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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2017-08-01</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001183765</issuerCik>
        <issuerName>Molecular Templates, Inc.</issuerName>
        <issuerTradingSymbol>MTEM</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001002637</rptOwnerCik>
            <rptOwnerName>MILLENNIUM PHARMACEUTICALS INC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>40 LANDSDOWNE STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02139</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001688140</rptOwnerCik>
            <rptOwnerName>Takeda Pharmaceuticals International AG</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>THURGAUERSTRASSE 130, 8152</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>GLATTPARK</rptOwnerCity>
            <rptOwnerState>V8</rptOwnerState>
            <rptOwnerZipCode></rptOwnerZipCode>
            <rptOwnerStateDescription>SWITZERLAND</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001716226</rptOwnerCik>
            <rptOwnerName>Takeda Pharma A/S</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>LANGEBJERG 1, 4000</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>ROSKILDE</rptOwnerCity>
            <rptOwnerState>G7</rptOwnerState>
            <rptOwnerZipCode></rptOwnerZipCode>
            <rptOwnerStateDescription>DENMARK</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001716380</rptOwnerCik>
            <rptOwnerName>Takeda A/S</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>DYBENDAL ALLE 10, 2630</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>TAASTRUP</rptOwnerCity>
            <rptOwnerState>G7</rptOwnerState>
            <rptOwnerZipCode></rptOwnerZipCode>
            <rptOwnerStateDescription>DENMARK</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001716379</rptOwnerCik>
            <rptOwnerName>Takeda Europe Holdings B.V.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>JUPITERSTRAAT 250, 2132 HK</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>HOOFDDORP</rptOwnerCity>
            <rptOwnerState>P7</rptOwnerState>
            <rptOwnerZipCode></rptOwnerZipCode>
            <rptOwnerStateDescription>NETHERLANDS</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001395064</rptOwnerCik>
            <rptOwnerName>TAKEDA PHARMACEUTICAL CO LTD</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>12-10, NIHONBASHI 2-CHOME, CHUO-KU</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>TOKYO</rptOwnerCity>
            <rptOwnerState>M0</rptOwnerState>
            <rptOwnerZipCode>103-8668</rptOwnerZipCode>
            <rptOwnerStateDescription>JAPAN</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001716229</rptOwnerCik>
            <rptOwnerName>Takeda Pharmaceuticals U.S.A., Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE TAKEDA PARKWAY</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>DEERFIELD</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60015</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>2922993</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">These shares are owned directly by Millennium Pharmaceuticals, Inc. (&quot;Millennium&quot;).   Millennium is a wholly-owned direct subsidiary of Takeda Pharmaceuticals U.S.A., Inc. (&quot;Takeda USA&quot;).  Takeda Pharmaceutical Company Limited (&quot;Takeda&quot;) owns 73.37% of Takeda USA, and Takeda Pharmaceuticals International AG (&quot;Takeda International&quot;) owns 26.63% of Takeda USA.  Takeda Pharma A/S (&quot;Takeda Denmark&quot;) owns 86.83% of Takeda International, and Takeda Europe Holdings B.V. (&quot;Takeda Europe&quot;) owns 13.17% of Takeda International.  Takeda Denmark is a wholly-owned direct subsidiary of Takeda A/S.  Takeda owns 76.09% of Takeda A/S, and Takeda Europe owns 23.91% of Takeda A/S.  Takeda Europe is a wholly-owned direct subsidiary of Takeda. Takeda, Takeda USA, Takeda International, Takeda Denmark, Takeda A/S and Takeda Europe each disclaims beneficial ownership of such shares except to the extent of its pecuniary interest therein.</footnote>
    </footnotes>

    <remarks>Exhibit List: Exhibit 24.1 Power of Attorney for Millennium Pharmaceuticals, Inc.; Exhibit 24.2 Power of Attorney for Takeda Pharmaceuticals U.S.A., Inc.; Exhibit 24.3 Power of Attorney for Takeda Pharmaceuticals International AG; Exhibit 24.4 Power of Attorney for Takeda Pharma A/S; Exhibit 24.5 Power of Attorney for Takeda A/S; Exhibit 24.6 Power of Attorney for Takeda Europe Holdings B.V.</remarks>

    <ownerSignature>
        <signatureName>/s/ James Kehoe, Chief Financial Officer, Takeda Pharmaceutical Company Limited</signatureName>
        <signatureDate>2017-09-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Brett R. Budzinski, Attorney-in-Fact for Millennium Pharmaceuticals, Inc.</signatureName>
        <signatureDate>2017-09-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Brett R. Budzinski, Attorney-in-Fact for Takeda Pharmaceuticals U.S.A., Inc.</signatureName>
        <signatureDate>2017-09-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Brett R. Budzinski, Attorney-in-Fact for Takeda Pharmaceutical International AG</signatureName>
        <signatureDate>2017-09-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Brett R. Budzinski, Attorney-in-Fact for Takeda Pharma A/S</signatureName>
        <signatureDate>2017-09-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Brett R. Budzinski, Attorney-in-Fact for Takeda A/S</signatureName>
        <signatureDate>2017-09-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Brett R. Budzinski, Attorney-in-Fact for Takeda Europe Holdings B.V.</signatureName>
        <signatureDate>2017-09-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
