire outstanding debt balance with Comerica, which is currently $14.6 million . We must also maintain a monthly liquidity ratio if we draw down on the revolving line of credit with Comerica. Summary of Significant Accounting Policies Fair Value Measurements We follow accounting guidance on fair value measurements for financial instruments measured on a recurring basis, as well as for certain assets and liabilities that are initially recorded at their estimated fair values. Fair value is defined as the exit price, or the amount that would be received from selling an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. We use the following three-level hierarchy that maximizes the use of observable inputs and minimizes the use of unobservable inputs to value our financial instruments: • Level 1: Observable inputs such as unadjusted quoted prices in active markets for identical instruments. • Level 2: Quoted prices for similar instruments that are directly or indirectly observable in the marketplace. • Level 3: Significant unobservable inputs which are supported by little or no market activity and that are financial instruments whose values are determined using pricing models, discounted cash flow methodologies, or similar techniques, as well as instruments for which the determination of fair value requires significant judgment or estimation. Financial instruments measured at fair value are classified in their entirety based on the lowest level of input that is significant to the fair value measurement. Our assessment of the significance of a particular input to the fair value measurement in its entirety requires us to make judgments and consider factors specific to the asset or liability. The use of different assumptions and/or estimation methodologies may have a material effect on estimated fair values. Accordingly, the fair value estimates disclosed or initial amounts recorded may not be indicative of the amount that we or holders of the instruments could realize in a current market exchange. The carrying amounts of cash equivalents and marketable securities approximate their fair value based upon quoted market prices. Certain of our financial instruments are not measured at fair value on a recurring basis, but are recorded at amounts that approximate their fair value due to their liquid or short-term nature, such as cash, accounts receivable and payable, and other financial instruments in current assets or current liabilities. Cash and Cash Equivalents and Concentration of Credit Risk Cash and cash equivalents consist of cash and short-term, highly-liquid financial instruments that are readily convertible to cash and have maturities of 90 days or less from the date of purchase. They may consist of money market funds, commercial paper, U.S. government agency obligations and corporate notes and bonds with high credit quality. We currently maintain all cash in several institutions in the U.S. Balances at these institutions may exceed Federal Deposit Insurance Corporation insured limits. Marketable Securities We have designated our marketable securities as of each balance sheet date as available-for-sale securities and account for them at their respective fair values. Marketable securities are classified as short-term or long-term based on the nature of the securities and their availability to meet current operating requirements. Marketable securities that are readily available for use in current operations are classified as short-term available-for-sale securities and are reported as a component of current assets in the accompanying balance sheets. Marketable securities that are not considered available for use in current operations are classified as long-term available-for-sale securities and are reported as a component of long-term assets in the accompanying balance sheets. Securities that are classified as available-for-sale are measured at fair value, including accrued interest, with temporary unrealized gains and losses reported as a component of stockholders' equity (deficit) until their disposition. We review all available-for-sale securities at each period end to determine if they remain available-for-sale based on our then current intent and ability to sell the security if it is required to do so. The cost of securities sold is based on the specific identification method. All of our marketable securities are subject to a periodic impairment review. We recognize an impairment charge when a decline in the fair value of our investments below the cost basis is judged to be other-than-temporary. Property and Equipment Property and equipment are stated at historical cost less accumulated depreciation and amortization. Additions and improvements are capitalized. Certain costs to internally develop software are also capitalized. Maintenance and repairs are expensed as incurred. Depreciation and amortization are computed on the straight-line method based on the following estimated useful lives: Furniture and fixtures 7 years Equipment 5 years Computer hardware and software 3 years We depreciate leasehold improvements associated with operating leases over the shorter of the expected useful life of the improvements or the remaining lease term. The carrying value for property and equipment is reviewed for impairment at least annually and when events or changes in circumstances indicate that the carrying value of the assets may not be recoverable. Equity Investments From time to time, we may enter into collaboration and other agreements or other arrangements under which we receive an equity interest as consideration for all or a portion of up-front, license or other fees or consideration under the terms of the agreement or arrangement. We report equity securities received from non-publicly traded companies in which we do not exercise a significant or controlling interest at cost in other long-term assets in the accompanying balance sheets. We monitor our investments for impairment at least annually, and consider events or changes in circumstances we know of that may have a significant adverse effect on the fair value. We make appropriate reductions in the carrying value if it is determined that an impairment has occurred, based primarily on the financial condition and near and long-term prospects of the issuer. We do not report the fair value of our equity investments in non-publicly traded companies because it is not practical to do so. Array received shares of Loxo Oncology Inc.'s ("Loxo") non-voting preferred stock as consideration for licensing rights we granted to Loxo under our July 2013 Drug Discovery Collaboration Agreement. We recorded the $4.5 million estimated fair value of the preferred shares as a long-term investment utilizing the cost method of accounting. In August 2014, Loxo completed an initial public offering ("IPO") of its common stock, which then began to trade on the NASDAQ Global Market. At the closing of the IPO, the preferred shares we held were converted into approximately 1.6 million shares of common stock and, based on the readily determinable fair value of the Loxo common stock following the IPO, we began to account for our investment in Loxo as available-for-sale securities. During the year ended June 30, 2015 , we sold all 1.6 million shares of Loxo common stock and received net proceeds of $20.8 million , resulting in a net realized gain of $16.3 million . As of both June 30, 2016 and 2015 , we held shares of preferred stock of VentiRx Pharmaceuticals, Inc. ("VentiRx") recorded at $1.5 million that we received under a February 2007 collaboration and licensing agreement with VentiRx. The Company does not have a controlling interest nor does it exert significant influence over VentiRx. Accrued Outsourcing Costs Substantial portions of our preclinical studies and clinical trials are performed by third-party laboratories, medical centers, contract research organizations and other vendors (collectively "CROs"). These CROs generally bill monthly or quarterly for services performed, or bill based upon milestone achievement. For preclinical studies, we accrue expenses based upon estimated percentage of work completed and the contract milestones remaining. For clinical studies, expenses are accrued based upon the number of patients enrolled and the duration of the study. We monitor patient enrollment, the progress of clinical studies and related activities to the extent possible through internal reviews of data reported to us by the CROs, correspondence with the CROs and clinical site visits. Our estimates depend on the timeliness and accuracy of the data provided by the CROs regarding the status of each program and total program spending. We periodically evaluate the estimates to determine if adjustments are necessary or appropriate based on information we receive. Convertible Senior Notes Our 3.00% convertible senior notes due 2020 are accounted for in accordance with FASB Accounting Standards Codification (“ASC”) 470-20, Debt – Debt with Conversion and Other Options. ASC 470-20 requires the issuer of convertible debt that may be settled in shares or cash upon conversion at the issuer's option, such as our notes, to account for the liability (debt) and equity (conversion option) components separately. The value assigned to the debt component is the estimated fair value, as of the issuance date, of a similar debt instrument without the conversion option. The amount of the equity component (and resulting debt discount) is calculated by deducting the fair value of the liability component from the principal amount of the convertible debt instrument. The resulting debt discount is amortized as additional non-cash interest expense over the expected life of the notes utilizing the effective interest method. Although ASC 470-20 has no impact on our actual past or future cash flows, it requires us to record non-cash interest expense as the debt discount is amortized. For additional information, see Note 7 – Long-term Debt . Binimetinib and Encorafenib Agreements The transactions contemplated by the asset transfer agreements Array entered into with Novartis International Pharmaceutical Ltd. ("Novartis") and Novartis Pharma AG ("Novartis Pharma"), for the re-acquisition of rights to binimetinib and encorafenib Agreements, which we refer to as the Binimetinib and Encorafenib Agreements, closed in March 2015. As a result of the closing, we received an $85 million cash payment, received $5 million for the reimbursement of certain transaction costs, extinguished net co-development liabilities of $21.6 million and recorded deferred revenue of $6.6 million in the third quarter of fiscal 2015. Also during the third quarter, we entered into a third party agreement to complete the Novartis transactions for a net consideration payment to the third party of $25 million . The Binimetinib and Encorafenib Agreements executed with Novartis Pharma and Novartis involved multiple elements. We therefore identified each item given and received and determined how each item should be recognized and classified. The sum of the above transactions was accounted for in a manner consistent with a settlement of a material liability or gain contingency. We deferred $6.6 million of the consideration received from Novartis Pharma to reflect the estimated fair value of certain future obligations we are required to perform under the Binimetinib and Encorafenib Agreements, including completion of certain trials that are partially funded by Novartis Pharma. The amount deferred was determined using the estimated fair value of the services to be provided by our full-time employees that we do not anticipate will be covered in the funding reimbursements we will receive from Novartis Pharma under the Binimetinib and Encorafenib Agreements. The estimated fair value was based on amounts we have billed to other third parties in other transactions for similar services. We anticipate recording revenue over the deferral period, which is based upon our estimated time to complete our performance with respect to the applicable clinical trials. The balance of deferred revenue was $1.8 million and $5.4 million at June 30, 2016 and 2015, respectively. As of March 2, 2015, prior to the closing of the Binimetinib and Encorafenib Agreements, we had an accounts receivable balance from Novartis of $6.7 million and a $28.3 million co-development liability balance that we owed to Novartis. On March 2, 2015, the termination of the License Agreement with Novartis relating to binimetinib and the effectiveness of the Binimetinib and Encorafenib Agreements resulted in the right to offset the accounts receivable and co-development liability balances. Because we and Novartis owed each other determinable amounts and we have the right to set off the amount payable with the amount receivable from Novartis, we set off these amounts resulting in a net co-development liability of $21.6 million that was extinguished in full upon termination of the License Agreement, which in turn increased our net gain. See Note 3 - Binimetinib and Encorafenib Agreements for further information. Revenue Recognition We recognize revenue for the performance of services or the shipment of products when each of the following four criteria is met: (i) persuasive evidence of an arrangement exists; (ii) products are delivered or as services are rendered; (iii) the sales price is fixed or determinable; and (iv) collectability is reasonably assured. We follow ASC 605-25, Revenue Recognition – Multiple-Element Arrangements and ASC 808, Collaborative Arrangements , if applicable, to determine the recognition of revenue under our collaborative research, development and commercialization agreements that contain multiple elements. These multiple elements, or deliverables, may include (i) grants of licenses, or options to obtain licenses, to our intellectual property, (ii) research and development services, (iii) drug product manufacturing, and/or (iv) participation on joint research and/or joint development committees. The payments we may receive under these arrangements typically include one or more of the following: non-refundable, up-front license fees; option exercise fees; funding of research and/or development efforts; amounts due upon the achievement of specified objectives; and/or royalties on future product sales. ASC 605-25 provides guidance relating to the separability of deliverables included in an arrangement into different units of accounting and the allocation of arrangement consideration to the units of accounting. The evaluation of multiple-element arrangements requires management to make judgments about (i) the identification of deliverables, (ii) whether such deliverables are separable from the other aspects of the contractual relationship, (iii) the estimated selling price of each deliverable, and (iv) the expected period of performance for each deliverable. To determine the units of accounting under a multiple-element arrangement, management evaluates certain separation criteria, including whether the deliverables have stand-alone value, based on the relevant facts and circumstances for each arrangement. Management then estimates the selling price for each unit of accounting and allocates the arrangement consideration to each unit utilizing the relative selling price method. The allocated consideration for each unit of accounting is recognized over the related obligation period in accordance with the applicable revenue recognition criteria. If there are deliverables in an arrangement that are not separable from other aspects of the contractual relationship, they are treated as a combined unit of accounting, with the allocated revenue for the combined unit recognized in a manner consistent with the revenue recognition applicable to the final deliverable in the combined unit. Payments received prior to satisfying the relevant revenue recognition criteria are recorded as deferred revenue in the accompanying balance sheets and recognized as revenue when the related revenue recognition criteria are met. We typically receive non-refundable, up-front payments when licensing our intellectual property, which often occurs in conjunction with a research and development agreement. When management believes that the license to our intellectual property has stand-alone value, we generally recognize revenue attributed to the license upon delivery provided that there are no future performance requirements for use of the license. When management believes that the license to our intellectual property does not have stand-alone value, we typically recognize revenue attributed to the license on a straight-line basis over the contractual or estimated performance period. When the performance period is not specifically identifiable from the agreement, we estimate the performance period based upon provisions contained within the agreement, such as the duration of the research or development term. Most of our agreements provide for non-refundable milestone payments. We recognize revenue that is contingent upon the achievement of a substantive milestone in its entirety in the period in which the milestone is achieved. A milestone is considered substantive when the consideration payable to us for such milestone (i) is consistent with our performance necessary to achieve the milestone or the increase in value to the collaboration resulting from our performance, (ii) relates solely to our past performance and (iii) is reasonable relative to all of the other deliverables and payments within the arrangement. In making this assessment, we consider all facts and circumstances relevant to the arrangement, including factors such as the scientific, regulatory, commercial and other risks that must be overcome to achieve the milestone, the level of effort and investment required to achieve the milestone and whether any portion of the milestone consideration is related to future performance or deliverables. For payments payable on achievement of milestones that do not meet all of the conditions to be considered substantive, we recognize a portion of the payment as revenue when the specific milestone is achieved, and the contingency is removed, based on the applicable percentage earned of the estimated research or development effort, or other performance obligations that have elapsed, to the total estimated research and/or development effort attributable to the milestone. In other cases, when a non-substantive milestone payment is attributed to our future research or development obligations, we recognize the revenue on a straight-line basis, or other appropriate method, over the estimated remaining research or development effort. Other contingent event-based payments for which payment is either contingent solely upon the passage of time or the result of collaborator's performance are recognized when earned. We periodically review the estimated performance periods under each of our agreements that provide for non-refundable up-front payments, license fees or milestone payments. We adjust the periods over which revenue should be recognized when appropriate to reflect changes in assumptions relating to the estimated performance periods. We could accelerate revenue recognition in the event of early termination of programs or if our expectations change. Alternatively, we could decelerate revenue recognition if programs are extended or delayed. While such changes to our estimates have no impact on our reported cash flows, the amount of revenue recorded in future periods could be materially impacted. We record as revenue amounts received for reimbursement of costs we incur from our license partners where we act as a principal, control the research and development activities, bear credit risk and may perform part of the services required in the transactions, consistent with ASC 605-45-15. Certain collaborators or other counterparties (currently, Novartis and Pierre Fabre) currently provide financial support to us in the form of reimbursement for associated out-of-pocket costs and for a certain amount of Array’s fully-burdened full-time equivalent ("FTE") costs based on an agreed-upon FTE rates. The gross amount of these pass-through reimbursed costs are reported as revenue in the accompanying statements of operations and comprehensive income (loss) in accordance with ASC 605-45-15. The actual expenses for which we are reimbursed are reflected as research and development for proprietary programs or cost of partnered programs, as applicable. See Note 5 – Collaboration and Other Agreements for further information. Research and Development Costs Research and development costs are expensed as incurred. Advance payments for goods and services that will be used in future research and development activities are expensed when the activity has been performed or when the goods have been received rather than when the payment is made. Upfront and milestone payments due to third parties that perform research and development services on our behalf will be expensed as services are rendered or when the milestone is achieved. Research and development costs primarily consist of personnel related expenses, including salaries, benefits, costs to recruit and relocate new employees, travel, and other related expenses, stock-based compensation, payments made to third party contract research organizations for preclinical and clinical studies, investigative sites for clinical trials, consultants, the cost of acquiring and manufacturing clinical trial materials, the cost of acquiring and manufacturing commercial drug supply, costs associated with regulatory filings and patents, software, facilities and laboratory costs and other supplies. We split our research and development costs between cost of partnered programs and research and development for proprietary programs on our statements of operations and comprehensive income (loss). Cost of partnered programs represents costs attributable to discovery and development activities, including preclinical and clinical trials we may conduct for or with our partners. Research and development expenses for proprietary programs include costs associated with our proprietary drug programs. Operating Leases We have negotiated certain landlord/tenant incentives and rent holidays and escalations in the base price of rent payments under our operating leases. For purposes of determining the period over which these amounts are recognized or amortized, the initial term of an operating lease includes the "build-out" period of leases, where no rent payments are typically due under the terms of the lease and includes additional terms pursuant to any options to extend the initial term if it is more likely than not that we will exercise such options. We recognize rent holidays and rent escalations on a straight-line basis over the initial lease term. The landlord/tenant incentives are recorded as an increase to deferred rent in the accompanying balance sheets and are amortized on a straight-line basis over the initial lease term. Deferred rent balances are classified as short-term or long-term in the accompanying balance sheets based upon the period when reversal of the liability is expected to occur. We completed the sale of our chemical manufacturing and control assets (the "CMC Assets") in June 2015, and in connection with the closing of the sale of the CMC Assets, we simultaneously entered into an amendment to our lease agreement for our facility in Boulder, Colorado and an early termination agreement for our Longmont, Colorado facility. The amended Boulder lease extended the term of our prior lease and provided for a reduction in the amount of leased space by the end of calendar year 2015. As both the amended Boulder lease and the Longmont termination were negotiated with the same landlord, we deferred our existing deferred rent liabilities rather than recognizing a gain on termination. Share-Based Compensation Share-based compensation awards include stock options and restricted stock units ("RSUs") granted under our Amended and Restated Stock Option and Incentive Plan ("Option and Incentive Plan") and purchases of common stock by our employees at a discount to the market price under the Amended and Restated Array BioPharma Inc. Employee Stock Purchase Plan ("ESPP"). We use the Black-Scholes option pricing model to determine the grant date fair value of stock options and ESPP awards. The determination of the fair value of share-based awards using an option pricing model is affected by our stock price, as well as assumptions regarding a number of complex and subjective variables. Share-based compensation expense is recognized on a straight-line basis over the requisite service period for each award. Further, compensation expense recognized in our statement of operations and comprehensive income (loss) is reduced for estimated forfeitures, which are based on historical experience and are revised in subsequent periods if actual forfeitures differ from our estimates. For stock-based compensation awards granted to non-employees, we remeasure the fair value of the non-employee awards at each reporting period prior to vesting and finally at the vesting date of the award. Changes in the estimated fair value of these non-employee awards are recognized as compensation expense in the period of change. The assumptions used in calculating the fair value of stock-based awards represent management’s best estimates and involve inherent uncertainties and the application of management’s judgment. Income Taxes We account for income taxes using the asset and liability method. We recognize the amount of income taxes payable (refundable) for the year as current income tax provision (benefit) and record a deferred income tax provision (benefit) based on changes in deferred tax assets and liabilities. Deferred tax assets and liabilities are determined based on the difference between the financial statement carrying value and the tax basis of assets and liabilities and, using enacted tax rate

MARKETABLE SECURITIES

MARKETABLE SECURITIES	12 Months Ended
	Jun. 30, 2016
Marketable Securities [Abstract]
MARKETABLE SECURITIES	MARKETABLE SECURITIES Marketable securities consisted of the following as of June 30, 2016 and 2015 (in thousands): June 30, 2016 Gross Gross Amortized Unrealized Unrealized Fair Cost Gains Losses Value Short-term available-for-sale securities: U.S. treasury securities $ 53,113 $ 8 $ (1 ) $ 53,120 Mutual fund securities 224 — — 224 53,337 8 (1 ) 53,344 Long-term available-for-sale securities: Mutual fund securities 596 — — 596 596 — — 596 Total $ 53,933 $ 8 $ (1 ) $ 53,940 June 30, 2015 Gross Gross Amortized Unrealized Unrealized Fair Cost Gains Losses Value Short-term available-for-sale securities: U.S. treasury securities $ 122,199 $ 8 $ (3 ) $ 122,204 Mutual fund securities 431 — — 431 122,630 8 (3 ) 122,635 Long-term available-for-sale securities: Mutual fund securities 496 — — 496 496 — — 496 Total $ 123,126 $ 8 $ (3 ) $ 123,131 The mutual fund securities shown in the above tables are securities held under the Array BioPharma Inc. Deferred Compensation Plan. The estimated fair value of our marketable securities was classified into fair value measurement categories as follows (in thousands): June 30, 2016 2015 Quoted prices in active markets for identical assets (Level 1) $ 53,940 $ 123,131 Quoted prices for similar assets observable in the marketplace (Level 2) — — Significant unobservable inputs (Level 3) — — Total $ 53,940 $ 123,131 The fair value of marketable securities are determined using quoted market prices from daily exchange-traded markets based on the closing price as of the balance sheet date and are classified as Level 1. The following table is a roll forward of the fair value of our prior investment, which consisted of Loxo common shares, in Level 3 equity securities (in thousands): Year Ended June 30, 2015 Balance, beginning of period $ — Transfer into Level 3 due to restriction period on trading 4,500 Change in unrealized gains and losses included in comprehensive income (loss) 13,205 Transfer out of Level 3 due to elimination of trading restrictions (17,705 ) Balance, end of period $ — As of June 30, 2016 , the amortized cost and estimated fair value of available-for-sale securities by contractual maturity were as follows (in thousands): Amortized Fair Cost Value Due in one year or less $ 53,113 $ 53,120 Due in one year to three years — — Total $ 53,113 $ 53,120

