Crinetics Pharmaceuticals, Inc.

6. Commitments and Contingencies

Litigation

From time to time, the Company may be subject to various claims and suits arising in the ordinary course of business. The Company does not expect that the resolution of these matters will have a material adverse effect on its financial position or results of operations.

7. Revenue Recognition

Sanwa Kagaku Kenkyusho Co., Ltd

On February 25, 2022, the Company and Sanwa Kagaku Kenkyusho Co., Ltd. (“Sanwa”), entered into a license agreement (the “Sanwa License”) whereby the Company granted Sanwa an exclusive license to develop and commercialize paltusotine in Japan.

In exchange, the Company received a $13.0 million nonrefundable, upfront payment and will be eligible to receive up to an additional $25.5 million in milestone payments related to the achievement of certain development, regulatory and commercial goals. In addition, upon market approval of paltusotine in Japan, the Company will be eligible to receive certain sales-based royalties.

Initially, the Company determined that the transaction price amounted to the upfront payment of $13.0 million. The Company determined that its performance obligations under the Sanwa License comprised the license and data exchange. The control of the license was transferred to Sanwa at the inception of the contract and the Company does not have an ongoing performance obligation to support or maintain the licensed intellectual property. Revenue allocated to the data exchange obligation is recognized over time using the cost-to-cost measure as this method represents a faithful depiction of progress toward certain ongoing paltusotine studies and related data transfer. Revenue is recognized on a gross basis as the Company is the principal. As there have been no sales of paltusotine in Japan to date, no sales-based milestones or royalties were recognized to date. Further, using the most-likely-method, the other developmental milestone payments are considered fully constrained.

During the nine months ended September 30, 2024, the Company achieved a $1.0 million milestone for the first indication of the development milestones. As of September 30, 2024, the Company updated its estimated transaction price to $14.0 million and recorded a cumulative catch-up adjustment of $0.4 million.

Deferred revenue consisted of the following (in thousands):

During the three and nine months ended September 30, 2025, $0.1 million and $1.1 million, respectively, of the $14.0 million estimated transaction price was recognized as revenues in the accompanying condensed consolidated statements of operations and comprehensive loss, all of which were included in the fiscal year 2024 deferred revenue balance. During the nine months ended September 30, 2024, $0.9 million of the $14.0 million estimated transaction price was recognized as revenues in the accompanying condensed consolidated statements of operations and comprehensive loss, of which $0.5 million was included in the fiscal year 2023 deferred revenue balance. There wereno revenues recognized related to the Sanwa License for the three months ended September 30, 2024. Deferred revenues are expected to be recognized over the duration of certain paltusotine studies conducted by the Company.

On June 14, 2022, the Company and Sanwa, entered into a clinical supply agreement (the “Sanwa Clinical Supply Agreement”) whereby the Company is responsible for manufacturing and supplying certain materials to Sanwa for specified activities under the Sanwa License. During the nine months ended September 30, 2025 and September 30, 2024, $0.4 million and $0.1 million, respectively, was recognized as revenues in the accompanying condensed consolidated statements of operations and comprehensive loss related to the Sanwa Clinical Supply Agreement. There wereno revenues recognized related to the Sanwa Clinical Supply Agreement for the three months ended September 30, 2025 and 2024.

Cellular Longevity, Inc., doing business as Loyal

On March 24, 2023, the Company granted Cellular Longevity Inc., doing business as Loyal (“Loyal”) an exclusive license to develop and commercialize CRN01941, a somatostatin receptor type 2 agonist, for veterinary use. In return, the Company received a $0.1 million upfront payment and Loyal preferred stock valued at $2.0 million. The Company may also earn single-digit sales-based royalties if the product is approved.

No revenue was recognized under this license for the three and nine months ended September 30, 2025 and 2024. As of September 30, 2025, the shares of Loyal preferred stock issued and to be issued to the Company valued at $2.0 million is included in prepaid expense and other assets, net of current portion, in the accompanying condensed consolidated balance sheets. The Loyal preferred stock does not have a readily determinable fair value and is recorded at cost less impairment. The Company assesses equity securities without a readily determinable fair value for changes in observable prices each period, noting none for the three and nine months ended September 30, 2025.

