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PDBeChem: Ligand Dictionary (PDB Ligand Chemistry - chemical component dictionary)
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style="color:#006666">Summary</text></b></li> <li><a href="/pdbe-srv/pdbechem/atom/list/WIW">Atoms</a></li> <li><a href="/pdbe-srv/pdbechem/bond/list/WIW">Bonds</a></li> <li><a href="/pdbe-srv/pdbechem/PDBEntry/list/WIW">In PDB Entries</a></li> <li><a href="/pdbe-srv/pdbechem/chemicalCompound/names/WIW">Names</a></li> <li><a href="/pdbe-srv/pdbechem/chemicalCompound/descriptors/WIW">Descriptors</a></li> <li class="leftmenudivider"></li> <li><a href="/pdbe-srv/pdbechem/chemicalCompound/complete/WIW">Complete Listing</a></li> <li class="leftmenudivider"></li> <li><a href="/pdbe-srv/pdbechem/">Modify Search</a></li> <li class="leftmenudivider"></li> </ul> <div class="slidecontainer"> <div class="iconbox2heading" > <span class="headerToggle" onclick="toggleSideDiv(this)" id="links"> <img id="links_image" class="headerToggleImage" src="http://www.ebi.ac.uk/inc/images/plus.gif" alt="Collapse" /></span> <a onclick="toggleSideDiv(document.getElementById('links'));" style="cursor:pointer;">Download Links</a> </div> <div class="iconbox2contents" id="links_content" style="display: hidden"> <ul> <li>Molfile:<br/><a href="/pdbe/static/files/pdbechem_v2/WIW_ideal.sdf" target=_blank>Ideal</a><br/><a href="/pdbe/static/files/pdbechem_v2/WIW_model.sdf" target=_blank>Representative</a></li> <li>PDB:<br/><a href="/pdbe/static/files/pdbechem_v2/WIW_ideal.pdb" target=_blank>Ideal</a><br/><a href="/pdbe/static/files/pdbechem_v2/WIW_model.pdb" target=_blank>Representative</a></li> <li>Other:<br/><a href="/pdbe/static/files/pdbechem_v2/WIW.cif" target=_blank>mmCif</a><br/><a href="/pdbe/static/files/pdbechem_v2/WIW.cml" target=_blank>CML</a></li> </ul> </div> </div> <div class="slidecontainer"> <div class="iconbox2heading" > <span class="headerToggle" onclick="toggleSideDiv(this)" id="stereo"> <img id="stereo_image" class="headerToggleImage" src="http://www.ebi.ac.uk/inc/images/plus.gif" alt="Collapse" /></span> <a onclick="toggleSideDiv(document.getElementById('stereo'));" style="cursor:pointer;">Related compounds</a> </div> <div class="iconbox2contents" id="stereo_content" style="display: hidden"> Could not find any related compound in the PDB. </div> </div> <div class="slidecontainer"> <div class="iconbox2heading" > <span class="headerToggle" onclick="toggleSideDiv(this)" id="3d"> <img id="3d_image" class="headerToggleImage" src="http://www.ebi.ac.uk/inc/images/plus.gif" alt="Collapse" /></span> <a onclick="toggleSideDiv(document.getElementById('3d'));" style="cursor:pointer;">3D-Views</a> </div> <div class="iconbox2contents" id="3d_content" style="display: hidden"> <ul> <li><a href="javascript::void(0)" onclick='window.open("../JMol/?type=ideal&code=WIW","","height=550,width=518");'>Ideal</a></li> <li><a href="javascript::void(0)" onclick='window.open("../JMol/?type=rep&code=WIW","","height=550,width=518");'>Representative</a></li> </ul> </div> </div> <div class="slidecontainer"> <div 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style="table-layout:fixed;width:100%;word-wrap:break-word;"> <tr VALIGN=BOTTOM> <td width=145px> <h3>Code <span id="cod"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td> WIW </td> </tr> <tr VALIGN=BOTTOM> <td > <h3>One-letter code <span id="olc"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td> X </td> </tr> <tr VALIGN=BOTTOM> <td> <h3>Molecule name <span id="mn"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td colspan="2"> (5~{S},5~{a}~{R},8~{a}~{R},9~{R})-5-pyrimidin-2-ylsulfanyl-9-(3,4,5-trimethoxyphenyl)-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[5,6-f][1,3]benzodioxol-8-one </td> </tr> <tr VALIGN=middle> <td > <h3>Systematic names <span id="sn"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td colspan="2"> <table id="tnameTable" class="tablesorter" style="table-layout:fixed;width:100%;word-wrap:break-word;"> <thead><tr><th width="80px">Program</th><th width="80px">Version</th><th>Name</th></tr></thead> <tbody> <tr> <td> OpenEye OEToolkits </td> <td> 2.0.7 </td> <td > (5~{S},5~{a}~{R},8~{a}~{R},9~{R})-5-pyrimidin-2-ylsulfanyl-9-(3,4,5-trimethoxyphenyl)-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[5,6-f][1,3]benzodioxol-8-one </td> </tr> </tbody> </table> </td> </tr> <tr VALIGN=BOTTOM> <td> <h3>Formula <span id="formula"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td colspan="2"> C26 H24 N2 O7 S </td> </tr> <tr VALIGN=BOTTOM> <td> <h3>Formal charge <span id="fc"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td