BINIMETINIB AND ENCORAFENIB AGR

BINIMETINIB AND ENCORAFENIB AGREEMENTS	12 Months Ended
	Jun. 30, 2016
Termination and Asset Transfer Agreement [Abstract]
BINIMETINIB AND ENCORAFENIB AGREEMENTS	BINIMETINIB AND ENCORAFENIB AGREEMENTS Effective March 2, 2015 (the "Effective Date"), Array regained all development and commercialization rights to binimetinib pursuant to the Termination and Asset Transfer Agreement with Novartis Pharma and Novartis, as amended on January 19, 2015 (as amended, the “Binimetinib Agreement”), and acquired all development and commercialization rights to encorafenib pursuant to the Asset Transfer Agreement with Novartis Pharma dated January 19, 2015 (the “Encorafenib Agreement”). As a result of the closing of the Binimetinib Agreement, we received an $85 million up-front payment from Novartis. On the Effective Date, Novartis Pharma transferred or exclusively licensed to Array all assets, including intellectual property, regulatory filings, technology, inventory and contract rights, owned by Novartis Pharma or its affiliates that relate to binimetinib and to encorafenib worldwide. Also upon the Effective Date, our existing License Agreement with Novartis dated April 19, 2010, under which we licensed development and commercialization rights to binimetinib and other compounds to Novartis, terminated; as a result of the termination of this License Agreement, we were not required to pay our portion of accrued co-development costs that we had previously accrued under that agreement. In connection with the closing of the Binimetinib Agreement and the Encorafenib Agreement, Array and Novartis Pharma entered into two Transition Agreements dated March 2, 2015, one associated with the Binimetinib Agreement and the other associated with the Encorafenib Agreement. Under these agreements, Novartis Pharma and its affiliates are providing certain regulatory assistance, development technology transfer, companion diagnostic transfer and other transition services to Array in connection with the continued development of binimetinib and encorafenib after the Effective Date. Novartis Pharma will provide substantial financial support to Array under the Transition Agreements for all clinical trials involving binimetinib and encorafenib in the form of reimbursement to Array for all associated out-of-pocket costs and for one-half of Array’s fully-burdened full-time equivalent ("FTE") costs based on an annual FTE rate. As of June 30, 2016, Novartis Pharma has transitioned responsibility for all previously Novartis-conducted trials and will provide this continuing financial support to Array for completing the trials. Novartis Pharma will remain responsible for conducting and funding development of the NRAS melanoma companion diagnostic until Premarket Approval is received from the U.S. Food and Drug Administration. Following approval, Novartis Pharma will transfer the product and Premarket Approval to a diagnostic vendor of our designation. Novartis Pharma also retains binimetinib and encorafenib supply obligations for all clinical and commercial needs for up to 30 months after the Effective Date and will also assist us in the technology and manufacturing transfer of binimetinib and encorafenib. Novartis Pharma will also provide Array continued clinical supply of several Novartis Pharma pipeline compounds including, LEE011 (CDK 4/6 inhibitor) and BYL719 (α-PI3K inhibitor), for use in currently ongoing combination studies, and possible future studies, including Phase 3 trials, with binimetinib and encorafenib. Each party has agreed to indemnify and hold the other party and its affiliates harmless from and against certain liabilities identified in the Binimetinib Agreement, the Encorafenib Agreement and the Transition Agreements and to a general release of claims relating to the existing License Agreement. The Binimetinib Agreement and the Encorafenib Agreement as well as the Transition Agreements may be terminated only upon the mutual agreement of Novartis Pharma and Array and will remain in effect until the respective obligations of the parties under them have been completed. We recorded the following amounts in the third quarter of fiscal 2015, resulting in a net gain on the Binimetinib and Encorafenib Agreements as follows (in thousands): Cash received from the termination of the binimetinib License Agreement with Novartis $ 85,000 Net cost of third party agreement to complete the Novartis transactions (25,000 ) Extinguishment of co-development obligation due to Novartis (net of a $6.7 million accounts receivable balance) 21,610 Reimbursement of certain transaction costs 5,000 Subtotal 86,610 Less: Deferred revenue related to ongoing obligations (6,600 ) Gain on the Binimetinib and Encorafenib Agreements, net $ 80,010 Array also entered into a Development and Commercialization Agreement with Pierre Fabre Medicament SAS, (“Pierre Fabre” or "PFM"), which became effective in December 2015 (the "PF Agreement"), pursuant to which we granted Pierre Fabre rights to commercialize binimetinib and encorafenib in all countries except for the United States, Canada, Japan, Korea and Israel, where Array will retain its ownership rights. The PF Agreement satisfied our commitment to secure a development and commercialization partner for the European market for both encorafenib and binimetinib acceptable to European Commission regulatory agencies made in connection with the Novartis Agreements. All clinical trials involving binimetinib and encorafenib that were active or planned when the Novartis Agreement became effective in March 2015, including the NEMO and COLUMBUS trials and other then active Novartis sponsored and investigator sponsored clinical studies, continue to be reimbursed pursuant to the terms of the Novartis Agreements. Further worldwide development activities of binimetinib and encorafenib will be governed by a Global Development Plan (GDP) with Pierre Fabre. Pierre Fabre and Array will jointly fund worldwide development costs under the GDP, with Array covering 60% and Pierre Fabre covering 40% of such costs. The initial GDP includes multiple trials, including the BEACON CRC trial, and Pierre Fabre and Array have agreed to commit at least €100 million in combined funds for these studies in colorectal cancer (CRC) and melanoma.

SALE OF CMC ASSETS

SALE OF CMC ASSETS	12 Months Ended
	Jun. 30, 2016
Discontinued Operations and Disposal Groups [Abstract]
SALE OF CMC ASSETS	SALE OF CMC ASSETS On June 1, 2015, we entered into an Asset Purchase Agreement (the “Purchase Agreement”) with Accuratus Lab Services, Inc. (“Accuratus”), pursuant to which Accuratus acquired certain assets and assumed certain liabilities relating to our chemistry, manufacturing and controls (“CMC”) activities in a transaction that closed on June 1, 2015. The transaction included the transfer of equipment, inventory and third party contracts relating to our CMC activities, as well as the termination of our facilities lease in Longmont, Colorado and the retention of 33 of our CMC employees by Accuratus following the closing. Accuratus paid us a $3.75 million cash purchase price at closing for the CMC assets, and we are entitled to receive additional consideration contingent upon achievement of revenue targets for the CMC activities during the first and second year following the closing. Array did not earn additional contingent consideration during the fiscal year ended June 30, 2016. As part of the transaction, Accuratus hired certain Array employees who were engaged in CMC activities for Array. We issued stock options to these transitioning employees to purchase an aggregate of 133,209 shares of common stock. The stock options vest one year after the date of grant and have a term that expires 90 days upon vesting at an exercise of price of $7.74 , which is equal to the closing price of our common stock on the date of grant. The stock options issued to the CMC employees hired by Accuratus did not have a substantive service condition; therefore, the grant date fair value was immediately expensed against the gain on sale of the CMC assets. We determined the grant date fair value of the stock options of $278 thousand based on the Black-Scholes valuation model using the following assumptions: strike price $7.74 , volatility 61.2% , risk-free interest rate 0.4% , effective life 1.25 years and dividend yield 0% . As part of this transaction, we are required to purchase a minimum of $7 million of CMC services from Accuratus over a 24 -month period (“Minimum Revenue Guarantee”). We are required to recognize this Minimum Revenue Guarantee at fair value in accordance with ASC 460-10. We determined that the price of the estimated future services approximates fair value and that we currently expect to use services in excess of this Minimum Revenue Guarantee amount. As of June 30, 2016, we have made payments related to the Minimum Revenue Guarantee which exceed the value of services received. Consequently, we have recorded a prepaid asset in the amount of $2.9 million . Our remaining obligation will result in payments totaling $1.9 million during fiscal year 2017. We recorded the following amounts in the fourth quarter of fiscal 2015, resulting in a net gain of $1.6 million on the sale of the CMC assets calculated as the difference between the allocated non-contingent consideration amount for the assets and liabilities and the net carrying amount of the assets and liabilities assumed or extinguished. The following sets forth the calculation of the gain on sale as of the closing (in thousands): Non-contingent cash consideration received $ 3,750 Fixed assets or related lease costs sold or written off (1,818 ) Fair value of stock options issued to retained CMC employees (278 ) Other extinguished employee liabilities 276 Estimated transaction costs (342 ) Deferred revenue associated with undelivered elements 144 Other (91 ) Gain on sale of CMC, net $ 1,641 The net gain on the sale of the CMC assets may be adjusted in future periods by the contingent consideration, based upon the achievement of pre-determined revenue milestones. The sale of the CMC assets does not qualify as a discontinued operation as the sale is not a strategic shift that has (or will have) a major effect on our operations and financial results.

COLLABORATION AND OTHER AGREEME

COLLABORATION AND OTHER AGREEMENTS	12 Months Ended
	Jun. 30, 2016
Collaboration and Other Agreements [Abstract]
COLLABORATION AND OTHER AGREEMENTS	COLLABORATION AND OTHER AGREEMENTS The following table summarizes our total revenues for the periods indicated (in thousands): Year Ended June 30, 2016 2015 2014 Novartis (1) $ 110,930 $ 8,220 $ 12,053 Loxo Oncology 12,635 9,223 9,708 Pierre Fabre 3,724 — — Mirati 3,557 1,200 — Celgene 3,126 4,132 3,742 Biogen Idec 2,816 4,593 282 Asahi Kasei 600 — — Cascadian Therapeutics (previously known as Oncothyreon Inc.) 183 21,955 3,464 AstraZeneca, PLC (2) 152 73 5,104 Genentech 24 367 3,568 Other partners 132 2,146 4,157 Total revenue $ 137,879 $ 51,909 $ 42,078 (1) Includes $107.3 million and $7.0 million of reimbursement revenue consisting of FTE and out-of-pocket costs that are reimbursable by Novartis under the Binimetinib and Encorafenib Agreements during the years ended June 30, 2016 and 2015, respectively. All other prior year amounts represent the amortization of the up-front and milestone payments under the April 2010 License Agreement with Novartis that was terminated on the Effective Date of the Binimetinib and Encorafenib Agreements in March 2015. (2) 2014 includes a $5.0 million milestone from AstraZeneca for the start of a Phase 3 clinical study. Novartis International Pharmaceutical Ltd. Array entered into a License Agreement with Novartis in April 2010, which granted Novartis the exclusive worldwide right to develop and commercialize binimetinib, as well as other specified MEK inhibitors. Array regained these rights and the 2010 License Agreement terminated on the Effective Date of the Binimetinib Agreement in March 2015, as discussed in Note 3 - Binimetinib and Encorafenib Agreements. As a result, our co-development liability under the License Agreement described below, and any receivables from Novartis then outstanding under the License Agreement, were eliminated as of the Effective Date. In consideration for the rights granted to Novartis under the prior License Agreement, we received an aggregate of $60 million in an up-front fee and in milestone payments between the fourth quarter of fiscal 2010 and the first quarter of fiscal 2014. We recognized the up-front fee and milestone payments under the License Agreement on a straight-line basis from April 2010 through April 2014. Co-Development Arrangement The License Agreement contained co-development rights whereby we could elect to pay a share of the combined total development costs, subject to a maximum amount with annual caps. During the first two years of the co-development, Novartis reimbursed us for 100% of our development costs. We began to pay our share of the combined development costs that had accrued since inception of the program, with payments to Novartis of $9.2 million and $11.3 million in the second quarters of fiscal 2013 and fiscal 2014, respectively, in accordance with the terms of the License Agreement. During fiscal 2014, we committed to continue our co-development contribution through fiscal 2015. We continued to record an estimate of our co-development liability under the License Agreement until our liability terminated upon the Effective Date of the Binimetinib Agreement as discussed in Note 3 - Binimetinib and Encorafenib Agreements . Our co-development liability was $28.3 million as of the Effective Date of the Binimetinib Agreement and was $0 as of June 30, 2015 . For periods prior to termination of the License Agreement, we recorded a receivable in accounts receivable on the balance sheet for the amounts due from Novartis for the reimbursement of our development costs in excess of the annual cap. We recorded expense in cost of partnered programs on the statement of operations and comprehensive income (loss) for our share of the combined development costs and accrued these costs on our balance sheet in co-development liability. Up until the Effective Date of the Binimetinib Agreement, our share of the combined development costs was $13.1 million and $18.9 million during the years ended June 30, 2015 and 2014 , respectively. We continued to record an estimate of our receivable from Novartis under the License Agreement until termination of the receivable upon the Effective Date, as discussed above and in Note 3 - Binimetinib and Encorafenib Agreements . Our receivable balance from Novartis was $6.7 million as of the Effective Date of the Binimetinib Agreement. Loxo Oncology, Inc. In July 2013, Array entered into a Drug Discovery Collaboration Agreement with Loxo and granted Loxo exclusive rights to develop and commercialize certain Array-invented compounds targeted at the tropomyosin kinase ("Trk") family of receptors, including LOXO-101, which is currently in Phase 1 and Phase 2 clinical trials. In November 2013, April 2014, October 2014, March 2015, and February 2016, Array and Loxo amended the agreement to expand the research activities under the agreement. Under the terms of the amended agreement, Loxo is funding further discovery and preclinical programs to be conducted by Array, including LOXO-195, a next generation selective TRK inhibitor, RET and FGFR programs, during the remainder of the three -year discovery research phase, which ends in September 2017, which may be extended by Loxo for up to one additional one -year renewal period. In addition, Loxo will fund further discovery and preclinical research to be conducted by Array directed at other targets during the research phase of the agreement. Loxo will be responsible for all additional preclinical and clinical development and commercialization. In consideration of the exclusive license and rights granted to Loxo under the agreement, Array received shares of Loxo non-voting preferred stock representing an initial 19.9% interest in the newly-formed entity and following additional financings by Loxo, Array's ownership interest in Loxo as of June 30, 2014 was 15.3% . All of the shares of preferred stock held by Array converted into shares of common stock on the closing date of Loxo's IPO. After certain trading restrictions ended following Loxo's IPO, we sold all of our shares of common stock of Loxo and as of June 30, 2015 , Array has no remaining ownership interest in Loxo. Array also receives advance payments for preclinical research and other services that Array is providing during the term of the discovery program and is eligible to receive up to $434.0 million in milestone payments if certain clinical, regulatory and sales milestones are achieved plus royalties on sales of any resulting drugs. Pursuant to the accounting guidance for revenue recognition for multiple-element arrangements, we determined that Array is obligated to deliver three non-contingent deliverables related to the Loxo agreement. These deliverables are (i) the conduct of the research activities under the discovery program, including related technology transfer (the "research services deliverable"), (ii) an exclusive worldwide license granted to Loxo to certain Array technology and Array's interest in collaboration technology, as well as exclusive worldwide marketing rights (the "license deliverable") and (iii) participation on the JRC. The Loxo agreement provides for no general right of return for any non-contingent deliverable. All of the identified non-contingent deliverables meet the separation criteria; therefore, they are each treated as separate units of accounting. Delivery of the research services and JRC participation obligations will be completed throughout the remainder of the three -year discovery program term which ends in September 2017. The license deliverable was complete as of September 30, 2013. To determine the stand-alone value of the license, we considered our negotiation discussions with Loxo that led to the final terms of the agreement, publicly-available data for similar licensing arrangements between other companies and the economic terms of previous collaborations Array has entered into with other partners. We also considered the estimated valuation of the preferred shares performed by an independent third-party and concluded that this value reasonably approximated the estimated selling price of the related license. We determined a selling price for the research services deliverable using our established annual FTE rate, which represents vendor-specific objective evidence for any FTE costs related to activities to be performed by Array scientists. We determined an estimated selling price for the JRC deliverable by estimating the time required for our scientists to perform their obligations and utilized our established FTE rate for research services as an estimate of what we would bill for this time if we sold this deliverable on a stand-alone basis. The receipt of the preferred shares was in consideration for the license deliverable. We allocated an amount of consideration under the Loxo agreement to the license deliverable equal to the fair value of the shares received after consideration of the other factors above. We chose the fair value of the shares received as this was a more evident and readily determinable measure as compared to the alternative method for determining the consideration to allocate to the license deliverable, which was the fair value for the exclusive license. The valuation of the preferred shares required the use of significant assumptions and estimates, including assumptions about the estimated volatility of the equity, the estimated time to a liquidity event, and the likelihood of Loxo obtaining additional future financing. During the first quarter of fiscal 2014, we recognized the full $4.5 million estimated fair value of the preferred shares received in license revenue as delivery of the shares was not contingent upon either the delivery of additional items or meeting other specified performance conditions. The remaining consideration under the amended Loxo agreement, which Loxo pays to Array in advance quarterly payments, is allocated between the research services and JRC participation deliverables and will be recognized as the services are rendered throughout the discovery program term. We had deferred revenue balances of $4.0 million and $0.9 million for Loxo at June 30, 2016 and 2015 , respectively. The April 2014 amendment added several contingent deliverables related to rights to discontinue research activities for fewer targets in exchange for additional payments to be made to Array. All of the obligations added to the arrangement by the amendment were considered contingent because the likelihood and timing of these deliverables is uncertain and therefore the potential consideration associated with these obligations was not included in the total allocable consideration. The April 2015 amendment increased the number of FTEs performing research services through December 31, 2015. The most recent amendment was treated as a new agreement. The February 2015 agreement extended the term of the additional FTEs. In July 2014, we began performing additional CMC-related services for Loxo that were agreed to between the parties on a project level basis. Each project consisted of a single deliverable or multiple deliverables and each was evaluated for proper revenue recognition as a multiple-element arrangement when appropriate. All unfinished Loxo CMC projects were assigned to the purchaser of our CMC assets effective June 1, 2015, as discussed in Note 4 - Sale of CMC Assets . The amended Loxo agreement will continue on a country-by-country basis until the termination of the royalty payment obligations, unless terminated earlier by the parties in accordance with its terms. The agreement may be terminated by either party upon the failure of the other party to cure any material breach of its obligations under the agreement, provided that, so long as Loxo is reasonably able to pay its debts as they are due, Array will only be entitled to seek monetary damages, and will not have the right to terminate the amended agreement in the event of Loxo's breach after expiration of the discovery program term. Loxo also has the right to terminate the amended agreement or to terminate discovery research with respect to any targets under development with six months ' notice to Array. If Loxo terminates the amended agreement for convenience, all licenses granted to Loxo will terminate and Array will have all rights to further develop and commercialize the licensed programs. The period of exclusivity to be observed by Array under the amended Loxo agreement will continue as long as Loxo either has an active research and/or development program for a target and the program could result in the receipt of milestones or royalties under the program by Array, or as long as Loxo is commercializing a product for a target under the amended agreement. Pierre Fabre On November 10, 2015, the Company entered into the PF Agreement with Pierre Fabre pursuant to which the Company granted Pierre Fabre rights to commercialize binimetinib and encorafenib in all countries except for the United States, Canada, Japan, Korea and Israel, where Array retains its ownership rights. The PF Agreement satisfies the Company’s commitment to secure a development and commercialization partner for the European market for both encorafenib and binimetinib acceptable to European Commission regulatory agencies made in connection with the Novartis Agreements. The PF Agreement closed in December 2015. All clinical trials involving binimetinib and encorafenib that were ongoing or planned at the Effective Date, including the NEMO and COLUMBUS trials and other then-ongoing Novartis sponsored and investigator sponsored clinical studies, continue to be conducted pursuant to the terms of the Novartis Agreements. Further worldwide development activities will be governed by a Global Development Plan (GDP) with Pierre Fabre. Pierre Fabre and the Company will jointly fund worldwide development costs under the GDP, with the Company covering 60% and Pierre Fabre covering 40% of such costs. The initial GDP includes multiple trials, including the BEACON CRC trial, and Pierre Fabre and Array have agreed to commit at least €100 million in combined funds for these studies in colorectal cancer (CRC) and melanoma. Pierre Fabre is responsible for seeking regulatory and pricing and reimbursement approvals in the European Economic Area and its other licensed territories. The Company and Pierre Fabre will also enter into a clinical and commercial supply agreement pursuant to which the Company will supply or procure the supply of clinical and commercial supplies of drug substance and drug product for Pierre Fabre, the costs of which will be borne by Pierre Fabre. The Company has also agreed to cooperate with Pierre Fabre to ensure the supply of companion diagnostics for use with binimetinib and encorafenib in certain indications. Each party has also agreed not to distribute, sell or promote competing products in each party’s respective markets during a period of exclusivity. Each party has also agreed to indemnify the other party from certain liabilities specified in the Agreement. In connection with the PF Agreement, Array received $30.0 million as an up-front payment during the year ended June 30, 2016. The terms of the PF Agreement include substantial ongoing collaboration and cost-sharing activities between the companies, and require Array to perform future development and commercialization activities. In accordance with the revenue recognition criteria under ASC Topic 605, the Company determined that the PF Agreement is a multi-deliverable arrangement with the following deliverables: (1) the license rights, and (2) clinical development and other services. The Company determined that the license granted to PF does not have stand-alone value apart from the services that Array will provide. Accordingly, non-refundable upfront amounts received under the PF agreement are recorded as deferred revenue and are being recognized on a straight-line basis over ten years, the period during which management expects that substantial development activities will be performed. License revenue recognized under this agreement was $1.6 million for the year ended June 30, 2016; at June 30, 2016 deferred revenue associated with this agreement was approximately $28.4 million . Collaboration revenue of $2.1 million was recognized for Pierre Fabre's share of co-development costs incurred during fiscal 2016. The PF Agreement contains substantive potential milestone payments of up to $35.0 million for achievement of three regulatory milestones relating to EC marketing approvals for three specified indications and of up to $390.0 million for achievement of seven commercialization milestones if certain net sales amounts are achieved for any licensed indications. Array is also entitled to double-digit royalties based on net sales under the agreement. Mirati Therapeutics, Inc. The Company is party to an agreement with Mirati Therapeutics, Inc. ("Mirati") whereby Array conducted a feasibility program for Mirati related to a particular target in exchange for an up-front payment of $1.6 million that was received in October 2014 (which was recognized as revenue over the subsequent twelve months ) and other payments and potential payments as described below. In September 2015, Mirati exercised an option to extend the feasibility program for six months , for which Array received a $750 thousand option extension fee (which was recognized as revenue over the subsequent six months ). During April 2016, Mirati elected to exercise an option to take an exclusive, worldwide license to an active compound under the agreement and Array received $2.5 million ("Option Exercise Fee") and will receive additional fess as reimbursement for research and development services. In accordance with the revenue recognition criteria under ASC Topic 605, the Company determined that the Mirati agreement is a multi-deliverable arrangement with multiple deliverables: (1) the license rights, (2) services related to obtaining enhanced intellectual property rights through the issuance of a particular patent and (3) clinical development services. The Company determined that the license granted under the Mirati Agreement does not have stand-alone value apart from the services Array will provide. Accordingly, the Option Exercise Fee, received in the quarter ended June 30, 2016, is recorded as deferred revenue and is being recognized on a straight-line basis over three years, the period during which management expects that substantial development activities will be performed. Revenue recognized under this agreement was $3.6 million and $1.2 million for the years ended June 30, 2016 and June 30, 2015, respectively; at June 30, 2016 deferred revenue associated with this agreement was approximately $3.2 million . In addition to the $1.6 million upfront payment, the $750 thousand option extension fee and the $2.5 million Option Exercise Fee, the Mirati Agreement contains substantive potential milestone payments of up to $9.3 million for four remaining developmental milestones and up to $337.0 million for the achievement of seven commercialization milestones if certain net sales amounts are achieved in the United States, the European Union and Japan. Dr. Charles Baum, a current member of Array’s Board of Directors, is the President and Chief Executive Officer of Mirati. Celgene Array and Celgene Corporation and Celgene Alpine Investment Co., LLC (collectively "Celgene") entered into a Drug Discovery and Development Option and License Agreement in July 2013 to collaborate on development of an Array-invented preclinical development program targeting a novel inflammation pathway. The agreement provides Celgene an option to select multiple clinical development candidates that Celgene may further develop on an exclusive basis under the agreement. Celgene also had the option to obtain exclusive worldwide rights to commercialize one or more of the development compounds it could select upon payment of an option exercise fee to Array. Array was responsible for funding and conducting preclinical discovery research on compounds directed at the target, and Celgene was responsible for all clinical development and commercialization of any compounds it could select. During July 2016, Celgene notified Array that it would not exercise the option to obtain exclusive worldwide rights to commercialize any of the development compounds. As a result, Array retains all rights to the program. Array received a non-refundable up-front payment of $11.0 million from Celgene during the first quarter of fiscal 2014. The majority of the up-front payment received was for the performance of research services, which we recognized as collaboration revenue over the estimated option term which originally was estimated to be three years . During the three months ended December 31, 2014, we revised this estimate to just over two years and prospectively adjusted recognition of the unrecognized portion of the up-front payment at the time of the change in estimate over the revised remaining option period. Due to additional information obtained during the three months ended March 31, 2015, we revised our estimate back to the original estimate of three years . Deferred revenue balances were $0 and $3.1 million as of June 30, 2016 and 2015, respectively. Biogen Idec Array entered into a Drug Discovery Collaboration Agreement with Biogen Idec MA Inc. ("Biogen") in May 2014 for the discovery and development of Array-discovered inhibitors targeting a novel kinase for the treatment of autoimmune disorders. Under the terms of the agreement, Biogen and Array collaborated on the discovery of the novel kinase inhibitors. Biogen was responsible for all aspects of clinical development and commercialization. Pursuant to advance quarterly funding from Biogen, Array provided staffing to support the discovery program during the anticipated three -year discovery program term, which could have been extended for an additional 12 -month period upon consent from both parties. The agreement included research funding for three years, various milestone payments payable upon achievement of certain development and commercial milestones, and royalties to Array. The collaboration terminated in November 2015. Pursuant to the accounting guidance for revenue recognition for multiple-element arrangements, we identified two non-contingent deliverables that met the separation criteria, the first being conduct of discovery and pre-IND manufacturing activities under the discovery program (the “discovery program deliverable”), and participation on the joint research committee ("JRC") as the second. The discovery program deliverable and the JRC deliverable are both expected to be delivered throughout the duration of the discovery program term. Revenue recognized under the Biogen agreement during the periods presented was based upon the level of staffing provided during those periods and our established FTE rate for research services. Deferred revenue balances were $0 and $1.1 million as of June 30, 2016 and 2015 , respectively. Asahi Kasei Pharma On March 31, 2016, the Company announced a strategic collaboration with Asahi Kasei Pharma Corporation ("AKP") to develop and commercialize select Tropomyosin receptor kinase A (TrkA) inhibitors, including Array-invented ARRY-954, for pain, inflammation and other non-cancer indications. The Company received a $12.0 million up-front payment in April 2016 and may receive cost sharing payments, up to $63.5 million in additional development and commercialization milestone payments, and up to double-digit royalties on future sales. Array will retain full commercialization rights for all compounds in all indications in territories outside of Asia and within Asia retain full rights to cancer indications for all compounds excluding those being developed by AKP. In accordance with the revenue recognition criteria under ASC Topic 605, the Company determined that the AKP agreement is a multi-deliverable arrangement with the following deliverables: (1) the license rights, and (2) clinical development and other services. The Company determined that the license granted to AKP does not have stand-alone value apart from the services Array will provide. Accordingly, non-refundable upfront amounts received under the AKP agreement are recorded as deferred revenue and are being recognized on a straight-line basis over five years , the period during which management expects that substantial development activities will be performed. Revenue recognized under this agreement was $0.6 million for the year ended June 30, 2016; at June 30, 2016 deferred revenue associated with this agreement was approximately $11.4 million . The milestone payments include up to $11.0 million related to the achievement of four regulatory milestones for up to five drug candidates and up to $52.5 million for a milestone payment at the time of the first commercial sale and the achievement of three commercialization milestones if certain net sales amounts are achieved for any licensed drug candidates. Cascadian Therapeutics (formerly Oncothyreon Inc.) License Agreement Effective December 11, 2014, Array entered into a License Agreement with Cascadian Therapeutics (" Cascadian "). Pursuant to the License Agreement, Array has granted Cascadian an exclusive license to develop, manufacture and commercialize ONT-380 (previously known also as ARRY-380), an orally active, reversible and selective small-molecule HER2 inhibitor currently in Phase 2 clinical trials. The License Agreement replaces and terminates the prior Development and Commercialization Agreement under which Cascadian and Array were jointly developing ONT-380, and going forward, Cascadian will be solely responsible for all preclinical and clinical development, regulatory and commercialization activities relating to ONT-380. Under the terms of the License Agreement, Cascadian paid Array a non-refundable, up-front fee of $20 million . In addition, if Cascadian sublicenses rights to ONT-380 to a third party, Cascadian will pay Array a percentage of any sublicense payments it receives, with the percentage varying according to the stage of development of ONT-380 at the time of the sublicense. If Cascadian is acquired within three years of the effective date of the License Agreement, and ONT-380 has not been sublicensed to another entity prior to such acquisition, then the acquirer will be required to make certain milestone payments of up to $280 million to Array, which are primarily based on potential ONT-380 sales. Array is also entitled to receive up to a double-digit royalty based on net sales of ONT-380. Pursuant to the accounting guidance for revenue recognition for multiple-element arrangements, we determined that the exclusive license is the only non-contingent deliverable with stand-alone value under the License Agreement. Array must also expend a nominal amount of effort related to technology transfer, which was completed as of December 31, 2014, but because the technology transfer deliverable does not meet the separation criteria, it was recognized as a combined unit of accounting with the license. Potential payments for a percentage of sublicensing rights, milestone payments and royalties cannot be estimated. Also, at its separate expense Cascadian may request additional technology transfer and/or transition services from Array. Due to uncertainty of the likelihood and timing of all of the potential payments and additional services, their consideration is not considered fixed and determinable, therefore no portion of the up-front fee has been allocated to them. The entire $20.0 million up-front fee was allocated to the combined license/initial technology transfer unit of accounting, which we recognized in full in license revenue during December 2014. The License Agreement will expire on a country-by-country basis on the later of 10 years following the first commercial sale of the product in each respective country or expiration of the last to expire patent covering the product in such country, but may be terminated earlier by either party upon material breach of the License Agreement by the other party or the other party’s insolvency, or by Cascadian on 180 days ' notice to Array. Cascadian and Array have also agreed to indemnify the other party for certain of their respective warranties and obligations under the License Agreement. AstraZeneca In December 2003, we entered into a Collaboration and License Agreement with AstraZeneca to develop our MEK program. Under the agreement, AstraZeneca acquired exclusive worldwide rights to our clinical development candidate, selumetinib (previously known as AZD6244, or ARRY- 142886), together with two other compounds, which we invented during the collaboration, for oncology indications. We retained the rights to all therapeutic indications for MEK compounds not selected by AstraZeneca for development, subject to the parties' agreement to work exclusively together. In April 2009, the exclusivity of the parties' relationship ended, and both companies are now free to independently research, develop and commercialize small molecule MEK inhibitors in the field of oncology. Our research obligations ended in 2004 and AstraZeneca is responsible for all future development and commercialization of the compounds under the collaboration. To date, we have earned $26.5 million in up-front and milestone payments. The agreement also provided for research funding, which is now complete, and provides potential additional development milestone payments of approximately $70.0 million (with $30 million specific for selumetinib) and royalties on product sales. Development Status: AstraZeneca is continuing to advance selumetinib in two registration trials: differentiated thyroid cancer (ASTRA) and Neurofibromatosis Type 1, or NF1. AstraZeneca estimates the availability of top-line results for both trials in 2017. In August 2016, AstraZeneca announced results from the Phase 3 SELECT-1 trial of selumetinib in combination with docetaxel chemotherapy as 2nd-line treatment in patients with KRAS mutation-positive locally-advanced or metastatic non-small cell lung cancer. The results showed that the trial did not meet its primary endpoint of progression-free survival, and selumetinib did not have a significant effect on overall survival. The adverse event profiles for selumetinib and docetaxel were consistent with those seen previously. The AstraZeneca Agreement contains substantive potential milestone payments of up to $36.0 million for nine remaining developmental milestones for Selumetinib and up to $34.0 million for the achievement of three commercialization milestones if certain net sales amounts are achieved in the United States, the European Union and Japan for Selumetinib. Genentech, Inc. We entered into a Licensing and Collaboration Agreement with Genentech Inc. ("Genentech") in December 2003 for development of small molecule drugs invented by Array directed at multiple therapeutic targets in the field of oncology. In August 2011, we entered into a License Agreement with Genentech for the development of each company’s small-molecule Checkpoint kinase 1 ("Chk-1") program in oncology. Under the 2003 agreement, Genentech made an up-front payment and provided research funding to Array, and we are entitled to receive additional milestone payments based on achievement of certain development and commercialization milestones and royalties on certain resulting product sales under the agreement. The 2003 agreement was expanded in 2005, 2008, and 2009 to develop clinical candidates directed against additional targets and, in 2010 the term of funded research was extended through January 2013, after which the research term ended. In February 2015, the parties again amended the 2003 agreement to terminate each party's continuing rights and obligations with respect to one of the molecular targets under the agreement in exchange for a payment by Array to Genentech that was made in March 2015 following the effectiveness of the amendment on March 2, 2015. Genentech is advancing 2 collaborative drugs: ipatasertib, an AKT inhibitor, in multiple Phase 2 trials and GDC-0994, an ERK inhibitor, in a Phase 1 trial. We have received up-front and milestone payments totaling $23.5 million under the 2003 agreement. We are eligible to earn an additional $23.0 million in payments if Genentech continues development and achieves the remaining milestones set forth in the 2003 agreement. The partnered drugs under the Chk-1 agreement included Genentech’s compound GDC-0425 and Array’s compound GDC-0575 (ARRY-575). In 2014, Genentech selected GDC-0575 over GDC-042

