<?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>0001339484</rptOwnerCik>
            <rptOwnerName>Poma Eric E</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>2019-02-23</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>152945</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>90514</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>34156</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>220560</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 February 23, 2009, Reporting Person was granted an option to purchase 216,125 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 152,945 shares of the Issuer's common stock at a per share exercise price of $0.42. One fifth of the total number of shares subject to the option shall vest on the one (1) year anniversary of the Vesting Commencement Date, which is February 23, 2009 and, thereafter, one sixtieth 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 127,904 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 90,514 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 48,266 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 34,156 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 311,670 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 220,560 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>Exhibit 24.1 - Power of Attorney

Chief Executive Officer and Chief Scientific Officer</remarks>

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