<SEC-DOCUMENT>0000899243-20-027886.txt : 20201009
<SEC-HEADER>0000899243-20-027886.hdr.sgml : 20201009
<ACCEPTANCE-DATETIME>20201009063045
ACCESSION NUMBER:		0000899243-20-027886
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20201001
FILED AS OF DATE:		20201009
DATE AS OF CHANGE:		20201009

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			LIGAND PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0000886163
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-36540
		FILM NUMBER:		201232063

	BUSINESS ADDRESS:	
		STREET 1:		3911 SORRENTO VALLEY BLVD
		STREET 2:		SUITE 110
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
		BUSINESS PHONE:		858-550-7500

	MAIL ADDRESS:	
		STREET 1:		3911 SORRENTO VALLEY BLVD
		STREET 2:		SUITE 110
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			Pfenex Inc.
		CENTRAL INDEX KEY:			0001478121
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				271356759
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		10790 ROSELLE STREET
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
		BUSINESS PHONE:		858-352-4400

	MAIL ADDRESS:	
		STREET 1:		10790 ROSELLE STREET
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
</SEC-HEADER>
<DOCUMENT>
<TYPE>3
<SEQUENCE>1
<FILENAME>doc3.xml
<DESCRIPTION>FORM 3 SUBMISSION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2020-10-01</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001478121</issuerCik>
        <issuerName>Pfenex Inc.</issuerName>
        <issuerTradingSymbol>PFNX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000886163</rptOwnerCik>
            <rptOwnerName>LIGAND PHARMACEUTICALS INC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>3911 SORRENTO VALLEY BOULEVARD,</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 110</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>27034437</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes></footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Charles S. Berkman, Senior Vice President, General Counsel and Secretary</signatureName>
        <signatureDate>2020-10-09</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