PROPERTY AND EQUIPMENT, NET

PROPERTY AND EQUIPMENT, NET	12 Months Ended
	Jun. 30, 2016
Property, Plant and Equipment [Abstract]
PROPERTY AND EQUIPMENT, NET	PROPERTY AND EQUIPMENT, NET Property and equipment, net consists of the following (in thousands): June 30, 2016 2015 Furniture and fixtures $ 2,647 $ 2,647 Equipment 26,120 26,120 Computer hardware and software 15,953 14,336 Leasehold improvements 15,577 15,335 Property and equipment, gross 60,297 58,438 Less: accumulated depreciation and amortization (53,617 ) (53,388 ) Property and equipment, net $ 6,680 $ 5,050

LONG-TERM DEBT

LONG-TERM DEBT	12 Months Ended
	Jun. 30, 2016
Debt Disclosure [Abstract]
LONG-TERM DEBT	LONG-TERM DEBT Long-term debt consists of the following (in thousands): June 30, 2016 2015 Comerica term loan $ 14,550 $ 14,550 Convertible senior notes 132,250 132,250 Long-term debt, gross 146,800 146,800 Less: Unamortized debt discount and fees (33,145 ) (39,520 ) Long-term debt, net $ 113,655 $ 107,280 Comerica Bank We entered into a Loan and Security Agreement with Comerica Bank dated June 28, 2005, which has been subsequently amended and provides for a $15 million term loan and a revolving line of credit of $2.8 million . The term loan bears interest at a variable rate and we currently have $14.6 million outstanding under the term loan. The revolving line of credit was established to support standby letters of credit in relation to our facilities leases, and has not been drawn upon. Under the terms of the amended Loan and Security Agreement, the term loan will mature in October 2017 and the revolving line of credit will mature in September 2016 unless extended. Effective December 31, 2013, the interest rate on the term loan was amended to be equal to the Prime Rate , if the balance of our cash, cash equivalents and marketable securities maintained at Comerica is greater than or equal to $10 million , or equal to the Prime Rate plus 2% if this balance is less than $10 million . As of June 30, 2016 , the term loan with Comerica had an interest rate of 3.5% per annum. All principal is due at maturity and interest is paid monthly. The Loan and Security Agreement requires us to maintain a balance of cash at Comerica that is at least equivalent to our total outstanding obligation under the term loan if our overall balance of cash, cash equivalents and marketable securities at Comerica and approved outside accounts is less than $22 million . Additionally, we are required to comply with a financial covenant that applies if we draw down on the revolving line of credit. In this event, we must maintain a ratio equal to at least 1.25 to 1.00 as of the last day of each month calculated as follows: (A) total cash, cash equivalents and marketable securities less all outstanding obligations to Comerica under the term loan, plus specified percentages of the respective values of eligible accounts, equipment and eligible inventory, divided by (B) the aggregate amount outstanding under the revolving letter of credit sublimit. No amounts are outstanding under the revolving line of credit and we do not expect to make any draws under this facility. Our obligations under the amended Loan and Security Agreement are secured by a first priority security interest in all of our assets, other than our intellectual property. The amended Loan and Security Agreement contains representations and warranties and affirmative and negative covenants that are customary for credit agreements of this type. Our ability to, among other things, sell certain assets, engage in a merger or change in control transaction, incur debt, pay cash dividends and make investments, are restricted by the Loan and Security Agreement as amended. The amended Loan and Security Agreement also contains events of default that are customary for credit agreements of this type, including payment defaults, covenant defaults, insolvency type defaults and events of default relating to liens, judgments, material misrepresentations and the occurrence of certain material adverse events. We use a discounted cash flow model to estimate the fair value of the Comerica term loan. The fair value was estimated at $14.6 million as of both June 30, 2016 and 2015 , and was determined using Level 2, observable inputs other than quoted prices in active markets. 3.00% Convertible Senior Notes Due 2020 On June 10, 2013, through a registered underwritten public offering, we issued and sold $132.3 million aggregate principal amount of 3.00% convertible senior notes due 2020 (the "Notes"), resulting in net proceeds to Array of approximately $128.0 million after deducting the underwriting discount and estimated offering expenses. The Notes are the general senior unsecured obligations of Array. The Notes bear interest at a rate of 3.00% per year, payable semi-annually on June 1 and December 1 of each year with all principal due at maturity. The Notes will mature on June 1, 2020, unless earlier converted by the holders or redeemed by us. Prior to March 1, 2020, holders may convert the Notes only upon the occurrence of certain events described in a supplemental indenture we entered into with Wells Fargo Bank, N.A., as trustee, upon issuance of the Notes. On or after March 1, 2020, until the close of business on the scheduled trading day immediately prior to the maturity date, holders may convert their Notes at any time. Upon conversion, the holders will receive, at our option, shares of our common stock, cash or a combination of shares and cash. The Notes will be convertible at an initial conversion rate of 141.8641 shares per $1,000 in principal amount of Notes, equivalent to a conversion price of approximately $7.05 per share. The conversion rate is subject to adjustment upon the occurrence of certain events described in the supplemental indenture. Holders of the Notes may require us to repurchase all or a portion of their Notes for cash at a price equal to 100% of the principal amount of the Notes to be purchased, plus accrued and unpaid interest, if there is a qualifying change in control or termination of trading of our common stock. On or after June 4, 2017, we may redeem for cash all or part of the outstanding Notes if the last reported sale price of our common stock exceeds 130% of the applicable conversion price for 20 or more trading days in a period of 30 consecutive trading days ending within seven trading days immediately prior to the date we provide the notice of redemption to holders. The redemption price will equal 100% of the principal amount of the Notes to be redeemed, plus all accrued and unpaid interest. If we were to provide a notice of redemption, the holders could convert their Notes up until the business day immediately preceding the redemption date. In accordance with ASC 470-20, we used an effective interest rate of 10.25% to determine the liability component of the Notes. This resulted in the recognition of $84.2 million as the liability component of the Notes and the recognition of the residual $48.0 million as the debt discount with a corresponding increase to additional paid-in capital for the equity component of the Notes. The underwriting discount and estimated offering expenses of $4.3 million were allocated between the debt and equity issuance costs in proportion to the allocation of the liability and equity components of the Notes. Debt issuance costs of $2.7 million were included in other long-term assets on our balance sheet as of the issuance date. Equity issuance costs of $1.6 million were recorded as an offset to additional paid-in capital. The debt discount and debt issuance costs will be amortized as non-cash interest expense through June 1, 2020. The balance of unamortized debt issuance costs was $1.8 million and $2.1 million as of June 30, 2016 and 2015 , respectively. The fair value of the Notes was $110.2 million and $142.2 million at June 30, 2016 and 2015 , respectively, and was determined using Level 2 inputs based on their quoted market values. Summary of Interest Expense The following table shows the details of our interest expense for all of our debt arrangements outstanding during the periods presented, including contractual interest, and amortization of debt discount, debt issuance costs and loan transaction fees that were charged to interest expense (in thousands): Year Ended June 30, 2016 2015 2014 Comerica Term Loan Simple interest $ 501 $ 480 $ 479 Amortization of fees paid for letters of credit 31 44 48 Total interest expense on the Comerica term loan 532 524 527 Convertible Senior Notes Contractual interest 3,967 3,968 3,979 Amortization of debt discount 6,033 5,447 4,932 Amortization of debt issuance costs 342 308 278 Total interest expense on the convertible senior notes 10,342 9,723 9,189 Total interest expense $ 10,874 $ 10,247 $ 9,716 Commitment Schedule We are required to make principal payments for our long-term debt as follows during the fiscal years ending June 30 (in thousands): Principal Due 2017 $ — 2018 14,550 2019 — 2020 132,250 2021 — Thereafter — $ 146,800

COMMITMENTS AND CONTINGENCIES

COMMITMENTS AND CONTINGENCIES	12 Months Ended
	Jun. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
COMMITMENTS AND CONTINGENCIES	COMMITMENTS AND CONTINGENCIES Operating Leases We lease facilities and equipment under various non-cancelable operating leases that expire through 2025. Our most significant lease in Boulder, Colorado was amended during the 2015 fiscal year, expires on March 31, 2025 and includes an option to extend the lease for up to two terms of five years each. We are currently leasing approximately 131,000 square feet. In addition to minimum lease payments, we are contractually obligated under some of our lease agreements to pay certain operating expenses during the term of the lease, such as maintenance, taxes and insurance. Future minimum rental commitments for our operating leases, by fiscal year and in the aggregate, as of June 30, 2016 , are (in thousands): Rental Payments 2017 $ 3,750 2018 3,540 2019 3,539 2020 3,581 2021 3,651 Thereafter 14,347 $ 32,408 Our facilities rent expense was as follows (dollars in thousands): Year Ended June 30, 2016 2015 2014 Cash paid for rent $ 4,785 $ 8,276 $ 8,878 Deferred rent credits (1,270 ) (3,236 ) (3,645 ) Rent expense, net $ 3,515 $ 5,040 $ 5,233 Legal Proceedings From time to time, we may be involved in claims or lawsuits that arise in the ordinary course of business. Accruals for claims or lawsuits are provided to the extent that losses are deemed both probable and estimable. Although the ultimate outcome of these claims or lawsuits cannot be ascertained, on the basis of present information and advice received from counsel, it is management's opinion that the disposition or ultimate determination of such claims or lawsuits will not have a material adverse effect on Array.