8. Stockholders’ Equity

Stock Offerings

On March 1, 2024, the Company completed a private placement of 8,333,334 shares of its common stock at a price of $42.00 per share (the “Private Placement”). Net proceeds from the Private Placement were approximately $335.5 million, after offering costs of approximately $14.5 million. On March 19, 2024, the Company registered for resale the shares issued and sold in the Private Placement, pursuant to the Registration Rights Agreement entered into with the Purchasers, dated February 27, 2024.

On October 10, 2024, the Company completed an underwritten public offering of 11,500,000 shares of its common stock at a price to the public of $50.00 per share, which included 1,500,000 shares of common stock issued pursuant to the underwriters' option to purchase additional shares. Net proceeds from the offering were approximately $542.8 million, after underwriting discounts and commissions and other offering costs of approximately $32.2 million.

ATM Offerings

On August 13, 2019, the Company entered into a Sales Agreement (as amended, the “2019 Sales Agreement”) with SVB Leerink LLC and Cantor Fitzgerald & Co. (collectively, the “Sales Agents”), under which the Company could, from time to time, sell up to $150.0 million of shares of its common stock through the Sales Agents (the “2019 ATM Offering”). The 2019 ATM Offering was terminated upon the filing by the Company of its Registration Statement on Form S-3ASR on June 21, 2024.

On June 21, 2024, the Company entered into a Sales Agreement (the “2024 Sales Agreement”) with the Sales Agents under which the Company may, from time to time, sell up to $350.0 million of shares of its common stock through the Sales Agents (the “2024 ATM Offering”).

During the three and nine months ended September 30, 2025, and as of date of this report, no shares of common stock have been issued pursuant to the 2024 ATM Offering.

9. Equity Incentive Plans

2021 Employment Inducement Incentive Award Plan

In December 2024, the Company amended the Company's 2021 Employment Inducement Incentive Award Plan (the “2021 Inducement Plan”) to increase the number of shares of the Company’s common stock available for future issuance under the 2021 Inducement Plan to 9,500,000 shares. As of September 30, 2025,2,080,995 shares of common stock were available for future issuance under the 2021 Inducement Plan.

2018 Incentive Award Plan

As of September 30, 2025,5,367,449 shares of common stock were available for future issuance under the Company's 2018 Incentive Award Plan (the “2018 Plan”).

The 2018 Plan contains a provision that allows annual increases in the number of shares available for issuance on the first day of each calendar year through January 1, 2028, in an amount equal to the lesser of: (i)5% of the aggregate number of shares of the Company’s common stock outstanding on December 31 of the immediately preceding calendar year, or (ii)

such lesser amount determined by the Company. Under this evergreen provision, on January 1, 2025, an additional 4,646,320 shares became available for future issuance under the 2018 Plan.

2018 Employee Stock Purchase Plan

As of September 30, 2025,2,865,513 shares of common stock were available for issuance under the Company's 2018 Employee Stock Purchase Plan (the “ESPP”).

The ESPP contains a provision that allows annual increases in the number of shares available for issuance on the first day of each calendar year through January 1, 2028, in an amount equal to the lesser of: (i)1% of the aggregate number of shares of the Company’s common stock outstanding on December 31 of the immediately preceding calendar year, or (ii) such lesser amount determined by the Company. Under this evergreen provision, on January 1, 2025, an additional 929,264 shares became available for future issuance under the ESPP.

Stock Awards

Stock Options

Activity under the Company’s stock option plans during the nine months ended September 30, 2025 was as follows:

Restricted Stock Units

The Company’s restricted stock unit (“RSU”) activity during the nine months ended September 30, 2025, was as follows:

Employee Stock Purchase Plan

During the nine months ended September 30, 2025, the Company issued 114,565 shares of our common stock under the ESPP. The shares were purchased by employees at an average purchase price of $25.14 per share, resulting in proceeds to the Company of approximately $2.9 million.

