<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2013-05-08</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001463729</issuerCik>
        <issuerName>Receptos, Inc.</issuerName>
        <issuerTradingSymbol>RCPT</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001508052</rptOwnerCik>
            <rptOwnerName>Flagship Ventures Fund 2007, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O RECEPTOS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>10835 ROAD TO THE CURE, SUITE 205</rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001508053</rptOwnerCik>
            <rptOwnerName>Flagship Ventures 2007 General Partner LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O RECEPTOS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>10835 ROAD TO THE CURE, SUITE 205</rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001255927</rptOwnerCik>
            <rptOwnerName>KANIA EDWIN M JR</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O RECEPTOS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>10835 ROAD TO THE CURE, SUITE 205</rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001222012</rptOwnerCik>
            <rptOwnerName>AFEYAN NOUBAR</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O RECEPTOS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>10835 ROAD TO THE CURE, SUITE 205</rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>114285</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>5.25</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1152039</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>7.73</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>550873</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The Series A Preferred Stock and the Series B Preferred Stock have no expiration date and are convertible at any time at the option of the holder and will convert upon the closing of the Issuer's initial public offering at a conversion ratio of 1 share of Common Stock for every 7.5 shares of Series A Preferred Stock and Series B Preferred Stock, for no additional consideration.</footnote>
        <footnote id="F2">Beneficial ownership consists of: (i) 114,285 shares of common stock held by Flagship Ventures Fund 2007, L.P. (&quot;Flagship Fund&quot;); and (ii) an aggregate of 1,702,912 shares of common stock issuable upon conversion of shares of Series A preferred stock and Series B preferred stock held by Flagship Fund. The general partner of Flagship Fund is Flagship Ventures 2007 General Partner LLC (&quot;Flagship GP&quot;), and the managing members of Flagship GP are Noubar B. Afeyan and Edwin M. Kania, Jr. Messrs. Afeyan and Kania have voting and investment control over the shares held by Flagship Fund and may be deemed to be the beneficial owners of such shares.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>FLAGSHIP VENTURES FUND 2007, L.P. /s/ Noubar B. Afeyan</signatureName>
        <signatureDate>2013-05-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>FLAGSHIP VENTURES 2007 GENERAL PARTNER LLC /s/ Noubar B. Afeyan</signatureName>
        <signatureDate>2013-05-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Edwin M. Kania, Jr.</signatureName>
        <signatureDate>2013-05-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Noubar B. Afeyan</signatureName>
        <signatureDate>2013-05-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
