<?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>0001713925</rptOwnerCik>
            <rptOwnerName>Kim Jason S.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O MOLECULAR TEMPLATES, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>9301 AMBERGLEN BLVD., SUITE 100</rptOwnerStreet2>
            <rptOwnerCity>AUSTIN</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>78729</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>See Remarks</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.42</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2020-03-09</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>54136</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.71</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2021-07-12</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>32038</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.71</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2022-07-10</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>12089</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.27</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <value>2024-11-19</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>78069</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Shares of common stock of the corporation then known as Molecular Templates, Inc. (&quot;Old Molecular&quot;) were converted into shares of the Issuer pursuant to that certain Agreement and Plan of Merger and Reorganization, dated as of March 16, 2017, by and among the Issuer, Trojan Merger Sub, Inc. and Old Molecular (the &quot;Merger Agreement&quot;). Pursuant to the terms of the Merger Agreement, each share of common stock was exchanged for 7.7844 shares of the Issuer's common stock, which then underwent a reverse split of 11-to-1.</footnote>
        <footnote id="F2">On March 9, 2010, Reporting Person was granted an option to purchase 76,500 shares of common stock of Old Molecular under the 2009 Stock Plan (the &quot;Plan&quot;) at an exercise price of $0.30 per share. Pursuant to the Merger Agreement, this option was converted into an option to purchase 54,136 shares of the Issuer's common stock at a per share exercise price of $0.42. One fourth of the total number of shares subject to the option shall vest on the one year anniversary of the Vesting Commencement Date, which is March 20, 2009 and, thereafter, one forty-eighth (1/48th) of the total number of Shares subject to the Option shall vest on the corresponding day of each month after such first anniversary, provided that at the relevant vesting dates the Reporting Person continues service to the Issuer and has not been terminated as defined in and as determined under the Plan. The option expires ten years after the date of the grant.</footnote>
        <footnote id="F3">On July 12, 2011, Reporting Person was granted an option to purchase 45,273 shares of common stock of Old Molecular under the 2009 Stock Plan (the &quot;Plan&quot;) at an exercise price of $0.50 per share. Pursuant to the Merger Agreement, this option was converted into an option to purchase 32,038 shares of the Issuer's common stock at a per share exercise price of $0.71. The shares subject to the option shall vest in 60 equal monthly installments beginning on the Vesting Commencement Date, which is July 12, 2011, provided that at the relevant vesting dates the Reporting Person continues service to the Issuer and has not been terminated as defined in and as determined under the Plan. The option expires ten years after the date of the grant.</footnote>
        <footnote id="F4">On July 10, 2012, Reporting Person was granted an option to purchase 17,084 shares of common stock of Old Molecular under the 2009 Stock Plan (the &quot;Plan&quot;) at an exercise price of $0.50 per share. Pursuant to the Merger Agreement, this option was converted into an option to purchase 12,089 shares of the Issuer's common stock at a per share exercise price of $0.71. The shares subject to the option shall vest in 60 equal monthly installments beginning on the Vesting Commencement Date, which is December 5, 2011, provided that at the relevant vesting dates the Reporting Person continues service to the Issuer and has not been terminated as defined in and as determined under the Plan. The option expires ten years after the date of the grant.</footnote>
        <footnote id="F5">On November 19, 2014, Reporting Person was granted an option to purchase 110,319 shares of common stock of Old Molecular under the 2009 Stock Plan (the &quot;Plan&quot;) at an exercise price of $0.90 per share. Pursuant to the Merger Agreement, this option was converted into an option to purchase 78,069 shares of the Issuer's common stock at a per share exercise price of $1.27. One fourth of the total number of shares subject to the option shall vest on the one year anniversary of the Vesting Commencement Date, which is September 19, 2013 and, thereafter, the remaining shares shall vest in 36 equal monthly installments, provided that at the relevant vesting dates the Reporting Person continues service to the Issuer and has not been terminated as defined in and as determined under the Plan. The option expires ten years after the date of the grant.</footnote>
    </footnotes>

    <remarks>President, Chief Operating Officer and Principal Financial Officer</remarks>

    <ownerSignature>
        <signatureName>/s/ Jason S. Kim</signatureName>
        <signatureDate>2017-08-11</signatureDate>
    </ownerSignature>
</ownershipDocument>
