<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType><periodOfReport>2004-01-16</periodOfReport><notSubjectToSection16>1</notSubjectToSection16>
    <issuer>
        <issuerCik>0001106917</issuerCik>
        <issuerName>PINNACOR INC</issuerName>
        <issuerTradingSymbol>PCOR</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001017645</rptOwnerCik>
            <rptOwnerName>GENERAL ATLANTIC PARTNERS LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O GENERAL ATLANTIC SERVICE CORPORATION</rptOwnerStreet1>
            <rptOwnerStreet2>3 PICKWICK PLAZA</rptOwnerStreet2>
            <rptOwnerCity>GREENWICH</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06830</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>0</isDirector><isOfficer>0</isOfficer><isTenPercentOwner>1</isTenPercentOwner><isOther>0</isOther></reportingOwnerRelationship></reportingOwner><nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2004-01-16</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>U</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>5835624</value></transactionShares><transactionPricePerShare><footnoteId id="F3"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>See </value><footnoteId id="F1"/></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2004-01-16</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>U</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>449403</value></transactionShares><transactionPricePerShare><footnoteId id="F3"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>See </value><footnoteId id="F2"/></natureOfOwnership></ownershipNature></nonDerivativeTransaction></nonDerivativeTable><footnotes><footnote id="F1">By General Atlantic Partners 69, L.P. (&quot;GAP 69&quot;), of which General Atlantic Partners, LLC (&quot;GAP LLC&quot;) is the general partner.</footnote><footnote id="F2">By GapStar, LLC (&quot;GapStar&quot;), of which GAP LLC is the sole member.</footnote><footnote id="F3">Disposed of as a result of the consummation of the Agreement and Plan of Merger, dated July 22, 2003 (the &quot;Merger Agreement&quot;), among Pinnacor, Inc. (the &quot;Company&quot;), NMP, Inc. (&quot;Holdco&quot;), MarketWatch.com, Inc. and the other parties thereto.  Pursuant to the Merger Agreement, stockholders of the Company were entitled to elect to receive, for each share of common stock of the Company, either $2.42 in cash, 0.2659 shares of common stock of the new MarketWatch.com, Inc. (the successor to Holdco) (&quot;MarketWatch&quot;) or a combination of both.  The final allocation of the consideration issued pursuant to the Merger Agreement has not been determined, but each of GAP 69 and GapStar elected to receive shares of common stock of MarketWatch and anticipates receiving 1,551,692 shares and 119,496 shares, respectively, having a market value of $9.87 per share, which is the closing price per share MarketWatch on January 16, 2004, the effective date of the merger.</footnote></footnotes><remarks/><ownerSignature><signatureName>Matthew Nimetz, A Managing Member</signatureName><signatureDate>2004-01-20</signatureDate></ownerSignature></ownershipDocument>