STOCKHOLDERS' EQUITY (DEFICIT)

STOCKHOLDERS' EQUITY (DEFICIT)	12 Months Ended
	Jun. 30, 2016
Equity [Abstract]
STOCKHOLDERS' EQUITY (DEFICIT)	STOCKHOLDERS’ EQUITY (DEFICIT) Stock Option and Incentive Plan In September 2000, our Board of Directors approved the Amended and Restated Stock Option and Incentive Plan (the "Option and Incentive Plan"). As of June 30, 2016 , 19,228,677 shares of common stock are reserved for future issuance under the Option and Incentive Plan to our eligible employees, consultants and directors. Of the shares available for future issuance, 2,282,592 are available for issuance as incentive stock options. The remaining shares can be used for other awards. In addition, the Option and Incentive Plan provides for the reservation of additional authorized shares on any given day in an amount equal to the difference between: (i) 25% of our issued and outstanding shares of common stock, on a fully diluted and as-converted basis; and (ii) the number of outstanding shares relating to awards under the Option and Incentive Plan plus the number of shares available for future grants of awards under the Option and Incentive Plan on that date. However, in no event shall the number of additional authorized shares determined pursuant to this formula exceed, when added to the number of shares of common stock outstanding and reserved for issuance under the Option and Incentive Plan other than pursuant to this formula, under the ESPP and upon conversion or exercise of outstanding warrants or convertible securities, the total number of shares of common stock authorized for issuance under our Amended and Restated Certificate of Incorporation. The Option and Incentive Plan provides for awards of both non-statutory stock options and incentive stock options within the meaning of Section 422 of the Internal Revenue Code of 1986, as amended, restricted stock and other incentive awards and rights to purchase shares of our common stock. The Option and Incentive Plan is administered by the Compensation Committee of the Board of Directors, which has the authority to select the individuals to whom awards will be granted, the number of shares, vesting terms, exercise price and term of each option grant. Generally, options have a four -year annual vesting term, an exercise price equal to the market value of the underlying shares at the grant date and a ten -year life from the date of grant. Warrants Associated with our previously outstanding long-term debt arrangements with Deerfield Capital, which have been paid in full, we issued warrants to Deerfield to purchase 6,000,000 shares of common stock at an exercise price of $3.65 and warrants to purchase 6,000,000 shares of common stock at an exercise price of $4.19 . The warrants contain the same terms, except for the lower per share exercise price. We valued the warrants at issuance based on a Black-Scholes option pricing model and then allocated a portion of the proceeds under the debt to the warrants based upon their relative fair values. The warrants were recorded in stockholders' deficit with the offset to debt discount. The debt discount was amortized using the effective interest method and recorded as interest expense in the accompanying statements of operations and comprehensive income (loss) from the respective draw dates until June 10, 2013, when the Deerfield credit facilities were repaid and the recognition of the remaining debt discount was accelerated. The warrants were sold by Deerfield Capital to an unrelated third party during the fiscal year 2015. During fiscal year 2016, 3,996,298 warrants with an exercise price of $3.65 were exercised on a cashless basis for approximately 223,000 common shares. Additionally, approximately 12,000 warrants with an exercise price of $3.65 were exercised for approximately 12,000 common shares. All of the remaining warrants expired on June 30, 2016. Controlled Equity Offering On March 27, 2013, we entered into a Sales Agreement with Cantor Fitzgerald & Co. ("Cantor"), pursuant to which we could sell up to $75 million in shares of our common stock from time to time through Cantor, acting as our sales agent, in an at-the-market offering. We completed the sale of all shares available under the Sales Agreement in June 2014. On August 15, 2014, we amended the Sales Agreement with Cantor to allow us to sell up to $47.5 million in additional shares under the Sales Agreement. All sales of shares have been made pursuant to an effective shelf registration statement on Form S-3 filed with the SEC. We paid Cantor a commission of approximately 2% of the aggregate gross proceeds we received from all sales of our common stock under the Sales Agreement. The amended Sales Agreement continues until the earlier of selling all shares available under the Sales Agreement, or March 27, 2016. We completed the sale of shares under the amended agreement in June 2015. In August 2015, the Company amended its Sales Agreement with Cantor Fitzgerald & Co. ("Cantor") dated March 27, 2013 to permit the sale by Cantor, acting as its sales agent, of up to $75 million in additional shares of the Company's common stock from time to time in an at-the-market offering under the Sales Agreement. All sales of shares have been and will continue to be made pursuant to an effective shelf registration statement on Form S-3 filed with the SEC. The Company pays Cantor a commission of approximately 2% of the aggregate gross proceeds the Company receives from all sales of the Company's common stock under the Sales Agreement. The amended Sales Agreement continues indefinitely until either party terminates the Sales Agreement, which may be done on 10 days prior written notice. From July 1, 2016 through July 31, 2016, the Company sold 1.3 million shares of common stock in accordance with the amended Sales Agreement for net proceeds of approximately $4.8 million . The following table summarizes our total sales under the Sales Agreement for the periods indicated (in thousands, except per share amounts): Year Ended June 30, 2016 2015 Total shares of common stock sold 566 8,965 Average price per share $ 5.28 $ 5.30 Gross proceeds $ 2,992 $ 47,500 Commissions earned by Cantor and other costs $ 100 $ 956

SHARE-BASED COMPENSATION

SHARE-BASED COMPENSATION	12 Months Ended
	Jun. 30, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
SHARE-BASED COMPENSATION	SHARE-BASED COMPENSATION Total share-based compensation expense recorded for employee equity awards issued pursuant to the Option and Incentive Plan and for shares issued under the ESPP was $7.3 million , $7.8 million and $4.3 million for the fiscal years ended June 30, 2016 , 2015 and 2014 , respectively. Share-based compensation for the year ending June 30, 2016 , 2015 and 2014 consisted of: Year Ended June 30, 2016 2015 2014 Awards issued to employees $ 7,283 $ 7,513 $ 4,331 Options issued to transitioned CMC employees, net of other CMC share-based compensation amounts — 251 — Other non-employee awards — 296 — Total share-based compensation expense $ 7,283 $ 8,060 $ 4,331 We use the Black-Scholes option pricing model to estimate the fair value of our share-based awards. In applying this model, we use the following assumptions: • Risk-free interest rate - We determine the risk-free interest rate by using a weighted average assumption equivalent to the expected term based on the U.S. Treasury constant maturity rate. • Expected term - We estimate the expected term of our options based upon historical exercises and post-vesting termination behavior. • Expected volatility - We estimate expected volatility using daily historical trading data of our common stock. • Dividend yield - We have never paid dividends and currently have no plans to do so; therefore, no dividend yield is applied. Option Awards The fair values of our employee option awards were estimated using the assumptions below, which yielded the following weighted average grant date fair values for the periods presented: Year Ended June 30, 2016 2015 2014 Risk-free interest rate 1.30% - 1.83% 1.5% - 2.1% 1.7% - 2.1% Expected option term in years 5.5 - 6.25 6.25 6.25 Expected volatility 55.7% - 60.1% 60.8% - 67.1% 67.8% - 68.9% Dividend yield 0% 0% 0% Weighted average grant date fair value $1.95 $3.86 $2.91 The fair values of our non-employee option awards were estimated using the assumptions below, which yielded the following weighted average grant date fair value for the period presented: Year Ended June 30, 2015 Risk-free interest rate 0.4% - 0.6% Expected option term in years 1.25 - 2.00 Expected volatility 58.9% - 61.2% Dividend yield 0% Weighted average grant date fair value $2.16 The following table summarizes our stock option activity under the Option and Incentive Plan for the year ended June 30, 2016 : Number of Options Weighted Average Exercise Price Weighted Average Remaining Contractual Term (in years) Aggregate Intrinsic Value (in thousands) Outstanding at June 30, 2015 10,750,863 $ 5.30 Granted 3,275,669 $ 3.69 Exercised (419,179 ) $ 3.43 Forfeited (1,245,008 ) $ 6.08 Expired or canceled (714,750 ) $ 5.82 Outstanding balance at June 30, 2016 11,647,595 $ 4.80 7.5 $ 1,777 Vested and expected to vest at June 30, 2016 9,816,010 $ 4.83 7.2 $ 1,310 Exercisable at June 30, 2016 5,627,819 $ 4.88 5.9 $ 521 The aggregate intrinsic value in the above table is calculated as the difference between the closing price of our common stock at June 30, 2016 , of $3.56 per share and the exercise price of the stock options that had strike prices below the closing price. The total intrinsic value of all options exercised during the years ended June 30, 2016 , 2015 and 2014 was $0.7 million , $2.3 million , and $2.0 million , respectively. As of June 30, 2016 , there was approximately $9.5 million of total unrecognized compensation expense, including estimated forfeitures, related to the unvested stock options in the table above, which is expected to be recognized over a weighted average period of 2.7 years . Restricted Stock Units ("RSUs") The Option and Incentive Plan provides for the issuance of RSUs that each represent the right to receive one share of Array common stock, cash or a combination of cash and stock, typically following achievement of time- or performance-based vesting conditions. Our RSU grants that vest subject to continued service over a defined period of time, will typically vest between two to four years, with a percentage vesting on each anniversary date of the grant, or they may be vested in full on the date of grant. RSUs will be settled upon the vesting date, upon a predetermined delivery date, upon a change in control of Array, or upon the employee leaving Array. All outstanding RSUs may only be settled through the issuance of common stock to recipients, and we intend to continue to grant RSUs that may only be settled in stock. RSUs are assigned the value of Array common stock at date of grant issuance, and the grant date fair value is amortized over the applicable vesting period. A summary of the status of our non-vested RSUs as of June 30, 2016 and changes during the year ended June 30, 2016 , is presented below: Number of RSUs Weighted Unvested at June 30, 2015 678,247 $ 5.35 Granted 329,597 $ 3.31 Vested (160,828 ) $ 5.12 Forfeited (14,916 ) $ 7.30 Unvested at June 30, 2016 832,100 $ 4.55 As of June 30, 2016 , there was $1.7 million of total unrecognized compensation cost related to non-vested RSUs granted under the Option and Incentive Plan. The cost is expected to be recognized over a weighted-average period of approximately 2.7 years . The fair value for RSUs that vested during the year ended June 30, 2016 and 2015 , was $0.8 million and $1.8 million , respectively. RSUs granted during the year ended June 30, 2016 and 2015 had a fair value of $1.1 million and $4.9 million at grant date, respectively. Employee Stock Purchase Plan Following approval by our shareholders at our 2014 Annual Meeting, an additional 600,000 shares of our common stock were reserved for issuance under the ESPP, bringing the total amount of our common shares reserved for issuance under the ESPP to an aggregate of 5,250,000 shares. The ESPP allows qualified employees (as defined in the ESPP) to purchase shares of our common stock at a price equal to 85% of the lower of (i) the closing price at the beginning of the offering period or (ii) the closing price at the end of the offering period. Effective each January 1, a new 12 -month offering period begins that will end on December 31 of that year. However, if the closing stock price on July 1 is lower than the closing stock price on the preceding January 1, then the original 12 -month offering period terminates, and the purchase rights under the original offering period roll forward into a new six -month offering period that begins July 1 and ends on December 31. As of June 30, 2016 , we had 586,104 shares available for issuance under the ESPP. We issued 265,179 , 240,366 and 309,287 shares under the ESPP during fiscal 2016 , 2015 and 2014 , respectively.

EMPLOYEE BENEFIT PLAN

EMPLOYEE BENEFIT PLAN	12 Months Ended
	Jun. 30, 2016
Compensation and Retirement Disclosure [Abstract]
EMPLOYEE BENEFIT PLAN	EMPLOYEE BENEFIT PLAN Employee Savings Plan Array has a 401(k) plan that allows participants to contribute from 1% to 60% of their salary, subject to eligibility requirements and annual IRS limits. Array matches up to 4% of employee contributions on a discretionary basis as determined by our Board of Directors. Company contributions are fully vested after four years of employment. We paid matching contributions of approximately $952 thousand , $ 1.1 million , and $1.2 million , during the years ended June 30, 2016 , 2015 and 2014 , respectively.

RESTRUCTURING CHARGES

RESTRUCTURING CHARGES	12 Months Ended
	Jun. 30, 2016
Restructuring and Related Activities [Abstract]
RESTRUCTURING CHARGES	RESTRUCTURING CHARGES On August 5, 2013, we implemented a 20% reduction in our workforce and the affected employees were immediately notified. The reduction in force supports our strategy to fund our development organization with strategic collaborations and to focus our resources to progress our hematology and oncology programs to later stage development. The actions associated with the reductions were substantially completed during the first quarter of fiscal 2014 and, as a result of the reductions, we recorded a one-time restructuring charge of $2.8 million for termination benefits in the same period. Of this charge, $2.2 million was recorded in research and development for proprietary programs and $602 thousand was recorded in general and administrative expense. The restructuring charge is associated with cash payments of $2.6 million and $194 thousand made during the first quarter and second quarter, respectively, of fiscal 2014.

INCOME TAXES

INCOME TAXES	12 Months Ended
	Jun. 30, 2016
Income Tax Disclosure [Abstract]
INCOME TAXES	INCOME TAXES We have accumulated net losses since inception and have not recorded an income tax provision or benefit during fiscal 2016 , 2015 and 2014 . A reconciliation of income taxes at the statutory federal income tax rate to net income taxes included in the accompanying statements of operations and comprehensive income (loss) is set forth in the following table: Year Ended June 30, 2016 2015 2014 U.S. federal income tax expense at the statutory rate 34.0 % 34.0 % 34.0 % Change in valuation allowance (53.4 ) 110.2 (37.5 ) Change in tax contingency reserve (releases) (5.7 ) 38.4 (0.3 ) State income taxes, net of federal taxes 2.1 11.1 3.1 Stock-based compensation (1.1 ) 10.5 (1.2 ) Available research and experimentation tax credits 5.0 (29.6 ) 2.0 Orphan drug credit 19.3 (176.0 ) — Rate change — 1.0 — Effect of other permanent differences — 0.4 (0.1 ) Other (0.2 ) — — Total 0.0 % 0.0 % 0.0 % Deferred tax assets and liabilities reflect the net tax effects of net operating losses, credit carryforwards and temporary differences between the carrying amounts of assets and liabilities for financial reporting purposes and amounts used for income tax purposes. The components of our deferred tax assets and liabilities are (in thousands): June 30, 2016 2015 Deferred tax assets Accrued benefits $ 2,568 $ 2,030 Inventory reserve 1,514 1,514 Net operating loss carryforwards 201,571 178,120 Capital loss carryforwards — 61 Research and experimentation credit carryforwards 33,834 31,004 Orphan drug credit carryforwards 45,420 21,838 Third party agreement payment 8,452 9,070 Deferred revenue 670 3,818 Deferred rent 1,772 1,707 Stock compensation 4,499 3,375 Depreciation of property and equipment 4,112 4,519 Loan costs on convertible senior notes 278 371 Other 35 12 Total deferred tax assets 304,725 257,439 Deferred tax liabilities Discount on convertible senior notes (11,639 ) (13,877 ) Unrealized gain (loss) on marketable securities (3 ) (2 ) Total deferred tax liabilities (11,642 ) (13,879 ) Less valuation allowance (293,083 ) (243,560 ) Net deferred tax assets $ — $ — As of each reporting date, we consider existing evidence, both positive and negative, that could impact our view with regard to future realization of deferred tax assets. We had a net loss of $92.8 million for the year ended June 30, 2016 . We continue to believe that it is more likely than not that the benefit for deferred tax assets will not be realized. In recognition of this uncertainty, we continue to provide a full valuation allowance on our deferred tax assets. We did not record a tax provision for the years ended June 30, 2016 , 2015 and 2014, due to our estimate that the effective tax rate for each year being 0% . Future realization depends on the future earnings of Array, if any, the timing and amount of which are uncertain as of June 30, 2016 . In the future, should management conclude that it is more likely than not that the deferred tax assets are partially or fully realizable, the valuation allowance would be reduced to the extent of such expected realization and the amount would be recognized as a deferred income tax benefit in our statements of operations and comprehensive income (loss). Certain tax benefits from employee stock option exercises are included in the deferred tax asset balances as of June 30, 2016 and 2015 as a component of our net operating loss carryforwards. The deferred tax asset balances as of June 30, 2016 and 2015 do not include excess tax benefits from stock option exercises of approximately $5.3 million and $5.3 million , respectively. Equity will be increased if and when management determines that it is more likely than not that such excess tax benefits will ultimately be realized. As of June 30, 2016 , we had available total net operating loss carryforwards of approximately $560.5 million , which expire in the years 2020 through 2036, federal research and experimentation credit carryforwards of $38.9 million , which expire in the years 2022 through 2036, and orphan drug credit carryforwards of $52.2 million , which begin to expire in 2033. The Tax Reform Act of 1986 and certain state tax statutes limit the utilization of net operating loss and tax credit carryforwards to offset future taxable income and tax, and may therefore result in the expiration of a portion of those carryforwards before they are utilized, if there has been a "change of ownership" as described in Section 382 of the Internal Revenue Code ("IRC"), and under similar state provisions. The Company has performed a detailed analysis of Section 382 of the IRC though June 30, 2016. Based on our analysis, approximately $40 thousand of our net operating losses as of the year ended June 30, 2016, may not be used to offset taxable income. We have provided a valuation allowance against the entire amount of our net operating loss and tax credit carryforwards. The effect of an ownership change would be the imposition of an annual limitation on the use of net operating loss carryforwards attributable to periods before the change. Any limitation may result in expiration of a portion of the net operating loss or research and development credit carryforwards before utilization. We will continue to evaluate future events that could limit our ability to utilize our net operating losses and tax credit carryforwards in future years. We follow a comprehensive model for recognizing, measuring, presenting and disclosing uncertain tax positions taken or expected to be taken on a tax return. Tax positions must initially be recognized in the financial statements when it is more likely than not that the position will be sustained upon examination by the tax authorities. Such tax positions must initially and subsequently be measured as the largest amount of tax benefit that has a greater than 50% likelihood of being realized upon ultimate settlement with the tax authority assuming full knowledge of the position and relevant facts. The cumulative effect of accounting for tax contingencies in this manner has been recorded in deferred tax assets, net of the full valuation allowance, which resulted in no liability being recorded on our accompanying balance sheets. The total amount of unrecognized tax benefits as of and for the years ended June 30, 2016 , 2015 , and 2014 are (in thousands): Year Ended June 30, 2016 2015 2014 Balance at beginning of year $ 7,311 $ 3,676 $ 3,428 Additions based on tax positions related to the current year 5,071 3,551 712 Additions for tax positions of prior year 1,323 559 — Reductions for tax positions of prior year (544 ) (475 ) (464 ) Balance at end of year $ 13,161 $ 7,311 $ 3,676 There are open statutes of limitations for taxing authorities in federal and state jurisdictions to audit our tax returns from inception of Array. Our policy is to account for income tax related interest and penalties in income tax expense in the accompanying statements of operations and comprehensive income (loss). There have been no income tax related interest or penalties assessed or recorded.

NET EARNINGS (LOSS) PER SHARE

NET EARNINGS (LOSS) PER SHARE	12 Months Ended
	Jun. 30, 2016
Earnings Per Share [Abstract]
NET EARNINGS (LOSS) PER SHARE	NET EARNINGS (LOSS) PER SHARE Basic and diluted earnings (loss) per common share are computed by dividing net income by the weighted average number of common shares outstanding during the period. Diluted earnings (loss) per share includes the determinants of basic net income (loss) per share and, in addition, gives effect to the potential dilution that would occur if securities or other contracts to issue common stock were exercised, vested or converted into common stock, unless they are anti-dilutive. Diluted weighted average common shares include common stock potentially issuable under our convertible notes, vested and unvested stock options and unvested RSUs. The following table sets forth the computation of earnings per share (amounts in thousands except per share data): Year Ended June 30, 2016 2015 2014 Net earnings (loss) - basic and diluted $ (92,840 ) $ 9,369 $ (85,257 ) Weighted average shares outstanding - basic 142,964 136,679 123,403 Warrants — 3,560 — Stock options — 1,300 — RSUs — 153 — Weighted average shares outstanding - diluted 142,964 141,692 123,403 Per share data: Basic $ (0.65 ) $ 0.07 $ (0.69 ) Diluted $ (0.65 ) $ 0.07 $ (0.69 ) For the periods where we reported losses, all common stock equivalents are excluded from the computation of diluted earnings (loss) per share, since the result would be anti-dilutive. Common stock equivalents (measured at the end of each fiscal period) that are not included in the calculations of diluted earnings (loss) per share because to do so would have been anti-dilutive, include the following (amounts in thousands): Year Ended June 30, 2016 2015 2014 Convertible senior notes 18,762 18,762 18,762 Warrants — — 12,000 Stock options 11,648 7,332 6,922 RSUs 832 275 — Total anti-dilutive common stock equivalents excluded from diluted loss per share calculation 31,242 26,369 37,684

SELECTED QUARTERLY FINANCIAL DA

SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED)	12 Months Ended
	Jun. 30, 2016
Quarterly Financial Information Disclosure [Abstract]
SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED)	SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED) The tables below summarize our unaudited quarterly operating results for the fiscal years ended June 30, 2016 and 2015 (dollars in thousands, except per share data): Fiscal Year Ended June 30, 2016 First Quarter Second Quarter Third Quarter Fourth Quarter Revenue $ 16,197 $ 35,430 $ 43,047 $ 43,205 Research and development for proprietary programs $ 20,998 $ 41,351 $ 48,802 $ 49,504 Total operating expenses $ 34,568 $ 56,952 $ 63,055 $ 65,513 Net loss $ (20,987 ) $ (24,164 ) $ (22,675 ) $ (25,014 ) Net earnings (loss) per share – basic $ (0.15 ) $ (0.17 ) $ (0.16 ) $ (0.17 ) Net earnings (loss) per share – diluted $ (0.15 ) $ (0.17 ) $ (0.16 ) $ (0.17 ) Weighted average shares outstanding – basic 142,216 142,833 143,338 143,475 Weighted average shares outstanding – diluted 142,216 142,833 143,338 143,475 Fiscal Year Ended June 30, 2015 First Quarter Second Quarter Third Quarter Fourth Quarter Revenue $ 6,069 $ 26,919 $ 6,601 $ 12,320 Research and development for proprietary programs $ 12,190 $ 11,817 $ 11,817 $ 18,618 Total operating expenses $ 31,166 $ 32,993 $ 32,144 $ 33,964 Net income (loss) $ (27,593 ) $ (8,611 ) $ 58,307 $ (12,734 ) Net earnings (loss) per share – basic $ (0.21 ) $ (0.06 ) $ 0.42 $ (0.09 ) Net earnings (loss) per share – diluted $ (0.21 ) $ (0.06 ) $ 0.37 $ (0.09 ) Weighted average shares outstanding – basic 131,826 133,815 139,769 141,393 Weighted average shares outstanding – diluted 131,826 133,815 166,265 141,393 The net earnings (loss) per share amounts above may not sum to the annual amounts presented in our accompanying statements of operations and comprehensive income (loss) due to rounding.

