RCPT (MM)

Item 1. Security and Issuer.

This statement on Schedule 13D relates to the Reporting Persons’ (as defined in Item 2 below) beneficial ownership interest in the 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.

Item 2. Identity and Background.

Each of the foregoing is referred to as a “Reporting Person” and collectively as the “Reporting Persons.”

Pursuant to the provisions of General Instruction C to Schedule 13D, information in Items 2 through 6 of this Schedule 13D is provided with respect to Flagship GP, Afeyan, and Kania.

Flagship Ventures

One Memorial Drive, 7 ^th Floor

Cambridge, Massachusetts 02142

Flagship Fund      Delaware, United States of America

Flagship GP         Delaware, United States of America

Afeyan                 United States of America

Kania                   United States of America

Additional information concerning the Reporting Persons is set forth on Attachment A hereto and is incorporated by reference herein.

Item 3. Source and Amount of Funds or Other Consideration.

On November 9, 2009, the Reporting Persons acquired 5,783,146 shares of the Issuer’s Series A convertible preferred stock at a price per share of $0.70, for an aggregate purchase price of $4,048,202.00. These shares were acquired with working capital.

On June 29, 2011, the Reporting Persons acquired 2,857,143 shares of the Issuer’s Series A convertible preferred stock at a price per share of $0.70, for an aggregate purchase price of $2,000,000.00. These shares were acquired with working capital.

On February 3, 2012, the Reporting Persons acquired 1,549,332 shares of the Issuer’s Series B convertible preferred stock at a price per share of $1.03, for an aggregate purchase price of $1,595,811.96. These shares were acquired with working capital.

On February 19, 2013, the Reporting Persons acquired 1,549,332 shares of the Issuer’s Series B convertible preferred stock at a price per share of $1.03, for an aggregate purchase price of $1,595,811.96. These shares were acquired with working capital.

On February 22, 2013, the Reporting Persons acquired 114,285 shares of the Issuer’s Common Stock through the exercise of 857,142 warrants underlying such shares. The shares were acquired with working capital at an exercise price per share of $0.075, for an aggregate purchase price of $8,571.38. The warrants were acquired by the Reporting Persons in conjunction with their purchase of the Issuer’s Series A convertible preferred stock on June 29, 2011.

Following completion of the Issuer’s initial public offering on May 9, 2013 (the “IPO”), the Reporting Persons’ shares of the Issuer’s Series A convertible preferred stock and Series B convertible preferred stock converted into shares of Common Stock on a 1-for-7.5 basis. After the conversion of the Series A convertible preferred stock and the Series B convertible preferred stock, the Reporting Persons owned, in aggregate, 1,817,197 shares of the Issuer’s Common Stock.

In conjunction with the Issuer’s IPO, the Reporting Persons acquired 107,142 shares of Common Stock. These shares were acquired with working capital at the initial public offering price of $14.00 per share for an aggregate purchase price of $1,499,988.00. Following the purchase of such shares in the IPO, the Reporting Persons owned, in aggregate, 1,924,339 shares of the Issuer’s Common Stock.

Item 4. Purpose of Transaction.

The shares of Common Stock reported herein were acquired solely for investment purposes. None of the Reporting Persons have any present plans or proposals that relate to or would result in any change in the business, policies, management, structure or capitalization of the Issuer. The Reporting Persons reserve the right to acquire, or dispose of, additional securities of the Issuer in the ordinary course of their business, to the extent deemed advisable in light of their general investment and trading policies, market conditions or other factors. The Reporting Persons may engage in discussions from time to time with other stockholders of the Issuer regarding the acquisition by the Reporting Persons of shares of the Issuer’s Common Stock or other securities of the Issuer held by such stockholders.

Douglas Cole, M.D. is a member of the Board of Directors of the Issuer and is also a member of Flagship GP. Mr. Cole does not own any shares of the Issuer’s Common Stock in his individual capacity and has no voting or investment control over the shares of Common Stock held by Flagship Fund.

The Reporting Persons may seek information from management and the Issuer’s Board of Directors, and may engage in further discussions with management, the Issuer’s Board of Directors, other stockholders of the Issuer and other relevant parties, concerning the business, operations, governance, management, strategy, capitalization and/or future plans of the Issuer, or in proposing one or more of the other actions described in subparagraphs (a) through (j) of this Item 4. In addition, the Reporting Persons may exercise their rights under the Investors’ Rights Agreement, as defined below.

