<?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>0001713599</rptOwnerCik>
            <rptOwnerName>Valacer David</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>Chief Medical Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.27</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2024-08-06</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>57321</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 August 6, 2014, Reporting Person was granted an option to purchase 81,000 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 57,321 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 vest on the first anniversary of Vesting Commencement Date, which is January 1, 2014 and, thereafter, in forty-eight 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</remarks>

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