OVERVIEW, BASIS OF PRESENTATI22

OVERVIEW, BASIS OF PRESENTATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Policies)	12 Months Ended
	Jun. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Basis of Presentation	The accompanying financial statements have been prepared in accordance with U.S. generally accepted accounting principles (“U.S. GAAP”) and include all adjustments necessary for the fair presentation of our financial position, results of operations and cash flows for the periods presented. Our management performed an evaluation of our activities through the date of filing of this Annual Report on Form 10-K and concluded that there are no subsequent events.
Use of Estimates	The preparation of financial statements in conformity with U.S. GAAP requires the Company's management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue and expenses, and related disclosure of contingent assets and liabilities. Management bases its estimates on the Company's historical experience and on various other assumptions that it believes are reasonable under the circumstances. These estimates are the basis for the Company's judgments about the carrying values of assets and liabilities, which in turn may impact its reported revenue and expenses. The Company's actual results could differ significantly from these estimates under different assumptions or conditions. The Company believes the financial statements are most significantly impacted by the following accounting estimates and judgments: (i) identifying deliverables under collaboration, license and other agreements involving multiple elements and determining whether such deliverables are separable from other aspects of the contractual relationship; (ii) estimating the selling price of deliverables for the purpose of allocating arrangement consideration for revenue recognition; (iii) estimating the periods over which the allocated consideration for deliverables is recognized; (iv) estimating accrued outsourcing costs for clinical trials and preclinical testing; and (v) estimating the fair value of non-marketable equity received from licensing or other transactions.
Reclassifications	Certain prior period amounts in the Company's financial statements have been reclassified to conform to the current period presentation. The $39.4 million balance attributable to outstanding warrants, which was presented historically as a separate item in stockholders' equity (deficit) on the Company's balance sheet, has been combined with additional paid-in capital for all periods presented in these financial statements.
Fair Value Measurements	We follow accounting guidance on fair value measurements for financial instruments measured on a recurring basis, as well as for certain assets and liabilities that are initially recorded at their estimated fair values. Fair value is defined as the exit price, or the amount that would be received from selling an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. We use the following three-level hierarchy that maximizes the use of observable inputs and minimizes the use of unobservable inputs to value our financial instruments: • Level 1: Observable inputs such as unadjusted quoted prices in active markets for identical instruments. • Level 2: Quoted prices for similar instruments that are directly or indirectly observable in the marketplace. • Level 3: Significant unobservable inputs which are supported by little or no market activity and that are financial instruments whose values are determined using pricing models, discounted cash flow methodologies, or similar techniques, as well as instruments for which the determination of fair value requires significant judgment or estimation. Financial instruments measured at fair value are classified in their entirety based on the lowest level of input that is significant to the fair value measurement. Our assessment of the significance of a particular input to the fair value measurement in its entirety requires us to make judgments and consider factors specific to the asset or liability. The use of different assumptions and/or estimation methodologies may have a material effect on estimated fair values. Accordingly, the fair value estimates disclosed or initial amounts recorded may not be indicative of the amount that we or holders of the instruments could realize in a current market exchange. The carrying amounts of cash equivalents and marketable securities approximate their fair value based upon quoted market prices. Certain of our financial instruments are not measured at fair value on a recurring basis, but are recorded at amounts that approximate their fair value due to their liquid or short-term nature, such as cash, accounts receivable and payable, and other financial instruments in current assets or current liabilities.
Cash and Cash Equivalents and Concentration of Credit Risk	Cash and cash equivalents consist of cash and short-term, highly-liquid financial instruments that are readily convertible to cash and have maturities of 90 days or less from the date of purchase. They may consist of money market funds, commercial paper, U.S. government agency obligations and corporate notes and bonds with high credit quality. We currently maintain all cash in several institutions in the U.S. Balances at these institutions may exceed Federal Deposit Insurance Corporation insured limits.
Marketable Securities	We have designated our marketable securities as of each balance sheet date as available-for-sale securities and account for them at their respective fair values. Marketable securities are classified as short-term or long-term based on the nature of the securities and their availability to meet current operating requirements. Marketable securities that are readily available for use in current operations are classified as short-term available-for-sale securities and are reported as a component of current assets in the accompanying balance sheets. Marketable securities that are not considered available for use in current operations are classified as long-term available-for-sale securities and are reported as a component of long-term assets in the accompanying balance sheets. Securities that are classified as available-for-sale are measured at fair value, including accrued interest, with temporary unrealized gains and losses reported as a component of stockholders' equity (deficit) until their disposition. We review all available-for-sale securities at each period end to determine if they remain available-for-sale based on our then current intent and ability to sell the security if it is required to do so. The cost of securities sold is based on the specific identification method. All of our marketable securities are subject to a periodic impairment review. We recognize an impairment charge when a decline in the fair value of our investments below the cost basis is judged to be other-than-temporary.
Property and Equipment	Property and equipment are stated at historical cost less accumulated depreciation and amortization. Additions and improvements are capitalized. Certain costs to internally develop software are also capitalized. Maintenance and repairs are expensed as incurred. Depreciation and amortization are computed on the straight-line method based on the following estimated useful lives: Furniture and fixtures 7 years Equipment 5 years Computer hardware and software 3 years We depreciate leasehold improvements associated with operating leases over the shorter of the expected useful life of the improvements or the remaining lease term. The carrying value for property and equipment is reviewed for impairment at least annually and when events or changes in circumstances indicate that the carrying value of the assets may not be recoverable.
Equity Investments	From time to time, we may enter into collaboration and other agreements or other arrangements under which we receive an equity interest as consideration for all or a portion of up-front, license or other fees or consideration under the terms of the agreement or arrangement. We report equity securities received from non-publicly traded companies in which we do not exercise a significant or controlling interest at cost in other long-term assets in the accompanying balance sheets. We monitor our investments for impairment at least annually, and consider events or changes in circumstances we know of that may have a significant adverse effect on the fair value. We make appropriate reductions in the carrying value if it is determined that an impairment has occurred, based primarily on the financial condition and near and long-term prospects of the issuer. We do not report the fair value of our equity investments in non-publicly traded companies because it is not practical to do so.
Accrued Outsourcing Costs	Substantial portions of our preclinical studies and clinical trials are performed by third-party laboratories, medical centers, contract research organizations and other vendors (collectively "CROs"). These CROs generally bill monthly or quarterly for services performed, or bill based upon milestone achievement. For preclinical studies, we accrue expenses based upon estimated percentage of work completed and the contract milestones remaining. For clinical studies, expenses are accrued based upon the number of patients enrolled and the duration of the study. We monitor patient enrollment, the progress of clinical studies and related activities to the extent possible through internal reviews of data reported to us by the CROs, correspondence with the CROs and clinical site visits. Our estimates depend on the timeliness and accuracy of the data provided by the CROs regarding the status of each program and total program spending. We periodically evaluate the estimates to determine if adjustments are necessary or appropriate based on information we receive.
Convertible Senior Notes	Our 3.00% convertible senior notes due 2020 are accounted for in accordance with FASB Accounting Standards Codification (“ASC”) 470-20, Debt – Debt with Conversion and Other Options. ASC 470-20 requires the issuer of convertible debt that may be settled in shares or cash upon conversion at the issuer's option, such as our notes, to account for the liability (debt) and equity (conversion option) components separately. The value assigned to the debt component is the estimated fair value, as of the issuance date, of a similar debt instrument without the conversion option. The amount of the equity component (and resulting debt discount) is calculated by deducting the fair value of the liability component from the principal amount of the convertible debt instrument. The resulting debt discount is amortized as additional non-cash interest expense over the expected life of the notes utilizing the effective interest method. Although ASC 470-20 has no impact on our actual past or future cash flows, it requires us to record non-cash interest expense as the debt discount is amortized.
Revenue Recognition	We recognize revenue for the performance of services or the shipment of products when each of the following four criteria is met: (i) persuasive evidence of an arrangement exists; (ii) products are delivered or as services are rendered; (iii) the sales price is fixed or determinable; and (iv) collectability is reasonably assured. We follow ASC 605-25, Revenue Recognition – Multiple-Element Arrangements and ASC 808, Collaborative Arrangements , if applicable, to determine the recognition of revenue under our collaborative research, development and commercialization agreements that contain multiple elements. These multiple elements, or deliverables, may include (i) grants of licenses, or options to obtain licenses, to our intellectual property, (ii) research and development services, (iii) drug product manufacturing, and/or (iv) participation on joint research and/or joint development committees. The payments we may receive under these arrangements typically include one or more of the following: non-refundable, up-front license fees; option exercise fees; funding of research and/or development efforts; amounts due upon the achievement of specified objectives; and/or royalties on future product sales. ASC 605-25 provides guidance relating to the separability of deliverables included in an arrangement into different units of accounting and the allocation of arrangement consideration to the units of accounting. The evaluation of multiple-element arrangements requires management to make judgments about (i) the identification of deliverables, (ii) whether such deliverables are separable from the other aspects of the contractual relationship, (iii) the estimated selling price of each deliverable, and (iv) the expected period of performance for each deliverable. To determine the units of accounting under a multiple-element arrangement, management evaluates certain separation criteria, including whether the deliverables have stand-alone value, based on the relevant facts and circumstances for each arrangement. Management then estimates the selling price for each unit of accounting and allocates the arrangement consideration to each unit utilizing the relative selling price method. The allocated consideration for each unit of accounting is recognized over the related obligation period in accordance with the applicable revenue recognition criteria. If there are deliverables in an arrangement that are not separable from other aspects of the contractual relationship, they are treated as a combined unit of accounting, with the allocated revenue for the combined unit recognized in a manner consistent with the revenue recognition applicable to the final deliverable in the combined unit. Payments received prior to satisfying the relevant revenue recognition criteria are recorded as deferred revenue in the accompanying balance sheets and recognized as revenue when the related revenue recognition criteria are met. We typically receive non-refundable, up-front payments when licensing our intellectual property, which often occurs in conjunction with a research and development agreement. When management believes that the license to our intellectual property has stand-alone value, we generally recognize revenue attributed to the license upon delivery provided that there are no future performance requirements for use of the license. When management believes that the license to our intellectual property does not have stand-alone value, we typically recognize revenue attributed to the license on a straight-line basis over the contractual or estimated performance period. When the performance period is not specifically identifiable from the agreement, we estimate the performance period based upon provisions contained within the agreement, such as the duration of the research or development term. Most of our agreements provide for non-refundable milestone payments. We recognize revenue that is contingent upon the achievement of a substantive milestone in its entirety in the period in which the milestone is achieved. A milestone is considered substantive when the consideration payable to us for such milestone (i) is consistent with our performance necessary to achieve the milestone or the increase in value to the collaboration resulting from our performance, (ii) relates solely to our past performance and (iii) is reasonable relative to all of the other deliverables and payments within the arrangement. In making this assessment, we consider all facts and circumstances relevant to the arrangement, including factors such as the scientific, regulatory, commercial and other risks that must be overcome to achieve the milestone, the level of effort and investment required to achieve the milestone and whether any portion of the milestone consideration is related to future performance or deliverables. For payments payable on achievement of milestones that do not meet all of the conditions to be considered substantive, we recognize a portion of the payment as revenue when the specific milestone is achieved, and the contingency is removed, based on the applicable percentage earned of the estimated research or development effort, or other performance obligations that have elapsed, to the total estimated research and/or development effort attributable to the milestone. In other cases, when a non-substantive milestone payment is attributed to our future research or development obligations, we recognize the revenue on a straight-line basis, or other appropriate method, over the estimated remaining research or development effort. Other contingent event-based payments for which payment is either contingent solely upon the passage of time or the result of collaborator's performance are recognized when earned. We periodically review the estimated performance periods under each of our agreements that provide for non-refundable up-front payments, license fees or milestone payments. We adjust the periods over which revenue should be recognized when appropriate to reflect changes in assumptions relating to the estimated performance periods. We could accelerate revenue recognition in the event of early termination of programs or if our expectations change. Alternatively, we could decelerate revenue recognition if programs are extended or delayed. While such changes to our estimates have no impact on our reported cash flows, the amount of revenue recorded in future periods could be materially impacted. We record as revenue amounts received for reimbursement of costs we incur from our license partners where we act as a principal, control the research and development activities, bear credit risk and may perform part of the services required in the transactions, consistent with ASC 605-45-15. Certain collaborators or other counterparties (currently, Novartis and Pierre Fabre) currently provide financial support to us in the form of reimbursement for associated out-of-pocket costs and for a certain amount of Array’s fully-burdened full-time equivalent ("FTE") costs based on an agreed-upon FTE rates. The gross amount of these pass-through reimbursed costs are reported as revenue in the accompanying statements of operations and comprehensive income (loss) in accordance with ASC 605-45-15. The actual expenses for which we are reimbursed are reflected as research and development for proprietary programs or cost of partnered programs, as applicable.
Research and Development Costs	Research and development costs are expensed as incurred. Advance payments for goods and services that will be used in future research and development activities are expensed when the activity has been performed or when the goods have been received rather than when the payment is made. Upfront and milestone payments due to third parties that perform research and development services on our behalf will be expensed as services are rendered or when the milestone is achieved. Research and development costs primarily consist of personnel related expenses, including salaries, benefits, costs to recruit and relocate new employees, travel, and other related expenses, stock-based compensation, payments made to third party contract research organizations for preclinical and clinical studies, investigative sites for clinical trials, consultants, the cost of acquiring and manufacturing clinical trial materials, the cost of acquiring and manufacturing commercial drug supply, costs associated with regulatory filings and patents, software, facilities and laboratory costs and other supplies. We split our research and development costs between cost of partnered programs and research and development for proprietary programs on our statements of operations and comprehensive income (loss). Cost of partnered programs represents costs attributable to discovery and development activities, including preclinical and clinical trials we may conduct for or with our partners. Research and development expenses for proprietary programs include costs associated with our proprietary drug programs.
Operating Leases	We have negotiated certain landlord/tenant incentives and rent holidays and escalations in the base price of rent payments under our operating leases. For purposes of determining the period over which these amounts are recognized or amortized, the initial term of an operating lease includes the "build-out" period of leases, where no rent payments are typically due under the terms of the lease and includes additional terms pursuant to any options to extend the initial term if it is more likely than not that we will exercise such options. We recognize rent holidays and rent escalations on a straight-line basis over the initial lease term. The landlord/tenant incentives are recorded as an increase to deferred rent in the accompanying balance sheets and are amortized on a straight-line basis over the initial lease term. Deferred rent balances are classified as short-term or long-term in the accompanying balance sheets based upon the period when reversal of the liability is expected to occur. We completed the sale of our chemical manufacturing and control assets (the "CMC Assets") in June 2015, and in connection with the closing of the sale of the CMC Assets, we simultaneously entered into an amendment to our lease agreement for our facility in Boulder, Colorado and an early termination agreement for our Longmont, Colorado facility. The amended Boulder lease extended the term of our prior lease and provided for a reduction in the amount of leased space by the end of calendar year 2015. As both the amended Boulder lease and the Longmont termination were negotiated with the same landlord, we deferred our existing deferred rent liabilities rather than recognizing a gain on termination.
Share-Based Compensation	Share-based compensation awards include stock options and restricted stock units ("RSUs") granted under our Amended and Restated Stock Option and Incentive Plan ("Option and Incentive Plan") and purchases of common stock by our employees at a discount to the market price under the Amended and Restated Array BioPharma Inc. Employee Stock Purchase Plan ("ESPP"). We use the Black-Scholes option pricing model to determine the grant date fair value of stock options and ESPP awards. The determination of the fair value of share-based awards using an option pricing model is affected by our stock price, as well as assumptions regarding a number of complex and subjective variables. Share-based compensation expense is recognized on a straight-line basis over the requisite service period for each award. Further, compensation expense recognized in our statement of operations and comprehensive income (loss) is reduced for estimated forfeitures, which are based on historical experience and are revised in subsequent periods if actual forfeitures differ from our estimates. For stock-based compensation awards granted to non-employees, we remeasure the fair value of the non-employee awards at each reporting period prior to vesting and finally at the vesting date of the award. Changes in the estimated fair value of these non-employee awards are recognized as compensation expense in the period of change. The assumptions used in calculating the fair value of stock-based awards represent management’s best estimates and involve inherent uncertainties and the application of management’s judgment.
Income Taxes	We account for income taxes using the asset and liability method. We recognize the amount of income taxes payable (refundable) for the year as current income tax provision (benefit) and record a deferred income tax provision (benefit) based on changes in deferred tax assets and liabilities. Deferred tax assets and liabilities are determined based on the difference between the financial statement carrying value and the tax basis of assets and liabilities and, using enacted tax rates in effect, reflect the expected effect these differences would have on future taxable income, if any. Valuation allowances are recorded to reduce the amount of deferred tax assets when management cannot conclude it is more likely than not that some or all of the deferred tax assets will be realized. Such allowances are based upon available objective evidence, the expected reversal of temporary differences and projections of future taxable income. Our policy is to account for income tax related interest and penalties in income tax expense in the accompanying statements of operations and comprehensive income (loss).
Segments	We operate in one operating segment and, accordingly, no segment disclosures have been presented herein. All of our equipment, leasehold improvements and other fixed assets are physically located within the U.S., and all agreements with our partners are denominated in U.S. dollars.
Concentration of Business Risks	The loss of one or more of our significant partners could have a material adverse effect on our business, operating results or financial condition. We do not require collateral from our partners, though most pay in advance. Although we are impacted by economic conditions in the biotechnology and pharmaceutical sectors, management does not believe significant credit risk exists as of June 30, 2016 .
Net Earnings (Loss) per Share	Basic net earnings (loss) per share is computed by dividing net income (loss) for the period by the weighted average number of common shares outstanding, excluding unvested restricted stock, during the period. Diluted net earnings (loss) per share reflects the additional dilution from potential issuances of common stock, such as stock issuable pursuant to the exercise of stock options or the vesting of restricted stock units, as well as from the possible conversion of our convertible senior notes and exercise of outstanding warrants. The treasury stock method and if-converted method are used to calculate the potential dilutive effect of these common stock equivalents. Potentially dilutive shares are excluded from the computation of diluted net earnings (loss) per share when their effect is anti-dilutive. In periods where a net loss is presented, all potentially dilutive securities were anti-dilutive and have been excluded from the computation of diluted net loss per share.
Comprehensive Income (Loss)	Comprehensive income (loss) is comprised of net income (loss) and adjustments for the change in unrealized gains and losses on our investments in available-for-sale marketable securities, net of taxes. We display comprehensive income (loss) and its components in our statements of operations and comprehensive income (loss).
Recent Accounting Pronouncements	In May 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers , an updated standard on revenue recognition. ASU No. 2014-09 provides enhancements to the quality and consistency of how revenue is reported by companies while also improving comparability in the financial statements of companies reporting using International Financial Reporting Standards or U.S. GAAP. The main purpose of the new standard is for companies to recognize revenue to depict the transfer of goods or services to customers in amounts that reflect the consideration to which a company expects to be entitled in exchange for those goods or services. The new standard also will result in enhanced disclosures about revenue, provide guidance for transactions that were not previously addressed comprehensively and improve guidance for multiple-element arrangements. In July 2015, the FASB voted to approve a one-year deferral of the effective date of ASU No. 2014-09, which will be effective for Array in the first quarter of fiscal year 2019 and may be applied on a full retrospective or modified retrospective approach. The Company is currently evaluating the impact of implementation and transition approach of this standard on its financial statements. In August 2014, the FASB issued ASU No. 2014-15, Presentation of Financial Statements-Going Concern , which defines management's responsibility to assess an entity's ability to continue as a going concern, and requires related footnote disclosures if there is substantial doubt about its ability to continue as a going concern. ASU No. 2014-15 is effective for Array for the fiscal year ending on June 30, 2017, with early adoption permitted. The Company is currently evaluating the impact of adopting ASU No. 2014-15 and its related disclosures. In November 2015, the FASB issued ASU No. 2015-17, Balance Sheet Classification of Deferred Taxes . ASU No. 2015-17 requires that deferred tax liabilities and assets be classified as noncurrent in a classified statement of financial position. ASU No. 2015-17 is effective for financial statements issued for fiscal years beginning after December 15, 2016, and interim periods within those fiscal years. The Company early adopted ASU No. 2015-17 during the fiscal year ended June 30, 2016. The early adoption of ASU 2015-17 had no impact to the statements of operations or cash flows for any period presented. In January 2016, the FASB issued ASU No. 2016-01, Recognition and Measurement of Financial Assets and Financial Liabilities . ASU No. 2016-01 requires equity investments to be measured at fair value with changes in fair value recognized in net income; simplifies the impairment assessment of equity investments without readily determinable fair values by requiring a qualitative assessment to identify impairment; eliminates the requirement for public business entities to disclose the method(s) and significant assumptions used to estimate the fair value that is required to be disclosed for financial instruments measured at amortized cost on the balance sheet; requires public business entities to use the exit price notion when measuring the fair value of financial instruments for disclosure purposes; requires an entity to present separately in other comprehensive income the portion of the total change in the fair value of a liability resulting from a change in the instrument-specific credit risk when the entity has elected to measure the liability at fair value in accordance with the fair value option for financial instruments; requires separate presentation of financial assets and financial liabilities by measurement category and form of financial assets on the balance sheet or the accompanying notes to the financial statements and clarifies that an entity should evaluate the need for a valuation allowance on a deferred tax asset related to available-for-sale securities in combination with the entity’s other deferred tax assets. ASU No. 2016-01 is effective for financial statements issued for fiscal years beginning after December 15, 2017, and interim periods within those fiscal years. The Company is currently evaluating the impact that ASU No. 2016-01 will have on its financial statements and related disclosures. In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842) which supersedes FASB ASC Topic 840, Leases (Topic 840) and provides principles for the recognition, measurement, presentation and disclosure of leases for both lessees and lessors. The new standard requires lessees to apply a dual approach, classifying leases as either finance or operating leases based on the principle of whether or not the lease is effectively a financed purchase by the lessee. This classification will determine whether lease expense is recognized based on an effective interest method or on a straight-line basis over the term of the lease, respectively. A lessee is also required to record a right-of-use asset and a lease liability for all leases with a term of greater than twelve months regardless of classification. Leases with a term of twelve months or less will be accounted for similar to existing guidance for operating leases. The standard is effective for annual and interim periods beginning after December 15, 2018, with early adoption permitted upon issuance. The Company is currently evaluating the impact this guidance will have on its financial statements. In March 2016, the FASB issued ASU No. 2016-08, Revenue from Contracts with Customers (Topic 606): Principal versus Agent Considerations . The purpose of ASU No. 2016-08 is to clarify the implementation of guidance on principal versus agent considerations. For public entities, the amendments in ASU No. 2016-08 are effective for interim and annual reporting periods beginning after December 15, 2017. The Company is currently evaluating the impact of ASU No. 2016-08 on its financial statements and related disclosures. In March 2016, the FASB issued ASU No. 2016-09, Compensation – Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting . The amendment is to simplify several aspects of the accounting for share-based payment transactions including the income tax consequences, classification of awards as either equity or liabilities, and classification on the statement of cash flows. The amendments in ASU No. 2016-09 are effective for interim and annual reporting periods beginning after December 15, 2016. The Company is currently assessing the impact of ASU No. 2016-09 on its financial statements and related disclosures. The Company does not expect the adoption of ASU 2016-09 to have a material effect on the financial statements. In April 2016, the FASB issued ASU No. 2016-10, Revenue from Contracts with Customer . The new guidance is an update to ASC 606 and provides clarity on: identifying performance obligations and licensing implementation. For public companies, ASU No. 2016-10 is effective for annual periods, including interim periods within those annual periods, beginning after December 15, 2016. The Company is currently evaluating the impact that ASU No. 2016-10 will have on its financial statements. In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses: Measurement of Credit Losses on Financial Instruments (ASU 2016-13). ASU 2016-13 requires that expected credit losses relating to financial assets measured on an amortized cost basis and available-for-sale debt securities be recorded through an allowance for credit losses. ASU 2016-13 limits the amount of credit losses to be recognized for available-for-sale debt securities to the amount by which carrying value exceeds fair value and also requires the reversal of previously recognized credit losses if fair value increases. The new standard will be effective for us on January 1, 2020. Early adoption will be available on January 1, 2019. The Company is currently evaluating the effect that the updated standard will have on our financial statements and related disclosures.
Uncertain Tax Positions	We follow a comprehensive model for recognizing, measuring, presenting and disclosing uncertain tax positions taken or expected to be taken on a tax return. Tax positions must initially be recognized in the financial statements when it is more likely than not that the position will be sustained upon examination by the tax authorities. Such tax positions must initially and subsequently be measured as the largest amount of tax benefit that has a greater than 50% likelihood of being realized upon ultimate settlement with the tax authority assuming full knowledge of the position and relevant facts.