Other than as described above and as set forth in the Investors’ Rights Agreement, as defined below, the Reporting Persons do not have any plans or proposals which would result in any of the following:

Item 5. Interest in Securities of the Issuer.

The aggregate percentage of shares of Common Stock reported beneficially owned by each person named herein has been determined in accordance with SEC rules and is based upon 17,604,643 shares of Common Stock outstanding, which is the total number of shares of Common Stock outstanding as reported in the Issuer’s final prospectus filed with the Securities and Exchange Commission on May 8, 2013 in connection with the Issuer’s IPO. 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.

Please see Attachment A for additional information.

Please see Attachment A for additional information.

Please see Attachment A for additional information.

D. Edwin M. Kania, Jr.

Please see Attachment A for additional information.

Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer.

Third Amended and Restated Investors’ Rights Agreement

Flagship Fund is party to a Third Amended and Restated Investors’ Rights Agreement, dated as of February 3, 2012, by and among the Issuer, certain other stockholders, the Issuer’s executive officers and directors, and certain entities with which the Issuer’s directors are affiliated (the “Investors’ Rights Agreement”). Upon completion of the Issuer’s IPO, the holders of 10,336,455 shares of Common Stock that was issued upon the conversion of the Issuer’s Series A convertible preferred stock and Series B convertible preferred stock became entitled to the rights described below with respect to registration of the resale of such shares under the Securities Act of 1933, as amended (the “Securities Act”), pursuant to the Investors’ Rights Agreement.

Registration of shares of Common Stock in response to the exercise of the following rights would result in the holders being able to trade these shares without restriction under the Securities Act when the applicable registration statement is declared effective. The Issuer generally must pay all expenses, other than underwriting discounts and commissions, related to any registration effected pursuant to the exercise of these registration rights.

The registration rights terminate upon the earlier of the fifth anniversary of the Issuer’s IPO, the occurrence of a deemed liquidation event (as such term is defined in the Issuer’s Certificate of Incorporation), or with respect to the registration rights of an individual holder, when such holder can sell all of its registrable securities in any 90-day period without registration, in compliance with Rule 144 of the Securities Act.

Demand registration rights

If, at any time beginning 180 days after the consummation of the Issuer’s IPO, the holders of not less than 60% of the outstanding registrable securities issued upon the conversion of the Issuer’s Series A convertible preferred stock and Series B convertible preferred stock request in writing that the Issuer file a Form S-1 registration statement with respect to the registrable securities then outstanding, the Issuer may be required to register such shares, subject to certain exceptions. The Issuer is only obligated to effect two such registrations in response to these demand registration rights of the holders of registrable securities. Depending on certain conditions, however, the Issuer may defer such registration for up to 45 days. The underwriters of any underwritten offering have the right to limit the number of shares registered by these holders for marketing reasons.

Piggyback registration rights

If at any time the Issuer proposes to register any shares of Common Stock under the Securities Act after the IPO, subject to certain exceptions, the holders of registrable securities will be entitled to notice of the registration and to include their share of registrable securities in the registration. The underwriters of any underwritten offering have the right to limit the number of shares registered by these holders for marketing reasons, subject to certain limitations.

Form S-3 registration rights

The holders of outstanding registrable securities issued upon conversion of the Issuer’s Series A convertible preferred stock or Series B convertible preferred stock may request in writing that the Issuer effect a registration on Form S-3 under the Securities Act, when registration of the Issuer’s shares under Form S-3 becomes possible, and when the proposed aggregate offering price of the shares to be registered by the holders requesting registration is at least $2,000,000, subject to certain exceptions. The Issuer is only obligated to effect two such registrations in any 12-month period in response to these Form S-3 registration rights.

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The foregoing description of the terms of the Investors’ Rights Agreement is intended as a summary only and is qualified in its entirety by reference to the Investors’ Rights Agreement, itself, which is filed as an exhibit to this Schedule 13D and incorporated by reference herein. Other than as described in this Schedule 13D, to the best of the Reporting Persons’ knowledge, there are no other contracts, arrangements, understandings or relationships (legal or otherwise) among the persons named in Item 2 and between such persons and any person with respect to any securities of the Issuer.

Item 7. Material to be Filed as Exhibits.

The following documents are filed as Exhibits to this statement:

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.