SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment     )*

Crinetics Pharmaceuticals, Inc.

(Name of Issuer)

Common Stock, $0.001 par value

(Title of Class of Securities)

22663K 107

(CUSIP Number)

Alexander Rakitin

Perceptive Advisors LLC

51 Astor Place, 10^th Floor

New York, NY 10003

(646) 205-5340

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

July 20, 2018

(Date of Event Which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box.    ☐

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See Section 240.13d-7 for other parties to whom copies are to be sent.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934, as amended (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

CUSIP No. 22663K 107

CUSIP No. 22663K 107

CUSIP No. 22663K 107

This Schedule 13D relates to the shares of common stock, $0.001 par value (“Common Stock”), of Crinetics Pharmaceuticals, Inc., a corporation incorporated under the laws of the State of Delaware (the “Company”), which has its principal executive offices at 10222 Barnes Canyon Road, Bldg. #2, San Diego, California 92121.

Schedule A attached hereto sets forth the information regarding the directors of the Master Fund.

The Reporting Persons acquired beneficial ownership of the shares of the Common Stock in the transactions described in Item 5(c) at an aggregate purchase price of $17.00. The source of these funds was the working capital of the Master Fund.

The Reporting Persons acquired the shares of Common Stock set forth in Item 5(c) and hold their shares of Common Stock for investment purposes. Subject to a number of factors, including market conditions and their general investment and trading policies, the Reporting Persons may, in the ordinary course of their business, acquire beneficial ownership of additional shares of Common Stock or dispose of the shares of Common Stock that they beneficially own. These acquisitions and dispositions may occur in open market transactions, privately negotiated transactions or through other methods.

Weston Nichols, Ph.D., who is an analyst at Perceptive Advisors, is a director of the Company. The Reporting Persons, either directly or indirectly through Dr. Nichols, may engage in discussions from time to time with the Company’s board of directors, the Company’s management or the Company’s other stockholders. These discussions may be with respect to (i) acquiring or disposing of shares of Common Stock or other securities of the Company (collectively, the “Securities”); (ii) maintaining or changing the Company’s business, operations, governance, management, strategy or capitalization; or (iii) implementing transactions that may relate to or may result in any matter set forth in paragraphs (a) through (j) of Item 4 of Schedule 13D.

Investor Rights Agreement

The Master Fund is party to an investors rights agreement (the “Investor Rights Agreement”) with the Company and certain other stockholders of the Company (collectively, the “Holders”). Pursuant to the terms of the Investor Rights Agreement, if at any time beginning six months following July 18, 2018, the holders of at least 30% of the registrable securities request in writing that the Company effect a registration with respect to their shares in an offering, the Company is obligated to effect at most two registrations for the holders of registrable securities in response to these demand registration rights, subject to certain exceptions. If at any time the Company becomes entitled under the Securities Act of 1933, as amended (the “Securities Act”), to register its shares on Form S-3, the holders of at least 30% of the registrable securities request in writing that the Company register their shares for public resale on Form S-3 and the price to the public of the offering is $2.0 million or more, the Company will be required to provide notice to all holders of registrable securities and to use all reasonable efforts to effect such registration; provided, however, that the Company will not be required to effect such a registration if, within the preceding 12 months, the Company has already effected two registrations on Form S-3 for the holders of registrable securities. In the case of an S-1 registration, if the holders requesting registration intend to distribute their shares by means of an underwriting, the underwriter of such offering will have the right to limit the numbers of shares to be underwritten for reasons related to the marketing of the shares. If at any time following the closing of this offering the Company proposes to register any shares of its Common Stock under the Securities Act, subject to certain exceptions, the holders of registrable securities will be entitled to notice of the registration and to include their shares of registrable securities in the registration. If the Company’s proposed registration involves an underwriting, the managing underwriter of such offering will have the right to limit the number of shares to be underwritten for reasons related to the marketing of the shares. The Investor Rights Agreement contains customary cross indemnification provisions, under which the Company is obligated to indemnify holders of registrable securities in the event of material misstatements or omissions in the registration statement attributable to the Company, and the holders are obligated to indemnify us for material misstatements or omissions attributable to them. The registration rights terminate upon the earlier of three years after the closing of the Company’s initial public offering or upon the closing of an acquisition of the Company.

Lock-up Agreement

In connection with the Company’s initial public offering, the Master Fund entered into a lock-up agreement (the “Lock-up Agreement”) with the representatives of the several underwriters. Pursuant to the Lock-up Agreement, the Master Fund, subject to certain exceptions, agreed not to sell or otherwise transfer any shares of Common Stock or securities convertible into, exchangeable for or exercisable for Common Stock, for 180 days after the date of the prospectus relating to the initial public offering without the prior consent of the representatives.

The foregoing summaries of the Shareholder Agreement and Lock-up Agreement do not purport to be complete and are qualified in their entirety by reference to the Investor Rights Agreement and the Lock-up Agreement, each of which is filed as an exhibit hereto and incorporated by reference herein.

SIGNATURES

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Dated: July 30, 2018

PERCEPTIVE ADVISORS LLC

PERCEPTIVE LIFE SCIENCES MASTER FUND, LTD.

Schedule A

The following sets forth the name, address, principal occupation, citizenship and beneficial ownership of the shares of Common Stock (to the extent not pursuant to Item 5(a)) of each director of the Master Fund.

Master Fund

Schedule B

Exhibit 1

JOINT FILING AGREEMENT

The persons below hereby agree that the Schedule 13D to which this agreement is attached as an exhibit, as well as all future amendments to such Schedule 13D, shall be filed jointly on behalf of each of them. This agreement is intended to satisfy the requirements of Rule 13d-1(k)(1)(iii) under the Securities Exchange Act of 1934.

Dated: July 30, 2018

PERCEPTIVE ADVISORS LLC

PERCEPTIVE LIFE SCIENCES MASTER FUND, LTD.