OVERVIEW, BASIS OF PRESENTATI23

OVERVIEW, BASIS OF PRESENTATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Tables)	12 Months Ended
	Jun. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Schedule of estimated useful lives of property and equipment	Depreciation and amortization are computed on the straight-line method based on the following estimated useful lives: Furniture and fixtures 7 years Equipment 5 years Computer hardware and software 3 years Property and equipment, net consists of the following (in thousands): June 30, 2016 2015 Furniture and fixtures $ 2,647 $ 2,647 Equipment 26,120 26,120 Computer hardware and software 15,953 14,336 Leasehold improvements 15,577 15,335 Property and equipment, gross 60,297 58,438 Less: accumulated depreciation and amortization (53,617 ) (53,388 ) Property and equipment, net $ 6,680 $ 5,050
Schedule of partners that contributed greater than 10% of total revenue	The following significant partners contributed greater than 10% of our total revenue during at least one of the periods set forth below. The revenue from these partners as a percentage of total revenue was as follows: Year Ended June 30, 2016 2015 2014 Novartis 80.5 % 15.8 % 28.6 % Loxo 9.2 17.8 23.1 Cascadian Therapeutics (previously known as Oncothyreon Inc.) 0.1 42.3 8.2 AstraZeneca 0.1 0.1 12.1 89.9 % 76.0 % 72.0 %
Schedule of revenue by geographic area based on the country in which partners are located	The following table details revenue by geographic area based on the country in which our partners are located (in thousands): Year Ended June 30, 2016 2015 2014 North America $ 22,474 $ 43,386 $ 24,757 Europe 114,806 8,293 17,153 Asia Pacific 599 230 168 $ 137,879 $ 51,909 $ 42,078

MARKETABLE SECURITIES (Tables)

MARKETABLE SECURITIES (Tables)	12 Months Ended
	Jun. 30, 2016
Marketable Securities [Abstract]
Schedule of marketable securities	Marketable securities consisted of the following as of June 30, 2016 and 2015 (in thousands): June 30, 2016 Gross Gross Amortized Unrealized Unrealized Fair Cost Gains Losses Value Short-term available-for-sale securities: U.S. treasury securities $ 53,113 $ 8 $ (1 ) $ 53,120 Mutual fund securities 224 — — 224 53,337 8 (1 ) 53,344 Long-term available-for-sale securities: Mutual fund securities 596 — — 596 596 — — 596 Total $ 53,933 $ 8 $ (1 ) $ 53,940 June 30, 2015 Gross Gross Amortized Unrealized Unrealized Fair Cost Gains Losses Value Short-term available-for-sale securities: U.S. treasury securities $ 122,199 $ 8 $ (3 ) $ 122,204 Mutual fund securities 431 — — 431 122,630 8 (3 ) 122,635 Long-term available-for-sale securities: Mutual fund securities 496 — — 496 496 — — 496 Total $ 123,126 $ 8 $ (3 ) $ 123,131
Schedule of fair value measurement categories of marketable securities	The estimated fair value of our marketable securities was classified into fair value measurement categories as follows (in thousands): June 30, 2016 2015 Quoted prices in active markets for identical assets (Level 1) $ 53,940 $ 123,131 Quoted prices for similar assets observable in the marketplace (Level 2) — — Significant unobservable inputs (Level 3) — — Total $ 53,940 $ 123,131
Roll forward of fair value of investment in Level 3 equity securities	The following table is a roll forward of the fair value of our prior investment, which consisted of Loxo common shares, in Level 3 equity securities (in thousands): Year Ended June 30, 2015 Balance, beginning of period $ — Transfer into Level 3 due to restriction period on trading 4,500 Change in unrealized gains and losses included in comprehensive income (loss) 13,205 Transfer out of Level 3 due to elimination of trading restrictions (17,705 ) Balance, end of period $ —
Schedule of amortized cost and estimated fair value of available-for-sale securities by contractual maturity	As of June 30, 2016 , the amortized cost and estimated fair value of available-for-sale securities by contractual maturity were as follows (in thousands): Amortized Fair Cost Value Due in one year or less $ 53,113 $ 53,120 Due in one year to three years — — Total $ 53,113 $ 53,120

BINIMETINIB AND ENCORAFENIB A25

BINIMETINIB AND ENCORAFENIB AGREEMENTS (Tables)	12 Months Ended
	Jun. 30, 2016
Termination and Asset Transfer Agreement [Abstract]
Schedule of net gain	We recorded the following amounts in the third quarter of fiscal 2015, resulting in a net gain on the Binimetinib and Encorafenib Agreements as follows (in thousands): Cash received from the termination of the binimetinib License Agreement with Novartis $ 85,000 Net cost of third party agreement to complete the Novartis transactions (25,000 ) Extinguishment of co-development obligation due to Novartis (net of a $6.7 million accounts receivable balance) 21,610 Reimbursement of certain transaction costs 5,000 Subtotal 86,610 Less: Deferred revenue related to ongoing obligations (6,600 ) Gain on the Binimetinib and Encorafenib Agreements, net $ 80,010

SALE OF CMC ASSETS (Tables)

SALE OF CMC ASSETS (Tables)	12 Months Ended
	Jun. 30, 2016
Discontinued Operations and Disposal Groups [Abstract]
Calculation of Gain on Sale	The following sets forth the calculation of the gain on sale as of the closing (in thousands): Non-contingent cash consideration received $ 3,750 Fixed assets or related lease costs sold or written off (1,818 ) Fair value of stock options issued to retained CMC employees (278 ) Other extinguished employee liabilities 276 Estimated transaction costs (342 ) Deferred revenue associated with undelivered elements 144 Other (91 ) Gain on sale of CMC, net $ 1,641

COLLABORATION AND OTHER AGREE27

COLLABORATION AND OTHER AGREEMENTS (Tables)	12 Months Ended
	Jun. 30, 2016
Collaboration and Other Agreements [Abstract]
Schedule of total revenue	The following table summarizes our total revenues for the periods indicated (in thousands): Year Ended June 30, 2016 2015 2014 Novartis (1) $ 110,930 $ 8,220 $ 12,053 Loxo Oncology 12,635 9,223 9,708 Pierre Fabre 3,724 — — Mirati 3,557 1,200 — Celgene 3,126 4,132 3,742 Biogen Idec 2,816 4,593 282 Asahi Kasei 600 — — Cascadian Therapeutics (previously known as Oncothyreon Inc.) 183 21,955 3,464 AstraZeneca, PLC (2) 152 73 5,104 Genentech 24 367 3,568 Other partners 132 2,146 4,157 Total revenue $ 137,879 $ 51,909 $ 42,078 (1) Includes $107.3 million and $7.0 million of reimbursement revenue consisting of FTE and out-of-pocket costs that are reimbursable by Novartis under the Binimetinib and Encorafenib Agreements during the years ended June 30, 2016 and 2015, respectively. All other prior year amounts represent the amortization of the up-front and milestone payments under the April 2010 License Agreement with Novartis that was terminated on the Effective Date of the Binimetinib and Encorafenib Agreements in March 2015. (2) 2014 includes a $5.0 million milestone from AstraZeneca for the start of a Phase 3 clinical study.

PROPERTY AND EQUIPMENT, NET (Ta

PROPERTY AND EQUIPMENT, NET (Tables)	12 Months Ended
	Jun. 30, 2016
Property, Plant and Equipment [Abstract]
Schedule of property and equipment, net	Depreciation and amortization are computed on the straight-line method based on the following estimated useful lives: Furniture and fixtures 7 years Equipment 5 years Computer hardware and software 3 years Property and equipment, net consists of the following (in thousands): June 30, 2016 2015 Furniture and fixtures $ 2,647 $ 2,647 Equipment 26,120 26,120 Computer hardware and software 15,953 14,336 Leasehold improvements 15,577 15,335 Property and equipment, gross 60,297 58,438 Less: accumulated depreciation and amortization (53,617 ) (53,388 ) Property and equipment, net $ 6,680 $ 5,050

LONG-TERM DEBT (Tables)

LONG-TERM DEBT (Tables)	12 Months Ended
	Jun. 30, 2016
Debt Disclosure [Abstract]
Schedule of long-term debt	Long-term debt consists of the following (in thousands): June 30, 2016 2015 Comerica term loan $ 14,550 $ 14,550 Convertible senior notes 132,250 132,250 Long-term debt, gross 146,800 146,800 Less: Unamortized debt discount and fees (33,145 ) (39,520 ) Long-term debt, net $ 113,655 $ 107,280
Schedule of interest expense	The following table shows the details of our interest expense for all of our debt arrangements outstanding during the periods presented, including contractual interest, and amortization of debt discount, debt issuance costs and loan transaction fees that were charged to interest expense (in thousands): Year Ended June 30, 2016 2015 2014 Comerica Term Loan Simple interest $ 501 $ 480 $ 479 Amortization of fees paid for letters of credit 31 44 48 Total interest expense on the Comerica term loan 532 524 527 Convertible Senior Notes Contractual interest 3,967 3,968 3,979 Amortization of debt discount 6,033 5,447 4,932 Amortization of debt issuance costs 342 308 278 Total interest expense on the convertible senior notes 10,342 9,723 9,189 Total interest expense $ 10,874 $ 10,247 $ 9,716
Schedule of principal payments required for long-term debt	We are required to make principal payments for our long-term debt as follows during the fiscal years ending June 30 (in thousands): Principal Due 2017 $ — 2018 14,550 2019 — 2020 132,250 2021 — Thereafter — $ 146,800

COMMITMENTS AND CONTINGENCIES (

COMMITMENTS AND CONTINGENCIES (Tables)	12 Months Ended
	Jun. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
Schedule of future minimum rental commitments	Future minimum rental commitments for our operating leases, by fiscal year and in the aggregate, as of June 30, 2016 , are (in thousands): Rental Payments 2017 $ 3,750 2018 3,540 2019 3,539 2020 3,581 2021 3,651 Thereafter 14,347 $ 32,408
Schedule of rent expense	Our facilities rent expense was as follows (dollars in thousands): Year Ended June 30, 2016 2015 2014 Cash paid for rent $ 4,785 $ 8,276 $ 8,878 Deferred rent credits (1,270 ) (3,236 ) (3,645 ) Rent expense, net $ 3,515 $ 5,040 $ 5,233

STOCKHOLDERS' EQUITY (DEFICIT)

STOCKHOLDERS' EQUITY (DEFICIT) (Tables)	12 Months Ended
	Jun. 30, 2016
Equity [Abstract]
Schedule of sale of stock	The following table summarizes our total sales under the Sales Agreement for the periods indicated (in thousands, except per share amounts): Year Ended June 30, 2016 2015 Total shares of common stock sold 566 8,965 Average price per share $ 5.28 $ 5.30 Gross proceeds $ 2,992 $ 47,500 Commissions earned by Cantor and other costs $ 100 $ 956

SHARE-BASED COMPENSATION (Table

SHARE-BASED COMPENSATION (Tables)	12 Months Ended
	Jun. 30, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Schedule of share-based compensation	Share-based compensation for the year ending June 30, 2016 , 2015 and 2014 consisted of: Year Ended June 30, 2016 2015 2014 Awards issued to employees $ 7,283 $ 7,513 $ 4,331 Options issued to transitioned CMC employees, net of other CMC share-based compensation amounts — 251 — Other non-employee awards — 296 — Total share-based compensation expense $ 7,283 $ 8,060 $ 4,331
Schedule of fair value assumptions	The fair values of our employee option awards were estimated using the assumptions below, which yielded the following weighted average grant date fair values for the periods presented: Year Ended June 30, 2016 2015 2014 Risk-free interest rate 1.30% - 1.83% 1.5% - 2.1% 1.7% - 2.1% Expected option term in years 5.5 - 6.25 6.25 6.25 Expected volatility 55.7% - 60.1% 60.8% - 67.1% 67.8% - 68.9% Dividend yield 0% 0% 0% Weighted average grant date fair value $1.95 $3.86 $2.91 The fair values of our non-employee option awards were estimated using the assumptions below, which yielded the following weighted average grant date fair value for the period presented: Year Ended June 30, 2015 Risk-free interest rate 0.4% - 0.6% Expected option term in years 1.25 - 2.00 Expected volatility 58.9% - 61.2% Dividend yield 0% Weighted average grant date fair value $2.16
Summary of stock option activity	The following table summarizes our stock option activity under the Option and Incentive Plan for the year ended June 30, 2016 : Number of Options Weighted Average Exercise Price Weighted Average Remaining Contractual Term (in years) Aggregate Intrinsic Value (in thousands) Outstanding at June 30, 2015 10,750,863 $ 5.30 Granted 3,275,669 $ 3.69 Exercised (419,179 ) $ 3.43 Forfeited (1,245,008 ) $ 6.08 Expired or canceled (714,750 ) $ 5.82 Outstanding balance at June 30, 2016 11,647,595 $ 4.80 7.5 $ 1,777 Vested and expected to vest at June 30, 2016 9,816,010 $ 4.83 7.2 $ 1,310 Exercisable at June 30, 2016 5,627,819 $ 4.88 5.9 $ 521
Summary of status of non-vested shares of RSUs	A summary of the status of our non-vested RSUs as of June 30, 2016 and changes during the year ended June 30, 2016 , is presented below: Number of RSUs Weighted Unvested at June 30, 2015 678,247 $ 5.35 Granted 329,597 $ 3.31 Vested (160,828 ) $ 5.12 Forfeited (14,916 ) $ 7.30 Unvested at June 30, 2016 832,100 $ 4.55

INCOME TAXES (Tables)

INCOME TAXES (Tables)	12 Months Ended
	Jun. 30, 2016
Income Tax Disclosure [Abstract]
Schedule of reconciliation of income taxes at the statutory federal income tax rate to net income taxes	A reconciliation of income taxes at the statutory federal income tax rate to net income taxes included in the accompanying statements of operations and comprehensive income (loss) is set forth in the following table: Year Ended June 30, 2016 2015 2014 U.S. federal income tax expense at the statutory rate 34.0 % 34.0 % 34.0 % Change in valuation allowance (53.4 ) 110.2 (37.5 ) Change in tax contingency reserve (releases) (5.7 ) 38.4 (0.3 ) State income taxes, net of federal taxes 2.1 11.1 3.1 Stock-based compensation (1.1 ) 10.5 (1.2 ) Available research and experimentation tax credits 5.0 (29.6 ) 2.0 Orphan drug credit 19.3 (176.0 ) — Rate change — 1.0 — Effect of other permanent differences — 0.4 (0.1 ) Other (0.2 ) — — Total 0.0 % 0.0 % 0.0 %
Schedule of deferred tax assets and liabilities	The components of our deferred tax assets and liabilities are (in thousands): June 30, 2016 2015 Deferred tax assets Accrued benefits $ 2,568 $ 2,030 Inventory reserve 1,514 1,514 Net operating loss carryforwards 201,571 178,120 Capital loss carryforwards — 61 Research and experimentation credit carryforwards 33,834 31,004 Orphan drug credit carryforwards 45,420 21,838 Third party agreement payment 8,452 9,070 Deferred revenue 670 3,818 Deferred rent 1,772 1,707 Stock compensation 4,499 3,375 Depreciation of property and equipment 4,112 4,519 Loan costs on convertible senior notes 278 371 Other 35 12 Total deferred tax assets 304,725 257,439 Deferred tax liabilities Discount on convertible senior notes (11,639 ) (13,877 ) Unrealized gain (loss) on marketable securities (3 ) (2 ) Total deferred tax liabilities (11,642 ) (13,879 ) Less valuation allowance (293,083 ) (243,560 ) Net deferred tax assets $ — $ —
Schedule of unrecognized tax benefits	The total amount of unrecognized tax benefits as of and for the years ended June 30, 2016 , 2015 , and 2014 are (in thousands): Year Ended June 30, 2016 2015 2014 Balance at beginning of year $ 7,311 $ 3,676 $ 3,428 Additions based on tax positions related to the current year 5,071 3,551 712 Additions for tax positions of prior year 1,323 559 — Reductions for tax positions of prior year (544 ) (475 ) (464 ) Balance at end of year $ 13,161 $ 7,311 $ 3,676

NET EARNINGS (LOSS) PER SHARE (

NET EARNINGS (LOSS) PER SHARE (Tables)	12 Months Ended
	Jun. 30, 2016
Earnings Per Share [Abstract]
Computation of earnings per share	The following table sets forth the computation of earnings per share (amounts in thousands except per share data): Year Ended June 30, 2016 2015 2014 Net earnings (loss) - basic and diluted $ (92,840 ) $ 9,369 $ (85,257 ) Weighted average shares outstanding - basic 142,964 136,679 123,403 Warrants — 3,560 — Stock options — 1,300 — RSUs — 153 — Weighted average shares outstanding - diluted 142,964 141,692 123,403 Per share data: Basic $ (0.65 ) $ 0.07 $ (0.69 ) Diluted $ (0.65 ) $ 0.07 $ (0.69 )
Anti-dilutive common stock equivalents	Common stock equivalents (measured at the end of each fiscal period) that are not included in the calculations of diluted earnings (loss) per share because to do so would have been anti-dilutive, include the following (amounts in thousands): Year Ended June 30, 2016 2015 2014 Convertible senior notes 18,762 18,762 18,762 Warrants — — 12,000 Stock options 11,648 7,332 6,922 RSUs 832 275 — Total anti-dilutive common stock equivalents excluded from diluted loss per share calculation 31,242 26,369 37,684

SELECTED QUARTERLY FINANCIAL 35

SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED) (Tables)	12 Months Ended
	Jun. 30, 2016
Quarterly Financial Information Disclosure [Abstract]
Schedule of unaudited quarterly operating results	The tables below summarize our unaudited quarterly operating results for the fiscal years ended June 30, 2016 and 2015 (dollars in thousands, except per share data): Fiscal Year Ended June 30, 2016 First Quarter Second Quarter Third Quarter Fourth Quarter Revenue $ 16,197 $ 35,430 $ 43,047 $ 43,205 Research and development for proprietary programs $ 20,998 $ 41,351 $ 48,802 $ 49,504 Total operating expenses $ 34,568 $ 56,952 $ 63,055 $ 65,513 Net loss $ (20,987 ) $ (24,164 ) $ (22,675 ) $ (25,014 ) Net earnings (loss) per share – basic $ (0.15 ) $ (0.17 ) $ (0.16 ) $ (0.17 ) Net earnings (loss) per share – diluted $ (0.15 ) $ (0.17 ) $ (0.16 ) $ (0.17 ) Weighted average shares outstanding – basic 142,216 142,833 143,338 143,475 Weighted average shares outstanding – diluted 142,216 142,833 143,338 143,475 Fiscal Year Ended June 30, 2015 First Quarter Second Quarter Third Quarter Fourth Quarter Revenue $ 6,069 $ 26,919 $ 6,601 $ 12,320 Research and development for proprietary programs $ 12,190 $ 11,817 $ 11,817 $ 18,618 Total operating expenses $ 31,166 $ 32,993 $ 32,144 $ 33,964 Net income (loss) $ (27,593 ) $ (8,611 ) $ 58,307 $ (12,734 ) Net earnings (loss) per share – basic $ (0.21 ) $ (0.06 ) $ 0.42 $ (0.09 ) Net earnings (loss) per share – diluted $ (0.21 ) $ (0.06 ) $ 0.37 $ (0.09 ) Weighted average shares outstanding – basic 131,826 133,815 139,769 141,393 Weighted average shares outstanding – diluted 131,826 133,815 166,265 141,393

OVERVIEW, BASIS OF PRESENTATI36

OVERVIEW, BASIS OF PRESENTATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Additional Information) (Details) shares in Millions	Mar. 02, 2015USD ($)	Jun. 30, 2016USD ($)	Mar. 31, 2016USD ($)	Dec. 31, 2015USD ($)	Sep. 30, 2015USD ($)	Jun. 30, 2015USD ($)	Mar. 31, 2015USD ($)	Dec. 31, 2014USD ($)	Sep. 30, 2014USD ($)	Jun. 30, 2016USD ($)segment	Jun. 30, 2015USD ($)shares	Jun. 30, 2014USD ($)	Aug. 31, 2014shares	Jul. 31, 2013USD ($)	Jun. 30, 2013USD ($)	Jun. 10, 2013
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Balance, outstanding warrants		$ (37,932,000)				$ 42,653,000				$ (37,932,000)	$ 42,653,000	$ (25,721,000)			$ (21,909,000)
Accumulated deficit		(801,407,000)				(708,567,000)				(801,407,000)	(708,567,000)
Net income (loss)		(25,014,000)	$ (22,675,000)	$ (24,164,000)	$ (20,987,000)	(12,734,000)	$ 58,307,000	$ (8,611,000)	$ (27,593,000)	(92,840,000)	9,369,000	(85,257,000)
Long-term debt, gross		146,800,000				146,800,000				146,800,000	146,800,000
Extinguishment of co-development liabilities										$ 0	21,610,000	0
Net cost of third party agreement to complete the Novartis transactions							25,000,000
Number of reportable segments | segment										1
Line of credit [Member] | Term loan [Member] | Comerica Loan and Security Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Amount of cash, cash equivalents and marketable securities that must be maintained at Comerica and approved outside accounts, or an amount equal to the entire outstanding debt balance with Comerica must be maintained at Comerica		22,000,000								$ 22,000,000
Long-term debt, gross		14,550,000				14,550,000				14,550,000	14,550,000
Senior Notes [Member] | Convertible Senior Notes, due 2020 [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Long-term debt, gross		$ 132,250,000				132,250,000				$ 132,250,000	132,250,000
Stated interest rate		3.00%								3.00%						3.00%
Loxo Oncology [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Deferred revenue		$ 4,000,000				900,000				$ 4,000,000	$ 900,000
Loxo Oncology [Member] | Common Stock [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Estimated fair value of shares														$ 4,500,000
Conversion, number of shares received (in shares) | shares													1.6
Number of shares sold (in shares) | shares											1.6
Proceeds from sale of investment											$ 20,800,000
Gain (loss) on sale of investment											16,300,000
VentiRx Pharmaceuticals Inc [Member] | Preferred Stock [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Investment in preferred stock		1,500,000				1,500,000				1,500,000	1,500,000
Novartis [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Cash received from the termination of the binimetinib License Agreement with Novartis	$ 85,000,000						85,000,000
Reimbursement of certain transaction costs							5,000,000
Extinguishment of co-development liabilities	21,600,000						21,610,000
Up-front payment	6,600,000						6,600,000
Net cost of third party agreement to complete the Novartis transactions							25,000,000
Deferred revenue		1,800,000				5,400,000				$ 1,800,000	5,400,000
Accounts receivable	6,700,000						$ 6,700,000
Co-development liability	$ 28,300,000					0					$ 0
Novartis [Member] | Customer Concentration Risk [Member] | Accounts Receivable [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Concentration risk percentage										85.00%	95.00%
Additional Paid-in Capital [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Balance, outstanding warrants		763,324,000				751,073,000				$ 763,324,000	$ 751,073,000	692,081,000			610,655,000
Reclassification adjustment [Member] | Additional Paid-in Capital [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Balance, outstanding warrants		39,400,000				39,400,000				39,400,000	39,400,000	39,400,000			39,400,000
Reclassification adjustment [Member] | Warrants [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Balance, outstanding warrants		$ (39,400,000)				$ (39,400,000)				$ (39,400,000)	$ (39,400,000)	$ (39,400,000)			$ (39,400,000)

