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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <title>Ligand Expo Home</title> <link rel="stylesheet" type="text/css" href="/styles/twoColLd.css"/> <script type="text/javascript" src="/styles/ajaxtabs.js"></script> </head> <body class="twoColLd"> <div id="container"> <div id="header"> <div class="logo"><a href="http://www.rcsb.org/" target="_blank" ><img src="/icons-local/pdblogo.gif" alt="RCSB PDB" border="0" /></a></div> <div class="headercontent"><h1>Ligand Expo</h1></div> <div class="logolinks"> <a href="http://www.rcsb.org/" alt="RCSB PDB" target="_blank">RCSB PDB</a>  |  <a href="mailto:info@rcsb.org">Contact Us <img src="/icons-local/email.png" alt="Contact Us" align="bottom" border="0"/></a> </div> <div class="mainlinks"> <img src="/icons-local/img1.gif" alt="" /> <a href="/index.html"><span>Home</span></a> <a href="/ld-search.html"><span>Search</span></a>  <a href="/pyapps/ldHandler.py?formid=cc-browse-search&operation=smiles&target=$&category=aa&first=1"><span>Browse</span></a> <a href="/ld-download.html"><span>Download</span></a> <a href="/help.html"><span>Ligand Expo Help</span></a> </div> </div> <div id="mainContent">  <h1>Ligand Expo </h1>  <p> Ligand Expo (formerly Ligand Depot) provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components. The data in Ligand Expo are updated weekly. <br/><br/> LigandExpo is no longer maintained. <br/><br/> <b>Accessing Ligand Expo features</b><br/> Users are strongly encouraged to use RCSB.org <a href="https://www.rcsb.org/docs/programmatic-access/web-apis-overview#search-api" target="_blank">Search APIs</a> and <a href="https://www.rcsb.org/docs/programmatic-access/web-apis-overview#data-api" target="_blank">Data APIs</a> to obtain ligand information. <br/><br/> <b>Accessing Chemical Component Dictionary definitions from wwPDB.org</b><br/> Some file downloads are available at <a href="https://www.wwpdb.org/data/ccd" target="_blank">https://www.wwpdb.org/data/ccd</a> for all CCD definitions in a concatenated file or the variances of the standard residues. <br/><br/> To access SDF/MOL formatted CCD files with ideal coordinates:<br/> <ol> <li>Download individual CCD files in SDF/MOL format from the PDB archive at <a href="https://files.wwpdb.org/pub/pdb/refdata/chem_comp/" target="_blank">https://files.wwpdb.org/pub/pdb/refdata/chem_comp/</a></li> <li>Download a concatenated CCD file in SDF/MOL format at <a href="https://files.wwpdb.org/pub/pdb/data/monomers/components-pub.sdf.gz">https://files.wwpdb.org/pub/pdb/data/monomers/components-pub.sdf.gz</a> which is accessible from the wwPDB website at <a href="https://www.wwpdb.org/data/ccd" target="_blank">https://www.wwpdb.org/data/ccd</a></li> </ol> <br/><br/> <b>Searching Chemical Components at RCSB.org</b><br/><br/> <ol> <li>Use Data API to obtain SMILES/InChI descriptors <ol> <li>Use the example at <a href="https://data.rcsb.org/#gql-example-8" target="_blank">https://data.rcsb.org/#gql-example-8</a> and add the following to the return value, in parallel to chem_comp and rcsb_chem_comp_info groups:<br/> pdbx_chem_comp_descriptor{<br/> type<br/> descriptor<br/> }</li> </ol> </li> <li>Search for similar ligands based on formula, SMILES, InChI or 2D chemical drawing <ol> <li>Go to <a href="https://www.rcsb.org/search/advanced/chemical" target="_blank">Advanced Search -> Chemical Similarity</a> -> select query type “Formula” for formula search or “Descriptor” for SMILES or InChI search, then <b>choose the return type as "Molecular Definitions"</b> and click on the “Search” button.</li> <li>Go to <a href="https://www.rcsb.org/search/advanced/chemical" target="_blank">Advanced Search -> Chemical Similarity</a> -> Click on “Open Chemical Sketch Tool” button to launch 2D chemical drawing tool for substructure search. You can also preload a molecule using CCD ID, SMILES, or InChI for further modification.</li> </ol> </li> <li>Search for CCD ID, chemical name, synonyms, molecular weight, chemical component type, or InCheyKey <ol> <li>Go to <a href="https://www.rcsb.org/search/advanced/text_chem" target="_blank">Advanced Search -> Chemical Attributes</a> -> Chemical Components -> then select a search item (e.g., Chemical ID), then choose the return type as “Molecular Definitions” and click on the “Search” button.</li> </ol> </li> <li>If searching by CCD ID alone, type the ID at the RCSB.org top simple search bar, then choose “in Chemical ID” from the drop down list.</li> </ol> <p/> <p> </p> <p> <b>Getting Started:</b> <ul> <li> The <a href="/help.html">Ligand Expo Tutorial</a> contains a summary of query, report and download features. </li> <li> Select the <a href="/ld-search.html">Search</a> menu to find a chemical component or build a new chemical component.</li> <li> Select the <a href="/pyapps/ldHandler.py?formid=cc-browse-search&operation=smiles&target=$&category=aa&first=1"><span>Browse</span></a> menu to view tabulations of modified amino acids and nucleotides.</li> <li> Select the <a href="/ld-download.html">Download</a> for links to chemical dictionaries and resource files.</li> <li> Go <a href="http://deposit.rcsb.org/cc-dict-content-tutorial.pdf">here</a> for a brief tutorial on the content of the Chemical Component Dictionary. </li> </ul> </p> <br /><br /> <hr> <p style="font-size: 10px; text-align: center;"> | <a href="/acknowledgements.html">Citing and Acknowledgements<a> |  </p>  </div> <br class="clearfloat" />  <p> </p> <div id="footer"> <p> <a class="white" href="http://www.rcsb.org/index.html" target="_blank" style="float:right;"><i>© RCSB PDB   </i></a> </p> </div>  </div>  <script type="text/javascript"> var gaJsHost = (("https:" == document.location.protocol) ? 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