Stock-Based Compensation Expense

Stock-based compensation expense for the equity awards issued by the Company to employees and non-employees for the periods presented below was as follows (in thousands):

A summary of the Company's total unrecognized stock-based compensation expense, as of September 30, 2025, is as follows:

10. Investment In Radionetics

In October 2021, the Company licensed its radiotherapeutics technology to Radionetics Oncology, Inc. (“Radionetics”) in exchange for 50,500,000 shares of Radionetics' common stock, equivalent to a 64% initial stake, and a warrant to maintain up to 22% equity in Radionetics on a fully diluted basis (“Radionetics Warrant”).

In August 2023, the Company participated in a refinancing transaction, exercising the Radionetics Warrant to purchase 3,407,285 shares of Radionetics common stock, exchanging 32,344,371 shares of Radionetics common stock for Radionetics preferred stock, and investing $5.0 million for an additional 14,404,656 shares of Radionetics preferred stock. The Radionetics license was also amended to include up to $15.0 million in new sales milestones.

In June 2024, the license with Radionetics was amended to reduce development targets, reverting certain rights to the Company, and the Company is eligible to receive total potential sales milestones in excess of $300.0 million and single-digit royalties on net sales. In July 2024, Radionetics formed a strategic partnership with Eli Lilly and Company (“Lilly”), receiving a $140.0 million upfront payment and granting Lilly the exclusive right to acquire Radionetics for $1.0 billion.

Although Radionetics is a variable interest entity (“VIE”), the Company determined it is not the primary beneficiary and does not consolidate Radionetics’ results due to lack of control over key decisions, which rest with Radionetics’ independent board and management. As of September 30, 2025, the Company held a 25% ownership in Radionetics consisting of common and preferred stock and accounts for its investment under the equity method. The investment asset was previously written down to zero. No equity method losses were recorded for the three and nine months ended September 30, 2025 and the three months ended September 30, 2024, and $0.5 million in losses were recorded during the nine months ended September 30, 2024.

R. Scott Struthers, Ph.D., the Company’s President and Chief Executive Officer, serves as chairman of the Radionetics board of directors. Pursuant to such arrangement, Dr. Struthers receives consideration in the form of both equity and a $50,000 annual retainer for his service as a board member of Radionetics. As of September 30, 2025, Dr. Struthers has an approximately 1.3% ownership stake in Radionetics, consisting of common stock. Reimbursements from Radionetics were immaterial during the three and nine months ended September 30, 2025 and 2024.

11. Segment Reporting

The Company operates in a single reportable segment. The chief operating decision maker (“CODM”), its Founder and Chief Executive Officer, assesses performance based on condensed consolidated net loss as reported on the condensed consolidated statement of operations and comprehensive loss, supplemented by certain additional significant expense details reflected in the table below. There have been no changes in the determination of segmentation or the measurements used to determine reported segment loss or segment total assets discussed in the Company's FY 2024 Form 10-K.

Segment revenue and significant segment expenses which are regularly reported to the CODM are included within the table below and are reconciled to condensed consolidated net loss:

(1)Other research and development is comprised of non-personnel related research and development indirect costs incurred for the benefit of multiple research and development programs, including depreciation, and other facility-based expenses, such as rent expense.

12. Net Loss Per Share

Basic net loss per share is computed by dividing the net loss by the weighted-average number of common shares outstanding for the period, without consideration for potentially dilutive securities. Diluted net loss per share is computed by dividing the net loss by the weighted-average number of shares of common stock and dilutive common stock equivalents outstanding for the period determined using the treasury-stock and if-converted methods. For all periods presented, there is no difference in the number of shares used to calculate basic and diluted shares outstanding as inclusion of the potentially dilutive securities on loss per share would be antidilutive.

Potentially dilutive securities (in common stock equivalent shares) not included in the calculation of diluted net loss per share because to do so would be anti-dilutive are as follows (in thousands):