colspan="2"> 0 </td> </tr> <tr VALIGN=BOTTOM> <td> <h3>Molecular weight <span id="mw"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td colspan="2"> 508.543 Da </td> </tr> <tr VALIGN=middle> <td> <h3>SMILES <span id="smiles"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td colspan="2"> <table id="topDescTable" class="tablesorter" style="table-layout:fixed;width:100%;word-wrap:break-word;"> <thead><tr><th width="80px">Type</th><th width="80px">Program</th><th width="70px">Version</th><th>Descriptor</th></tr></thead> <tbody> <tr> <td> SMILES </td> <td width="80px">CACTVS</td> <td width="80px">3.385</td> <td>COc1cc(cc(OC)c1OC)[CH]2[CH]3[CH](COC3=O)[CH](Sc4ncccn4)c5cc6OCOc6cc25</td> </tr> <tr> <td> SMILES </td> <td width="80px">OpenEye OEToolkits</td> <td width="80px">2.0.7</td> <td>COc1cc(cc(c1OC)OC)C2c3cc4c(cc3C(C5C2C(=O)OC5)Sc6ncccn6)OCO4</td> </tr> <tr> <td> Canonical SMILES </td> <td width="80px">CACTVS</td> <td width="80px">3.385</td> <td>COc1cc(cc(OC)c1OC)[C@H]2[C@@H]3[C@H](COC3=O)[C@H](Sc4ncccn4)c5cc6OCOc6cc25</td> </tr> <tr> <td> Canonical SMILES </td> <td width="80px">OpenEye OEToolkits</td> <td width="80px">2.0.7</td> <td>COc1cc(cc(c1OC)OC)[C@@H]2c3cc4c(cc3[C@H]([C@@H]5[C@@H]2C(=O)OC5)Sc6ncccn6)OCO4</td> </tr> </tbody> </table> </td> </tr> <tr VALIGN=BOTTOM><td><h3>IUPAC InChI <span id="inchi"><img src="/pdbe/static/images/help.png" /></span></h3></td><td colspan="2">InChI=1S/C26H24N2O7S/c1-30-19-7-13(8-20(31-2)23(19)32-3)21-14-9-17-18(35-12-34-17)10-15(14)24(16-11-33-25(29)22(16)21)36-26-27-5-4-6-28-26/h4-10,16,21-22,24H,11-12H2,1-3H3/t16-,21+,22-,24+/m0/s1</td></tr> <tr VALIGN=BOTTOM><td><h3>IUPAC InChI key <span id="ikey"><img src="/pdbe/static/images/help.png" /></span></h3></td><td colspan="2">VJWQXPQIWVFAAY-JNTAVDMJSA-N</td></tr> </table> </div> </td> <td valign="top"><center> <img src="https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/WIW_400.svg" alt="WIW" width="350px"/> <br/> <ul id="sidemenuid" class="sidemenu"> <li class="leftmenudivider"></li> </ul> </center> <center> <table width="320px" border="0"> <tr><td colspan="2"><h1>wwPDB Information</h1></td></tr> <tr VALIGN="MIDDLE"> <td> <h3>Atom count <span id="ac"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td > 60 (36 without Hydrogen) </td> </tr> <tr VALIGN=BOTTOM> <td > <h3>Polymer type <span id="pt"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td colspan="2"> Bound ligand </td> </tr> <tr VALIGN=BOTTOM> <td> <h3>Type description <span id="td"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td colspan="2"> non-polymer </td> </tr> <tr VALIGN=BOTTOM> <td> <h3>Type code <span id="tc"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td colspan="2"> HETAIN </td> </tr> <tr VALIGN=BOTTOM> <td> <h3>Is modified <span id="im"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td > No </td> </tr> <tr VALIGN=BOTTOM> <td> <h3>Standard parent <span id="sp"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td > <span style="color:#D8D8D8">Not Assigned</span> </td> </tr> <tr VALIGN=BOTTOM> <td > <h3>Defined at <span id="da"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td > 2023-10-05 </td> </tr> <tr VALIGN=BOTTOM> <td> <h3>Last modified at <span id="lma"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td > 2024-10-04 </td> </tr> <tr VALIGN=BOTTOM> <td> <h3>Status <span id="sts"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td > Released </td> </tr> <tr VALIGN=BOTTOM> <td> <h3>Obsoleted <span id="obs"><img src="/pdbe/static/images/help.png" /></span></h3> </td> <td > <span style="color:#D8D8D8">Not Assigned</span> </td> </tr> </table> </center> <ul id="sidemenuid" class="sidemenu"> <li class="leftmenudivider"></li> </ul> </td> </tr></table> <div class="spacer" style="height: 5em;"></div> </div> </div> <div class="footerdiv" id="footerdiv"> <div class="footer"> <!-- Optional local footer (insert citation / project-specific copyright / etc here --> <div id="local-footer" class="grid_24 clearfix"></div> <script type="text/javascript" src="/pdbe/js/pdbe-script.js"></script> <!-- End optional local footer --> <div id="global-footer" class="grid_24 clearfix"> <div class="nav" id="global-nav-expanded"> <div class="grid_4 alpha"> <h3 class="embl-ebi"><a href="/" title="Go to the EMBL-EBI homepage">EMBL-EBI</a></h3> </div> <div 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</div> <script type="text/javascript"> var localFrameworkVersion = 'compliance'; // 1.1 or 1.2 or compliance or other // if you select compliance or other we will add some helpful // CSS styling, but you may need to add some CSS yourself var newDataProtectionNotificationBanner = document.createElement('script'); newDataProtectionNotificationBanner.src = 'https://dev.ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/js/ebi-global-includes/script/5_ebiFrameworkNotificationBanner.js?legacyRequest='+localFrameworkVersion; document.head.appendChild(newDataProtectionNotificationBanner); newDataProtectionNotificationBanner.onload = function() { ebiFrameworkRunDataProtectionBanner(); // invoke the banner }; </script> <script type="text/javascript"> function myfunction(){ new YAHOO.widget.Tooltip("tt0",{ context:"cod",text:"The short 3 letter code of the molecule as referenced in PDB, which uniquely identify each component in PDBeChem" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt1",{ context:"olc",text:"For standard polymer components, the one-letter code for the component. For non-standard polymer components, the one-letter code for parent component if this exists, otherwise, the one-letter code should be given as 'X'. Components that derived from multiple parents components are described by a sequence of one-letter-codes" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt2",{ context:"mn",text:"The standard molecule name" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt3",{ context:"sn",text:"The generated IUPAC systematic name" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt4",{ context:"formula",text:"Chemical formula of the molecule listing the number of atoms from each chemical element" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt5",{ context:"fc",text:"The net integer charge assigned to this component. This is the formal charge assignment normally found in chemical diagrams." , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt6",{ context:"mw",text:"Formula mass in daltons of the chemical component." , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt7",{ context:"smiles",text:"Representation of the molecule using the smile string notation that may or may not include stereochemistry information." , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt8",{ context:"inchi",text:"The IUPAC Inchi string for the molecule (http://www.iupac.org/inchi/)" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt9",{ context:"ikey",text:"It is a fixed length (25 character) condensed digital representation of the InChI that is not human-understandable, designed to facilitate search" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt10",{ context:"ac",text:"The total number of atoms in the molecule (including and excluding hydrogen atoms)" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt11",{ context:"pt",text:"The type of monomer." , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt12",{ context:"td",text:"For standard polymer components, the type of the monomer." , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt13",{ context:"tc",text:"A preliminary classification used by PDB." , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt14",{ context:"im",text:"Flag which indicates whether this molecule has been modified since it's initial definition" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt15",{ context:"sp",text:"The identifier for the parent component of the nonstandard component." , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt16",{ context:"da",text:"The initial date at which the molecule was first defined" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt17",{ context:"lma",text:"The date at which the molecule was last modified" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt18",{ context:"sts",text:"This data item holds the current release status for the component." , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt19",{ context:"obs",text:"Whether this molecule has been obsoleted and replaced by another molecule" , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt20",{ context:"sy",text:"Known synonyms for this chemical component." , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt21",{ context:"subcomps",text:"List of sub-components." , zIndex:99, width:"350px"}); new YAHOO.widget.Tooltip("tt22",{ context:"supcomps",text:"Super-ligands of which this compound is a part of." , zIndex:99, width:"350px"}); } </script> <script type="text/javascript"> $(document).ready(function() { $("#tnameTable").tablesorter({ widgets: ['zebra'], headers: { 0: { sorter: false }, 1: { sorter: false }, 2: { sorter: false } }}) }); </script> <script type="text/javascript"> $(document).ready(function() { $("#topDescTable").tablesorter({ widthFixed: true, widgets: ['zebra'], headers: { 0: { sorter: false }, 1: { sorter: false }, 2: { sorter: false }, 3: { sorter: false } }}) }); </script> </body> </html>