OVERVIEW, BASIS OF PRESENTATI37

OVERVIEW, BASIS OF PRESENTATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Estimated Useful Lives of Property and Equipment) (Details)	12 Months Ended
	Jun. 30, 2016
Furniture and fixtures [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives	7 years
Equipment [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives	5 years
Computer hardware and software [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives	3 years

OVERVIEW, BASIS OF PRESENTATI38

OVERVIEW, BASIS OF PRESENTATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Schedule of Concentration of Revenue) (Details) - Sales [Member] - Customer Concentration Risk [Member]	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Concentration Risk [Line Items]
Concentration risk percentage	89.90%	76.00%	72.00%
Novartis [Member]
Concentration Risk [Line Items]
Concentration risk percentage	80.50%	15.80%	28.60%
Loxo Oncology [Member]
Concentration Risk [Line Items]
Concentration risk percentage	9.20%	17.80%	23.10%
Cascadian Therapeutics (previously known as Oncothyreon Inc.) [Member]
Concentration Risk [Line Items]
Concentration risk percentage	0.10%	42.30%	8.20%
AstraZeneca, PLC [Member]
Concentration Risk [Line Items]
Concentration risk percentage	0.10%	0.10%	12.10%

OVERVIEW, BASIS OF PRESENTATI39

OVERVIEW, BASIS OF PRESENTATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Schedule of Revenue by Geographic Area) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2014	Sep. 30, 2014	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Concentration Risk [Line Items]
Total revenue	$ 43,205	$ 43,047	$ 35,430	$ 16,197	$ 12,320	$ 6,601	$ 26,919	$ 6,069	$ 137,879	$ 51,909	$ 42,078
North America [Member]
Concentration Risk [Line Items]
Total revenue									22,474	43,386	24,757
Europe [Member]
Concentration Risk [Line Items]
Total revenue									114,806	8,293	17,153
Asia Pacific [Member]
Concentration Risk [Line Items]
Total revenue									$ 599	$ 230	$ 168

MARKETABLE SECURITIES (Schedule

MARKETABLE SECURITIES (Schedule of Marketable Securities) (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Jun. 30, 2015
Marketable securities
Amortized Cost	$ 53,933	$ 123,126
Gross Unrealized Gains	8	8
Gross Unrealized Losses	(1)	(3)
Fair Value	53,940	123,131
Short-term investments [Member]
Marketable securities
Amortized Cost	53,337	122,630
Gross Unrealized Gains	8	8
Gross Unrealized Losses	(1)	(3)
Fair Value	53,344	122,635
Short-term investments [Member] | U.S. treasury securities [Member]
Marketable securities
Amortized Cost	53,113	122,199
Gross Unrealized Gains	8	8
Gross Unrealized Losses	(1)	(3)
Fair Value	53,120	122,204
Short-term investments [Member] | Mutual fund securities [Member]
Marketable securities
Amortized Cost	224	431
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	224	431
Long-term investments [Member]
Marketable securities
Amortized Cost	596	496
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	596	496
Long-term investments [Member] | Mutual fund securities [Member]
Marketable securities
Amortized Cost	596	496
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	$ 596	$ 496

MARKETABLE SECURITIES (Schedu41

MARKETABLE SECURITIES (Schedule of Fair Value Measurement Categories) (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Jun. 30, 2015
Fair value measurement categories
Fair value	$ 53,940	$ 123,131
Fair Value, Measurements, Recurring [Member]
Fair value measurement categories
Fair value	53,940	123,131
Fair Value, Measurements, Recurring [Member] | Quoted prices in active markets for identical assets (Level 1) [Member]
Fair value measurement categories
Fair value	53,940	123,131
Fair Value, Measurements, Recurring [Member] | Quoted prices for similar assets observable in the marketplace (Level 2) [Member]
Fair value measurement categories
Fair value	0	0
Fair Value, Measurements, Recurring [Member] | Significant unobservable inputs (Level 3) [Member]
Fair value measurement categories
Fair value	$ 0	$ 0

MARKETABLE SECURITIES (Roll For

MARKETABLE SECURITIES (Roll Forward of Fair Value of Investment in Level 3 Equity Securities) (Details) - Equity Securities [Member] $ in Thousands	12 Months Ended
	Jun. 30, 2015USD ($)
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Balance, beginning of period	$ 0
Transfer into Level 3 due to restriction period on trading	4,500
Change in unrealized gains and losses included in comprehensive income (loss)	13,205
Transfer out of Level 3 due to elimination of trading restrictions	(17,705)
Balance, end of period	$ 0

MARKETABLE SECURITIES (Schedu43

MARKETABLE SECURITIES (Schedule of Amortized Cost and Estimated Fair Value) (Details) $ in Thousands	Jun. 30, 2016USD ($)
Amortized Cost
Due in one year or less	$ 53,113
Due in one year to three years	0
Total	53,113
Fair Value
Due in one year or less	53,120
Due in one year to three years	0
Total	$ 53,120

BINIMETINIB AND ENCORAFENIB A44

BINIMETINIB AND ENCORAFENIB AGREEMENTS (Schedule of Net Gain) (Details) - USD ($) $ in Thousands	Mar. 02, 2015	Mar. 31, 2015	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Accounts, Notes, Loans and Financing Receivable [Line Items]
Net cost of third party agreement to complete the Novartis transactions		$ (25,000)
Extinguishment of co-development obligation due to Novartis (net of a $6.7 million accounts receivable balance)			$ 0	$ 21,610	$ 0
Gain on the Binimetinib and Encorafenib Agreements, net			$ 0	$ 80,010	$ 0
Novartis [Member]
Accounts, Notes, Loans and Financing Receivable [Line Items]
Cash received from the termination of the binimetinib License Agreement with Novartis	$ 85,000	85,000
Net cost of third party agreement to complete the Novartis transactions		(25,000)
Extinguishment of co-development obligation due to Novartis (net of a $6.7 million accounts receivable balance)	21,600	21,610
Reimbursement of certain transaction costs		5,000
Subtotal		86,610
Less: Deferred revenue related to ongoing obligations	(6,600)	(6,600)
Gain on the Binimetinib and Encorafenib Agreements, net		80,010
Accounts receivable	$ 6,700	$ 6,700

SALE OF CMC ASSETS (Additional

SALE OF CMC ASSETS (Additional Information) (Details) $ / shares in Units, $ in Thousands	Jun. 01, 2015USD ($)employee$ / sharesshares	Jun. 30, 2015USD ($)	Jun. 30, 2016USD ($)$ / sharesshares	Jun. 30, 2015USD ($)	Jun. 30, 2014USD ($)
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Cash purchase price			$ 0	$ 3,750	$ 0
Options granted (in shares) | shares			3,275,669
Exercise price (in dollars per share) | $ / shares			$ 3.69
Gain on sale of CMC, net			$ 0	$ 1,641	$ 0
Disposal Group, Disposed Of By Sale, Not Discontinued Operations [Member] | Chemistry, Manufacturing and Controls Activities [Member]
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Number of employees retained by acquiror after sale | employee	33
Cash purchase price	$ 3,750	$ 3,750
Options granted (in shares) | shares	133,209
Vesting period	1 year
Expiration term	90 days
Exercise price (in dollars per share) | $ / shares	$ 7.74
Fair value of stock options issued to retained CMC employees	$ 278	278
Strike price (in dollars per share) | $ / shares	$ 7.74
Volatility	61.20%
Risk-free interest rate	0.40%
Effective life	1 year 3 months
Dividend yield	0.00%
Gain on sale of CMC, net		$ 1,641
Disposal Group, Disposed Of By Sale, Not Discontinued Operations [Member] | Chemistry, Manufacturing and Controls Activities [Member] | Guarantee of Business Revenue [Member]
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Minimum purchase guarantee	$ 7,000
Minimum purchase guarantee, term	24 months
Prepaid asset			2,900
Remaining obligation - expected payments during fiscal year 2017			$ 1,900

BINIMETINIB AND ENCORAFENIB A46

BINIMETINIB AND ENCORAFENIB AGREEMENTS (Additional Information) (Details) $ in Thousands	Mar. 02, 2015USD ($)	Dec. 31, 2015EUR (€)	Mar. 31, 2015USD ($)
Novartis [Member]
Accounts, Notes, Loans and Financing Receivable [Line Items]
Asset transfer agreement, cash received | $	$ 85,000		$ 85,000
Percentage reimbursement of FTE costs	50.00%
Supply obligations from closing, maximum period	30 months
Pierre Fabre [Member]
Accounts, Notes, Loans and Financing Receivable [Line Items]
Cost sharing percentage		60.00%
Cost sharing percentage, collaboration partner		40.00%
Combined amount committed | €		€ 100,000,000

SALE OF CMC ASSETS (Calculation

SALE OF CMC ASSETS (Calculation of Gain on Sale) (Details) - USD ($) $ in Thousands	Jun. 01, 2015	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Non-contingent cash consideration received			$ 0	$ 3,750	$ 0
Gain on sale of CMC, net			$ 0	$ 1,641	$ 0
Disposal Group, Disposed Of By Sale, Not Discontinued Operations [Member] | Chemistry, Manufacturing and Controls Activities [Member]
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Non-contingent cash consideration received	$ 3,750	$ 3,750
Fixed assets or related lease costs sold or written off		(1,818)
Fair value of stock options issued to retained CMC employees	$ (278)	(278)
Other extinguished employee liabilities		276
Estimated transaction costs		(342)
Deferred revenue associated with undelivered elements		144
Other		(91)
Gain on sale of CMC, net		$ 1,641

COLLABORATION AND OTHER AGREE48

COLLABORATION AND OTHER AGREEMENTS (Schedule Of Total Revenue) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2014	Sep. 30, 2014	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue	$ 43,205	$ 43,047	$ 35,430	$ 16,197	$ 12,320	$ 6,601	$ 26,919	$ 6,069	$ 137,879	$ 51,909	$ 42,078
Reimbursement revenue									107,330	7,020	0
Novartis [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue									110,930	8,220	12,053
Reimbursement revenue									107,300	7,000
Loxo Oncology [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue									12,635	9,223	9,708
Pierre Fabre [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue									3,724	0	0
Mirati [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue									3,557	1,200	0
Celgene [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue									3,126	4,132	3,742
Biogen Idec [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue									2,816	4,593	282
Asahi Kasei [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue									600	0	0
Cascadian Therapeutics (previously known as Oncothyreon Inc.) [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue									183	21,955	3,464
AstraZeneca, PLC [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue									152	73	5,104
Milestone revenue											5,000
Genentech [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue									24	367	3,568
Other partners [Member]
Collaborative Arrangements and Non-collaborative Arrangements [Line Items]
Revenue									$ 132	$ 2,146	$ 4,157

COLLABORATION AND OTHER AGREE49

COLLABORATION AND OTHER AGREEMENTS (Additional Information) (Details)	Mar. 02, 2015USD ($)	Dec. 11, 2014USD ($)	Apr. 30, 2016USD ($)milestone	Dec. 31, 2015EUR (€)milestoneindication	Sep. 30, 2015USD ($)	Dec. 31, 2014USD ($)	Oct. 31, 2014USD ($)	May 31, 2014Deliverable	Jul. 31, 2013USD ($)DeliverableRenewal	Aug. 31, 2011USD ($)drugDeliverable	Dec. 31, 2003USD ($)drug_trialdrugmilestone	Jun. 30, 2016USD ($)	Mar. 31, 2016USD ($)drugmilestone	Dec. 31, 2015USD ($)	Sep. 30, 2015USD ($)	Jun. 30, 2015USD ($)	Mar. 31, 2015USD ($)	Dec. 31, 2014USD ($)	Sep. 30, 2014USD ($)	Dec. 31, 2013USD ($)	Sep. 30, 2013USD ($)	Dec. 31, 2012USD ($)	Sep. 30, 2011USD ($)	Jun. 30, 2016USD ($)	Jun. 30, 2015USD ($)	Jun. 30, 2014USD ($)	Mar. 31, 2012	Jun. 30, 2016USD ($)	Dec. 31, 2015USD ($)milestoneindication
Collaboration and License Agreements, by Type [Line Items]
Revenue												$ 43,205,000	$ 43,047,000	$ 35,430,000	$ 16,197,000	$ 12,320,000	$ 6,601,000	$ 26,919,000	$ 6,069,000					$ 137,879,000	$ 51,909,000	$ 42,078,000
License and milestone revenue																								3,876,000	20,367,000	25,111,000
Novartis [Member]
Collaboration and License Agreements, by Type [Line Items]
Up-front and milestone payments received, cumulative																					$ 60,000,000
Percentage of reimbursement of development costs by collaborator during first two years																											100.00%
Co-development payment issued to partner																				$ 11,300,000		$ 9,200,000
Co-development liability	$ 28,300,000															0									0
Share of combined development costs																									13,100,000	18,900,000
Reimbursement receivable	6,700,000
Deferred revenue												1,800,000				$ 5,400,000								1,800,000	5,400,000			$ 1,800,000
Up-front payment	$ 6,600,000																$ 6,600,000
Revenue																								110,930,000	$ 8,220,000	$ 12,053,000
Loxo Oncology [Member]
Collaboration and License Agreements, by Type [Line Items]
Discovery program term									3 years
Number of agreement extensions | Renewal									1
Discovery program renewal term									1 year
Cost method investment, ownership percentage									19.90%																	15.30%
Common stock investment, ownership percentage																0.00%									0.00%
Potential additional milestone payment									$ 434,000,000
Number of non-contingent deliverables | Deliverable									3
License revenue																					4,500,000
Deferred revenue												4,000,000				$ 900,000								4,000,000	$ 900,000			4,000,000
Termination notice period									6 months
Revenue																								12,635,000	9,223,000	$ 9,708,000
Pierre Fabre [Member]
Collaboration and License Agreements, by Type [Line Items]
Deferred revenue												28,400,000												28,400,000				28,400,000
Cost sharing percentage				60.00%
Cost sharing percentage, collaboration partner				40.00%
Combined amount committed | €				€ 100,000,000
Up-front payment																								30,000,000
Deferred revenue, recognition period				10 years
Up-front and milestone payments earned																								1,600,000
Collaboration revenue																								2,100,000
Revenue																								3,724,000	0	0
Pierre Fabre [Member] | Regulatory milestone [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment																													$ 35,000,000
Number of milestones | milestone				3																									3
Number of specified indications | indication				3																									3
Pierre Fabre [Member] | Commercialization milestone [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment																													$ 390,000,000
Number of milestones | milestone				7																									7
Mirati [Member]
Collaboration and License Agreements, by Type [Line Items]
Deferred revenue												3,200,000												3,200,000				3,200,000
Up-front payment							$ 1,600,000
Deferred revenue, recognition period			3 years		6 months		12 months
Option extension term					6 months
Option extension fee			$ 2,500,000		$ 750,000
Revenue																								3,557,000	1,200,000	0
Mirati [Member] | Commercialization milestone [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment			$ 337,000,000
Number of milestones | milestone			7
Mirati [Member] | Developmental milestone [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment			$ 9,300,000
Number of milestones | milestone			4
Celgene [Member]
Collaboration and License Agreements, by Type [Line Items]
Deferred revenue												0				3,100,000								0	3,100,000			0
Up-front payment																					$ 11,000,000
Deferred revenue, recognition period									3 years								3 years	2 years
Revenue																								3,126,000	4,132,000	3,742,000
Biogen Idec [Member]
Collaboration and License Agreements, by Type [Line Items]
Discovery program term								3 years
Discovery program renewal term								12 months
Number of non-contingent deliverables | Deliverable								2
Deferred revenue												0				$ 1,100,000								0	1,100,000			0
Revenue																								2,816,000	4,593,000	282,000
Asahi Kasei [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment													63,500,000
Deferred revenue												11,400,000												11,400,000				11,400,000
Up-front payment			$ 12,000,000
Deferred revenue, recognition period			5 years
Revenue																								600,000	0	0
Asahi Kasei [Member] | Regulatory milestone [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment													$ 11,000,000
Number of milestones | milestone													4
Number of drug candidates | drug													5
Asahi Kasei [Member] | Commercialization milestone [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment													$ 52,500,000
Number of milestones | milestone													3
Cascadian Therapeutics (previously known as Oncothyreon Inc.) [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment		$ 280,000,000
Termination notice period		180 days
Up-front payment		$ 20,000,000
Revenue																								183,000	21,955,000	3,464,000
Term from effective date, during which counterparty is acquired		3 years
License and milestone revenue						$ 20,000,000
Term of agreement		10 years
AstraZeneca, PLC [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment											$ 70,000,000
Up-front and milestone payments earned																												26,500,000
Revenue																								152,000	$ 73,000	$ 5,104,000
Number of drug trials | drug_trial											2
AstraZeneca, PLC [Member] | Selumetinib Drug [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment											$ 30,000,000
AstraZeneca, PLC [Member] | Commercialization milestone [Member] | Selumetinib Drug [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment											$ 34,000,000
Number of milestones | milestone											3
AstraZeneca, PLC [Member] | Developmental milestone [Member] | Selumetinib Drug [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment											$ 36,000,000
Number of milestones | milestone											9
Genentech 2003 Collaboration Agreement [Member]
Collaboration and License Agreements, by Type [Line Items]
Up-front and milestone payments received, cumulative												$ 23,500,000												$ 23,500,000				$ 23,500,000
Potential additional milestone payment											$ 23,000,000
Termination notice period											4 months
Number of drugs | drug											2
Genentech Chk-1 Agreement [Member]
Collaboration and License Agreements, by Type [Line Items]
Potential additional milestone payment										$ 380,000,000
Number of non-contingent deliverables | Deliverable										3
License revenue																	$ 99,000
Termination notice period										60 days
Up-front payment																							$ 28,000,000
Number of drugs | drug										2

PROPERTY AND EQUIPMENT, NET (De

PROPERTY AND EQUIPMENT, NET (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Jun. 30, 2015
Property and equipment, net:
Property and equipment, gross	$ 60,297	$ 58,438
Less: accumulated depreciation and amortization	(53,617)	(53,388)
Property and equipment, net	6,680	5,050
Furniture and fixtures [Member]
Property and equipment, net:
Property and equipment, gross	2,647	2,647
Equipment [Member]
Property and equipment, net:
Property and equipment, gross	26,120	26,120
Computer hardware and software [Member]
Property and equipment, net:
Property and equipment, gross	15,953	14,336
Leasehold improvements [Member]
Property and equipment, net:
Property and equipment, gross	$ 15,577	$ 15,335

