UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 1)*

Receptos, Inc.

(Name of Issuer)

Common Stock, $0.001 par value

(Title of Class of Securities)

756207106

(CUSIP Number)

Mark McDonnell

ARCH Venture Corporation

8725 W. Higgins Road Suite 290

Chicago, IL 60631

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

August 13, 2014

(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 §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 (“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).

Persons who respond to the collection of information contained in this form are not

required to respond unless the form displays a currently valid OMB control number.

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Schedule 13D

This Amendment No. 1 amends, supplements and restates (as applicable) the statement on Schedule 13D filed on May 14, 2013, (the “Original Filing”), and relates to the Reporting Persons’ (as defined in Item 2 of the Original Filing) beneficial ownership of common stock, par value $0.001 per share (the “Common Stock”), of Receptos, Inc., a Delaware corporation (the “Issuer”). The address of the principal executive office of the Issuer is 10835 Road to the Cure, Suite 205, San Diego, California 92121. Information given in response to each item shall be deemed incorporated by reference in all other items, as applicable. Capitalized terms used but not otherwise defined herein have the meanings assigned to such terms in the Original Filing.

There are no amendments to Item 2 of the Original Filing.

There are no amendments to Item 3 of the Original Filing.

There are no amendments to Item 4 of the Original Filing.

Item 5 of the Original Filing is hereby amended and restated to read in its entirety as follows:

“(a) ARCH Venture Fund VII is the record owner of 1,703,739 shares of Common Stock (the “ARCH VII Shares”) and ARCH Venture Fund VI is the record owner of 105,197 shares of Common Stock (the “ARCH VI Shares” and, collectively with the ARCH VII Shares, the “Record Shares”).

AVP VII LP, as the sole general partner of ARCH Venture Fund VII, may be deemed to beneficially own the ARCH VII Shares. AVP VII LLC, as the sole general partner of the AVP VII LP, may be deemed to beneficially own the ARCH VII Shares.

AVP VI LP, as the sole general partner of ARCH Venture Fund VI, may be deemed to beneficially own the ARCH VI Shares. AVP VI LLC, as the sole general partner of AVP VI LP, may be deemed to beneficially own the ARCH VI Shares.

By virtue of their relationship as affiliated entities who have overlapping general partners and managing directors, each entity Reporting Person may be deemed to share the power to direct the disposition and vote of the Record Shares. In addition, each of the Managing Directors may be deemed to share the power to direct the disposition and vote of the Record Shares. Each Reporting Person disclaims beneficial ownership of all securities except for the shares, if any, held of record by such Reporting Person.

The percentage of outstanding Common Stock of the Issuer which may be deemed to be beneficially owned by each Reporting Person is set forth on Line 13 of such Reporting Person’s cover sheet. Such percentage was calculated in accordance with SEC rules and is based upon 27,278,662 shares of the Issuer’s common stock outstanding as of July 31, 2014, as reported in the Issuer’s Form 10-Q filed with the SEC on August 12, 2014 pursuant to Rule 13a-13. The applicable SEC rules generally attribute beneficial ownership of securities to persons who possess sole or shared voting power or investment power with respect to those securities and include shares of Common Stock issuable upon the conversion or exercise of other securities that are immediately convertible or exercisable, or are convertible or exercisable within 60 days of the filing of this Report.

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(b) Regarding the number of shares as to which such person has:

(c) On May 13, 2014, ARCH Venture Fund VII sold 34,835 shares and ARCH Venture Fund VI sold 2,151 shares of the Issuer’s Common Stock in the open market at a weighted average price per share of $29.94.

On May 14, 2014, ARCH Venture Fund VII sold 7,907 shares and ARCH Venture Fund VI sold 488 shares of the Issuer’s Common Stock in the open market at a weighted average price per share of $28.39.

On May 27, 2014, ARCH Venture Fund VII sold 55,353 shares and ARCH Venture Fund VI sold 3,418 shares of the Issuer’s Common Stock in the open market at a weighted average price per share of $29.90.

On May 28, 2014, ARCH Venture Fund VII sold 63,386 shares and ARCH Venture Fund VI sold 3,914 shares of the Issuer’s Common Stock in the open market at a weighted average price per share of $29.41.

On May 29, 2014, ARCH Venture Fund VII sold 26,020 shares and ARCH Venture Fund VI sold 1,607 shares of the Issuer’s Common Stock in the open market at a weighted average price per share of $30.20.

On August 13, 2014, ARCH Venture Fund VI distributed to its partners, including AVP VI LP as its general partner, 12,980 in kind shares of the Issuer’s Common Stock without receipt of any consideration. The shares distributed to the general partner where distributed to its limited partners including Clinton Bybee, Keith Crandell and Robert Nelsen.

On August 13, 2014, ARCH Venture Fund VII distributed to its partners, including AVP VII LP as its general partner, 210,136 in kind shares of the Issuer’s Common Stock without receipt of any consideration. The shares distributed to the general partner where distributed to its limited partners including Clinton Bybee, Keith Crandell and Robert Nelsen.

Following such sales and distributions, each of ARCH Venture Fund VII, AVP VII LP, AVP VII LLC, ARCH Venture Fund VI, AVP VI LP and AVP VI LLC are deemed to beneficially own, in aggregate, 1,808,936 shares of the Issuer’s Common Stock, and each of Keith Crandell and Robert Nelsen are deemed to beneficially own, in aggregate, 1,810,198 shares of the Issuer’s Common Stock and Clinton Bybee combined with his affiliated entity is deemed to beneficially own, in aggregate, 1,810,197 shares of the Issuer’s Common Stock.”

Except for the transactions described in this Schedule, none of the Reporting Persons have any contract, arrangement, understanding or relationship (legal or otherwise) with any other person with respect to any securities of the Issuer, including but not limited to transfer or voting of any such securities, finder’s fees, joint ventures, loan or option arrangements, puts or calls, guarantees of profits, division of profits or loss or the giving or withholding of proxies.

Exhibit 1 – Agreement regarding filing of joint Schedule 13D.

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SIGNATURE

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.

Date: August 14, 2014

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Exhibit 1

AGREEMENT OF JOINT FILING

Pursuant to Rule 13d-1(k)(1) under the Securities Exchange Act of 1934, the undersigned hereby agree that only one statement containing the information required by Schedule 13D need be filed with respect to the ownership by each of the undersigned of shares of Common Stock of Receptos, Inc.

This Agreement may be executed in any number of counterparts, each of which shall be deemed an original.

Date: August 14, 2014

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