LONG-TERM DEBT (Additional Info

LONG-TERM DEBT (Additional Information) (Details)	Jun. 10, 2013USD ($)trading_day$ / shares	Jun. 30, 2016USD ($)	Jun. 30, 2015USD ($)
Debt Instrument [Line Items]
Long-term debt, outstanding		$ 146,800,000	$ 146,800,000
Comerica Loan and Security Agreement [Member] | Line of credit [Member] | Comerica Bank [Member]
Debt Instrument [Line Items]
Financial ratio required to be maintained under covenant		1.25
Comerica Loan and Security Agreement [Member] | Line of credit [Member] | Term loan [Member]
Debt Instrument [Line Items]
Long-term debt, outstanding		$ 14,550,000	14,550,000
Amount of cash, cash equivalents and marketable securities that must be maintained at Comerica and approved outside accounts, or an amount equal to the entire outstanding debt balance with Comerica must be maintained at Comerica		22,000,000
Comerica Loan and Security Agreement [Member] | Line of credit [Member] | Term loan [Member] | Comerica Bank [Member]
Debt Instrument [Line Items]
Maximum borrowing capacity		15,000,000
Long-term debt, outstanding		14,600,000
Balance of cash, cash equivalents and marketable securities maintained at Comerica, if amount is greater than or equal to, interest is Scenario One		10,000,000
Balance of cash, cash equivalents and marketable securities maintained at Comerica, if amount is less than, interest is Scenario Two		$ 10,000,000
Stated interest rate		3.50%
Amount of cash, cash equivalents and marketable securities that must be maintained at Comerica and approved outside accounts, or an amount equal to the entire outstanding debt balance with Comerica must be maintained at Comerica		$ 22,000,000
Comerica Loan and Security Agreement [Member] | Line of credit [Member] | Term loan [Member] | Comerica Bank [Member] | Quoted prices for similar assets observable in the marketplace (Level 2) [Member]
Debt Instrument [Line Items]
Fair value of term loan		$ 14,600,000	14,600,000
Comerica Loan and Security Agreement [Member] | Line of credit [Member] | Term loan [Member] | Comerica Bank [Member] | Prime rate [Member]
Debt Instrument [Line Items]
Basis spread on variable interest rate (up to)		2.00%
Comerica Loan and Security Agreement [Member] | Line of credit [Member] | Revolving line of credit [Member] | Comerica Bank [Member]
Debt Instrument [Line Items]
Maximum borrowing capacity		$ 2,800,000
Long-term debt, outstanding		0
Convertible Senior Notes, due 2020 [Member] | Senior Notes [Member]
Debt Instrument [Line Items]
Long-term debt, outstanding		$ 132,250,000	132,250,000
Stated interest rate	3.00%	3.00%
Debt instrument, face amount	$ 132,300,000
Proceeds from debt issuance	$ 128,000,000
Convertible debt, conversion rate	0.1418641
Convertible debt, conversion price | $ / shares	$ 7.05
Percentage of principal amount of convertible debt required to be repurchased upon qualifying change in control or termination of trading of common stock	100.00%
Convertible debt, threshold percentage of stock price trigger	130.00%
Convertible debt, threshold trading days | trading_day	20
Convertible debt, threshold consecutive trading days	30 days
Convertible debt, threshold consecutive trading days, number of days immediately prior to redemption notice date	7 days
Convertible debt, redemption price, percentage of principal amount to be redeemed	100.00%
Effective interest rate	10.25%
Convertible debt, liability component	$ 84,200,000
Convertible debt, equity component	48,000,000
Underwriting discount and offering expenses	4,300,000
Unamortized debt issuance costs		$ 1,800,000	2,100,000
Convertible Senior Notes, due 2020 [Member] | Senior Notes [Member] | Other noncurrent assets [Member]
Debt Instrument [Line Items]
Debt issuance costs	2,700,000
Convertible Senior Notes, due 2020 [Member] | Senior Notes [Member] | Additional paid-in capital [Member]
Debt Instrument [Line Items]
Underwriting discount and offering expenses	$ 1,600,000
Convertible Senior Notes, due 2020 [Member] | Senior Notes [Member] | Quoted prices for similar assets observable in the marketplace (Level 2) [Member]
Debt Instrument [Line Items]
Fair value of notes		$ 110,200,000	$ 142,200,000
Scenario One [Member] | Comerica Loan and Security Agreement [Member] | Line of credit [Member] | Term loan [Member] | Comerica Bank [Member] | Prime rate [Member]
Debt Instrument [Line Items]
Description of variable interest rate basis		Prime Rate
Scenario Two [Member] | Comerica Loan and Security Agreement [Member] | Line of credit [Member] | Term loan [Member] | Comerica Bank [Member] | Prime rate [Member]
Debt Instrument [Line Items]
Description of variable interest rate basis		Prime Rate

LONG-TERM DEBT (Schedule of Lon

LONG-TERM DEBT (Schedule of Long-Term Debt) (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Jun. 30, 2015
Debt Instrument [Line Items]
Long-term debt, gross	$ 146,800	$ 146,800
Less: Unamortized debt discount and fees	(33,145)	(39,520)
Long-term debt, net	113,655	107,280
Senior Notes [Member] | Convertible Senior Notes, due 2020 [Member]
Debt Instrument [Line Items]
Long-term debt, gross	132,250	132,250
Term loan [Member] | Line of credit [Member] | Comerica Loan and Security Agreement [Member]
Debt Instrument [Line Items]
Long-term debt, gross	$ 14,550	$ 14,550

LONG-TERM DEBT (Summary of Inte

LONG-TERM DEBT (Summary of Interest Expense) (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Debt Instrument [Line Items]
Total interest expense	$ 10,874	$ 10,247	$ 9,716
Line of credit [Member] | Comerica Loan and Security Agreement [Member] | Term loan [Member]
Debt Instrument [Line Items]
Simple interest	501	480	479
Amortization of fees and debt issuance costs	31	44	48
Total interest expense	532	524	527
Senior Notes [Member] | Convertible Senior Notes, due 2020 [Member]
Debt Instrument [Line Items]
Simple interest	3,967	3,968	3,979
Amortization of debt discount	6,033	5,447	4,932
Amortization of fees and debt issuance costs	342	308	278
Total interest expense	$ 10,342	$ 9,723	$ 9,189

LONG-TERM DEBT (Commitment Sche

LONG-TERM DEBT (Commitment Schedule) (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Jun. 30, 2015
Debt Disclosure [Abstract]
2,017	$ 0
2,018	14,550
2,019	0
2,020	132,250
2,021	0
Thereafter	0
Long-term debt, gross	$ 146,800	$ 146,800

COMMITMENTS AND CONTINGENCIES55

COMMITMENTS AND CONTINGENCIES (Details) ft² in Thousands, $ in Thousands	12 Months Ended
	Jun. 30, 2016USD ($)ft²	Jun. 30, 2015USD ($)Term	Jun. 30, 2014USD ($)
Commitments and Contingencies Disclosure [Abstract]
Option to extend lease, number of terms | Term		2
Option to extend lease, lease term		5 years
Approximate square footage of leased real estate (in sqft) | ft²	131
Future minimum rental commitments
2,017	$ 3,750
2,018	3,540
2,019	3,539
2,020	3,581
2,021	3,651
Thereafter	14,347
Total minimum rental commitments	32,408
Rent expense
Cash paid for rent	4,785	$ 8,276	$ 8,878
Deferred rent credits	(1,270)	(3,236)	(3,645)
Rent expense, net	$ 3,515	$ 5,040	$ 5,233

STOCKHOLDERS' EQUITY (DEFICIT56

STOCKHOLDERS' EQUITY (DEFICIT) (Additional Information) (Details) - USD ($)	1 Months Ended		12 Months Ended
	Jul. 31, 2016	Aug. 31, 2015	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014	Aug. 15, 2014	Mar. 27, 2013
Controlled Equity Offering
Proceeds from the issuance of common stock			$ 2,992,000	$ 47,500,000	$ 75,000,000
Common Stock [Member]
Controlled Equity Offering
Dollar amount of stock that may be sold under the agreement		$ 75,000,000				$ 47,500,000	$ 75,000,000
Commission under sales agreement		2.00%				2.00%
Sales agreement termination notice period		10 days
Issuance of common stock, net of offering costs (in shares)			566,000	8,965,000
Proceeds from the issuance of common stock			$ 2,992,000	$ 47,500,000
Warrant Issuance One [Member]
Warrants
Number of warrants			6,000,000
Exercise price of warrants (in dollars per share)			$ 3.65
Warrant Issuance Two [Member]
Warrants
Number of warrants			6,000,000
Exercise price of warrants (in dollars per share)			$ 4.19
Warrant Exercise One [Member]
Warrants
Exercise price of warrants (in dollars per share)			$ 3.65
Number of warrants exercised (in shares)			3,996,298
Warrants exercised - cashless (in shares)			223,000
Warrant Exercise Two [Member]
Warrants
Exercise price of warrants (in dollars per share)			$ 3.65
Number of warrants exercised (in shares)			12,000
Warrants exercised for cash (in shares)			12,000
Stock Option and Incentive Plan [Member]
Stock Option and Incentive Plan
Shares of common stock reserved for future issuance under the Option and Incentive Plan			19,228,677
Additional shares authorized as a percentage of shares issued and outstanding			25.00%
Vesting period			4 years
Expiration term			10 years
Stock Option and Incentive Plan [Member] | Incentive Stock Options [Member]
Stock Option and Incentive Plan
Shares of common stock reserved for future issuance under the Option and Incentive Plan			2,282,592
Subsequent Event [Member]
Controlled Equity Offering
Issuance of common stock, net of offering costs (in shares)	1,300,000
Proceeds from the issuance of common stock	$ 4,800,000

STOCKHOLDERS' EQUITY (DEFICIT57

STOCKHOLDERS' EQUITY (DEFICIT) (Schedule of Sale of Stock) (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Class of Stock [Line Items]
Gross proceeds	$ 2,992	$ 47,500	$ 75,000
Common Stock [Member]
Class of Stock [Line Items]
Total shares of common stock sold	566	8,965
Average price per share (in dollars per share)	$ 5.28	$ 5.30
Gross proceeds	$ 2,992	$ 47,500
Commissions earned by Cantor and other costs	$ 100	$ 956

SHARE-BASED COMPENSATION (Alloc

SHARE-BASED COMPENSATION (Allocated Share-based Compensation) (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Awards issued to employees	$ 7,283	$ 7,513	$ 4,331
Total share-based compensation expense	7,283	8,060	4,331
Options issued to transitioned CMC employees, net of other CMC share-based compensation amounts [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Other non-employee awards	0	251	0
Other non-employee awards [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Other non-employee awards	$ 0	$ 296	$ 0

SHARE-BASED COMPENSATION (Fair

SHARE-BASED COMPENSATION (Fair Value Assumptions) (Details) - $ / shares	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Stock options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate, minimum	1.30%	1.50%	1.70%
Risk-free interest rate, maximum	1.83%	2.10%	2.10%
Expected option term in years		6 years 3 months	6 years 3 months
Expected volatility, minimum	55.70%	60.80%	67.80%
Expected volatility, maximum	60.10%	67.10%	68.90%
Dividend yield	0.00%	0.00%	0.00%
Weighted-average grant date fair value (in dollars per share)	$ 1.95	$ 3.86	$ 2.91
Stock options [Member] | Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected option term in years	5 years 6 months
Stock options [Member] | Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected option term in years	6 years 3 months
Non-employee stock options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate, minimum		0.40%
Risk-free interest rate, maximum		0.60%
Expected volatility, minimum		58.90%
Expected volatility, maximum		61.20%
Dividend yield		0.00%
Weighted-average grant date fair value (in dollars per share)		$ 2.16
Non-employee stock options [Member] | Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected option term in years		1 year 3 months
Non-employee stock options [Member] | Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected option term in years		2 years

SHARE-BASED COMPENSATION (Stock

SHARE-BASED COMPENSATION (Stock Option Activity) (Details) $ / shares in Units, $ in Thousands	12 Months Ended
	Jun. 30, 2016USD ($)$ / sharesshares
Number of Options [Roll Forward]
Outstanding at beginning of period (in shares) | shares	10,750,863
Granted (in shares) | shares	3,275,669
Exercised (in shares) | shares	(419,179)
Forfeited (in shares) | shares	(1,245,008)
Expired or canceled (in shares) | shares	(714,750)
Outstanding at end of period (in shares) | shares	11,647,595
Number of options, vested and expected to vest at end of period | shares	9,816,010
Number of options, exercisable at end of period | shares	5,627,819
Weighted Average Exercise Price [Roll Forward]
Outstanding at beginning of period (in dollars per share) | $ / shares	$ 5.30
Granted (in dollars per share) | $ / shares	3.69
Exercised (in dollars per share) | $ / shares	3.43
Forfeited (in dollars per share) | $ / shares	6.08
Expired or canceled (in dollars per share) | $ / shares	5.82
Outstanding at end of period (in dollars per share) | $ / shares	4.80
Weighted average exercise price, vested and expected to vest at end of period (in dollars per share) | $ / shares	4.83
Weighted average exercise price, exercisable at end of period (in dollars per share) | $ / shares	$ 4.88
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Weighted average remaining contractual term, outstanding at end of period (in years)	7 years 5 months 18 days
Weighted average remaining contractual term, vested and expected to vest at end of period (in years)	7 years 2 months 6 days
Weighted average remaining contractual term, exercisable at end of period (in years)	5 years 11 months
Aggregate intrinsic value, outstanding at end of period | $	$ 1,777
Aggregate intrinsic value, vested and expected to vest at end of period | $	1,310
Aggregate intrinsic value, exercisable at end of period | $	$ 521

SHARE-BASED COMPENSATION (Non-v

SHARE-BASED COMPENSATION (Non-vested RSUs) (Details) - RSUs [Member]	12 Months Ended
	Jun. 30, 2016$ / sharesshares
Number of RSUs {Roll Forward]
Unvested at beginning of period (in shares) | shares	678,247
Granted (in shares) | shares	329,597
Vested (in shares) | shares	(160,828)
Forfeited (in shares) | shares	(14,916)
Unvested at end of period (in shares) | shares	832,100
Weighted Average Grant Date Fair Value [Roll Forward]
Unvested at beginning of period (in dollars per share) | $ / shares	$ 5.35
Granted (in dollars per share) | $ / shares	3.31
Vested (in dollars per share) | $ / shares	5.12
Forfeited (in dollars per share) | $ / shares	7.30
Unvested at end of period (in dollars per share) | $ / shares	$ 4.55

SHARE-BASED COMPENSATION (Addit

SHARE-BASED COMPENSATION (Additional Information) (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based compensation expense	$ 7,283	$ 7,513	$ 4,331
Closing stock price (in dollars per share)	$ 3.56
Total intrinsic value of all options exercised	$ 700	$ 2,300	$ 2,000
Total unrecognized compensation expense	$ 9,500
Weighted-average period for recognition of unrecognized compensation expense (in years)	2 years 8 months 6 days
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of additional shares reserved for issuance			600,000
Shares of common stock reserved for issuance under the ESPP	5,250,000
Purchase price of common stock (as a percent)	85.00%
Original offering period (in months)	12 months
New offering period on termination of original offering period (in months)	6 months
Common shares available for issuance under ESPP (in shares)	586,104
Shares issued under ESPP (in shares)	265,179	240,366	309,287
Employee and non-employee awards [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based compensation expense	$ 7,300	$ 7,800	$ 4,300
RSUs [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total unrecognized compensation expense	$ 1,700
Weighted-average period for recognition of unrecognized compensation expense (in years)	2 years 8 months 24 days
RSUs vested, fair market value	$ 800	1,800
RSUs granted, value at grant date	$ 1,100	$ 4,900
RSUs [Member] | Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period	2 years
RSUs [Member] | Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period	4 years

EMPLOYEE BENEFIT PLAN (Details)

EMPLOYEE BENEFIT PLAN (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Compensation and Retirement Disclosure [Abstract]
Minimum percentage of salary that participants can contribute under the 401(k) plan	1.00%
Maximum percentage of salary that participants can contribute under the 401(k) plan	60.00%
Employer matching contribution, percent of employee contributions	4.00%
Employer matching contribution, vesting period	4 years
Matching contributions by company	$ 952	$ 1,100	$ 1,200

RESTRUCTURING CHARGES (Details)

RESTRUCTURING CHARGES (Details) - Reduction in workforce - Fiscal 2014 restructuring - USD ($) $ in Thousands	Aug. 05, 2013	Dec. 31, 2013	Sep. 30, 2013
Restructuring Cost and Reserve [Line Items]
Number of positions eliminated, percentage	20.00%
Restructuring charges			$ 2,800
Payments for restructuring		$ 194	2,600
Research and development
Restructuring Cost and Reserve [Line Items]
Restructuring charges			2,200
General and administrative expense
Restructuring Cost and Reserve [Line Items]
Restructuring charges			$ 602

INCOME TAXES (Schedule of Recon

INCOME TAXES (Schedule of Reconciliation of Income Taxes at the Statutory Federal Income Tax Rate to Net Income Taxes) (Details)	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Income Tax Disclosure [Abstract]
U.S. federal income tax expense at the statutory rate	34.00%	34.00%	34.00%
Change in valuation allowance	(53.40%)	110.20%	(37.50%)
Change in tax contingency reserve (releases)	(5.70%)	38.40%	(0.30%)
State income taxes, net of federal taxes	2.10%	11.10%	3.10%
Stock-based compensation	(1.10%)	10.50%	(1.20%)
Available research and experimentation tax credits	5.00%	(29.60%)	2.00%
Orphan drug credit	19.30%	(176.00%)	(0.00%)
Rate change	0.00%	1.00%	0.00%
Effect of other permanent differences	0.00%	0.40%	(0.10%)
Other	(0.20%)	0.00%	0.00%
Total	0.00%	0.00%	0.00%

INCOME TAXES (Schedule of Defer

INCOME TAXES (Schedule of Deferred Tax Assets and Liabilities) (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Jun. 30, 2015
Deferred Tax Assets, Net [Abstract]
Accrued benefits	$ 2,568	$ 2,030
Inventory reserve	1,514	1,514
Net operating loss carryforwards	201,571	178,120
Capital loss carryforwards	0	61
Research and experimentation credit carryforwards	33,834	31,004
Orphan drug credit carryforwards	45,420	21,838
Third party agreement payment	8,452	9,070
Deferred revenue	670	3,818
Deferred rent	1,772	1,707
Stock compensation	4,499	3,375
Depreciation of property and equipment	4,112	4,519
Loan costs on convertible senior notes	278	371
Other	35	12
Total deferred tax assets	304,725	257,439
Deferred tax liabilities
Discount on convertible senior notes	(11,639)	(13,877)
Unrealized gain (loss) on marketable securities	(3)	(2)
Total deferred tax liabilities	(11,642)	(13,879)
Less valuation allowance	(293,083)	(243,560)
Net deferred tax assets	$ 0	$ 0

INCOME TAXES (Unrecognized Tax

INCOME TAXES (Unrecognized Tax Benefits) (Details) - USD ($) $ in Thousands	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Unrecognized tax benefits
Balance at beginning of year	$ 7,311	$ 3,676	$ 3,428
Additions based on tax positions related to the current year	5,071	3,551	712
Additions for tax positions of prior year	1,323	559	0
Reductions for tax positions of prior year	(544)	(475)	(464)
Balance at end of year	$ 13,161	$ 7,311	$ 3,676

INCOME TAXES (Additional Inform

INCOME TAXES (Additional Information) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2014	Sep. 30, 2014	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Tax Credit Carryforward [Line Items]
Net income (loss)	$ (25,014)	$ (22,675)	$ (24,164)	$ (20,987)	$ (12,734)	$ 58,307	$ (8,611)	$ (27,593)	$ (92,840)	$ 9,369	$ (85,257)
Effective tax rate									0.00%	0.00%	0.00%
Unrealized excess tax benefits from stock option exercises, before valuation allowance									$ 5,300	$ 5,300
Net operating loss carryforwards	560,500								560,500
Net operating losses limited in ability to offset taxable income	40								40
Orphan drug credit carryforward [Member]
Tax Credit Carryforward [Line Items]
Tax credit carryforwards	52,200								52,200
Federal [Member] | Research and experimentation [Member]
Tax Credit Carryforward [Line Items]
Tax credit carryforwards	$ 38,900								$ 38,900

NET EARNINGS (LOSS) PER SHARE -

NET EARNINGS (LOSS) PER SHARE - Computation of Earnings Per Share (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2014	Sep. 30, 2014	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Net Income (Loss) Attributable to Parent, Diluted [Abstract]
Net earnings (loss) - basic and diluted	$ (25,014)	$ (22,675)	$ (24,164)	$ (20,987)	$ (12,734)	$ 58,307	$ (8,611)	$ (27,593)	$ (92,840)	$ 9,369	$ (85,257)
Weighted Average Number of Shares Outstanding Reconciliation [Abstract]
Weighted average shares outstanding – basic (in shares)	143,475	143,338	142,833	142,216	141,393	139,769	133,815	131,826	142,964	136,679	123,403
Warrants (in shares)									0	3,560	0
Weighted average shares outstanding – diluted (in shares)	143,475	143,338	142,833	142,216	141,393	166,265	133,815	131,826	142,964	141,692	123,403
Per share data:
Basic (in dollars per share)	$ (0.17)	$ (0.16)	$ (0.17)	$ (0.15)	$ (0.09)	$ 0.42	$ (0.06)	$ (0.21)	$ (0.65)	$ 0.07	$ (0.69)
Diluted (in dollars per share)	$ (0.17)	$ (0.16)	$ (0.17)	$ (0.15)	$ (0.09)	$ 0.37	$ (0.06)	$ (0.21)	$ (0.65)	$ 0.07	$ (0.69)
Stock options [Member]
Weighted Average Number of Shares Outstanding Reconciliation [Abstract]
Equity awards (in shares)									0	1,300	0
RSUs [Member]
Weighted Average Number of Shares Outstanding Reconciliation [Abstract]
Equity awards (in shares)									0	153	0

NET EARNINGS (LOSS) PER SHARE70

NET EARNINGS (LOSS) PER SHARE - Anti-dilutive Common Stock Equivalents (Details) - shares shares in Thousands	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total anti-dilutive common stock equivalents excluded from diluted earnings per share calculation	31,242	26,369	37,684
Convertible senior notes [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total anti-dilutive common stock equivalents excluded from diluted earnings per share calculation	18,762	18,762	18,762
Warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total anti-dilutive common stock equivalents excluded from diluted earnings per share calculation	0	0	12,000
Stock options [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total anti-dilutive common stock equivalents excluded from diluted earnings per share calculation	11,648	7,332	6,922
RSUs [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total anti-dilutive common stock equivalents excluded from diluted earnings per share calculation	832	275	0

SELECTED QUARTERLY FINANCIAL 71

SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED) (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2014	Sep. 30, 2014	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2014
Quarterly Financial Information Disclosure [Abstract]
Revenue	$ 43,205	$ 43,047	$ 35,430	$ 16,197	$ 12,320	$ 6,601	$ 26,919	$ 6,069	$ 137,879	$ 51,909	$ 42,078
Research and development for proprietary programs	49,504	48,802	41,351	20,998	18,618	11,817	11,817	12,190	160,655	54,442	49,824
Total operating expenses	65,513	63,055	56,952	34,568	33,964	32,144	32,993	31,166	220,088	130,267	117,696
Net income (loss)	$ (25,014)	$ (22,675)	$ (24,164)	$ (20,987)	$ (12,734)	$ 58,307	$ (8,611)	$ (27,593)	$ (92,840)	$ 9,369	$ (85,257)
Net earnings (loss) per share – basic (in dollars per share)	$ (0.17)	$ (0.16)	$ (0.17)	$ (0.15)	$ (0.09)	$ 0.42	$ (0.06)	$ (0.21)	$ (0.65)	$ 0.07	$ (0.69)
Net earnings (loss) per share – diluted (in dollars per share)	$ (0.17)	$ (0.16)	$ (0.17)	$ (0.15)	$ (0.09)	$ 0.37	$ (0.06)	$ (0.21)	$ (0.65)	$ 0.07	$ (0.69)
Weighted average shares outstanding – basic (in shares)	143,475	143,338	142,833	142,216	141,393	139,769	133,815	131,826	142,964	136,679	123,403
Weighted average shares outstanding – diluted (in shares)	143,475	143,338	142,833	142,216	141,393	166,265	133,815	131,826	142,964	141,692	123,403