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id="618271c92a7d828464a7d146" onclick="toggle("618271c92a7d828464a7d146")"><table><tr><td style="padding-left: 4px">Exploring a 3D Structure</td><td><span class="glyphicon glyphicon-triangle-top" id="glyph618271c92a7d828464a7d146"></span></td></tr></table></div><div class="item show" id="618274c904fb9835c6ae189a"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/overview">Overview</a></td></tr></table></div><div class="item show" id="618271f904fb9835c6ae1892"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/structure-summary-page">Structure Summary Page</a></td></tr></table></div><div class="item show" id="6182729704fb9835c6ae1893"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/structure">Structure</a></td></tr></table></div><div class="item show" id="618272c004fb9835c6ae1894"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/annotations">Annotations</a></td></tr></table></div><div class="item show" id="618272e004fb9835c6ae1895"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/experiment">Experiment</a></td></tr></table></div><div class="item show" id="618272fb04fb9835c6ae1896"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/sequence">Sequence</a></td></tr></table></div><div class="item show" id="6182730904fb9835c6ae1897"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/genome">Genome</a></td></tr></table></div><div class="item show" id="6182731a04fb9835c6ae1898"><table><tr><td class="title" style="padding-left: 24px"><a class="docs-index-link" href="/docs/exploring-a-3d-structure/ligands">Ligands</a></td><td><span class="glyphicon glyphicon-chevron-right"></span></td></tr></table></div><div class="item show" id="6182732a04fb9835c6ae1899"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/versions">Versions</a></td></tr></table></div><div class="group show" id="6256b2b3b4396e45e97bf3de" onclick="toggle("6256b2b3b4396e45e97bf3de")"><table><tr><td style="padding-left: 4px">Grouping Structures</td><td><span class="glyphicon glyphicon-triangle-bottom" id="glyph6256b2b3b4396e45e97bf3de"></span></td></tr></table></div><div class="item hidden" id="62fbafaf3b6e49562fa5c055"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/grouping-structures/overview-grouping-structures">Overview: Grouping Structures</a></td></tr></table></div><div class="item hidden" id="6081c10aec901916050494be"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/grouping-structures/sequence-based-clustering">Sequence-based Clustering</a></td></tr></table></div><div class="item hidden" id="6256b3269c3931864b07285b"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/grouping-structures/grouping-search-results">Grouping Search Results</a></td></tr></table></div><div class="item hidden" id="6256b35e9c3931864b07285c"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/grouping-structures/group-summary-pages">Group Summary Pages</a></td></tr></table></div><div class="item hidden" id="6364336066d6046810db7f11"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/grouping-structures/explore-sequence-alignments-in-3d">Explore Sequence Alignments in 3D</a></td></tr></table></div><div class="group show" id="5fd3e3a6eb210c2c5632d098" onclick="toggle("5fd3e3a6eb210c2c5632d098")"><table><tr><td style="padding-left: 4px">3D Viewers</td><td><span class="glyphicon glyphicon-triangle-bottom" id="glyph5fd3e3a6eb210c2c5632d098"></span></td></tr></table></div><div class="group hidden" id="5f98cc9614cc37a34de620ea" onclick="toggle("5f98cc9614cc37a34de620ea")"><table><tr><td style="padding-left: 24px">Mol*</td><td><span class="glyphicon glyphicon-triangle-bottom" id="glyph5f98cc9614cc37a34de620ea"></span></td></tr></table></div><div class="item hidden" id="5ee0fc4d25aa7b208a9fe39e"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/3d-viewers/mol*/getting-started">Getting Started</a></td></tr></table></div><div class="item hidden" id="5ee107b225aa7b208a9fe3a1"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/3d-viewers/mol*/maneuvering-in-mol*">Maneuvering in Mol*</a></td></tr></table></div><div class="item hidden" id="5ee10ad725aa7b208a9fe3a2"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/3d-viewers/mol*/making-selections">Making Selections</a></td></tr></table></div><div class="item hidden" id="5ee1046625aa7b208a9fe3a0"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/3d-viewers/mol*/navigating-by-sequence">Navigating by Sequence</a></td></tr></table></div><div 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class="item hidden" id="65a4b499c76ca3abcc925d0d"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/3d-viewers/ngl-to-mol*-ui-migration-guide">NGL to Mol* UI Migration Guide</a></td></tr></table></div><div class="group show" id="5fd3e3f4eb210c2c56332c65" onclick="toggle("5fd3e3f4eb210c2c56332c65")"><table><tr><td style="padding-left: 4px">Sequence Viewers</td><td><span class="glyphicon glyphicon-triangle-bottom" id="glyph5fd3e3f4eb210c2c56332c65"></span></td></tr></table></div><div class="item hidden" id="60103d1ab1afe64903398251"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/sequence-viewers/sequence-annotations-viewer">Sequence Annotations Viewer</a></td></tr></table></div><div class="item hidden" id="60342ff52087e87def0d0b09"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/sequence-viewers/sequence-annotations-in-3d">Sequence Annotations in 3D</a></td></tr></table></div><div class="item hidden" id="5fc7f2843fb4b83beb6a7a3d"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/sequence-viewers/genome-view">Genome View</a></td></tr></table></div><div class="item hidden" id="60182dc1ecb9a74be53123aa"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/sequence-viewers/protein-sequence-alignment-view">Protein Sequence Alignment View</a></td></tr></table></div><div class="group show" id="60132e62aeeea33d3f095fa8" onclick="toggle("60132e62aeeea33d3f095fa8")"><table><tr><td style="padding-left: 4px">Tools</td><td><span class="glyphicon glyphicon-triangle-bottom" id="glyph60132e62aeeea33d3f095fa8"></span></td></tr></table></div><div class="item hidden" id="60132e6a610d04019e01d4c2"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/tools/pairwise-structure-alignment">Pairwise Structure Alignment</a></td></tr></table></div><div class="group show" id="601024f3244a4309df5d6630" 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data-elastic-include><h5 class="menu-path">Exploring a 3D Structure</h5><h1>Ligands</h1><div><div style="padding-left:20px;">● <a href="#introduction">Introduction</a></div> <div style="padding-left:40px;">○ <a href="#what-are-ligands">What are Ligands?</a></div> <div style="padding-left:40px;">○ <a href="#why-learn-about-ligands">Why learn about ligands?</a></div> <div style="padding-left:40px;">○ <a href="#what-are-ligands-of-interest">What are ligands of interest?</a></div> <div style="padding-left:20px;">● <a href="#documentation">Documentation</a></div> <div style="padding-left:40px;">○ <a href="#the-interface">The Interface</a></div> <div style="padding-left:40px;">○ <a href="#learning-about-the-structure">Learning about the Structure</a></div> <div style="padding-left:40px;">○ <a href="#exploring-other-structures">Exploring other structures</a></div> <a class="content-anchor" id="introduction"></a> <h2>Introduction</h2> <a class="content-anchor" id="what-are-ligands"></a> <h3>What are Ligands?</h3> <p>Small molecules such as ions, cofactors, inhibitors, drugs, etc. are called ligands in the PDB. They are often found interacting with biological polymers (like proteins and nucleic acids) and may have structurally stabilizing or functional roles in their interactions with macromolecules.</p> <a class="content-anchor" id="why-learn-about-ligands"></a> <h3>Why learn about ligands?</h3> <p>Ligands often bind to pockets, cavities, and surfaces to facilitate their structural or functional roles. Thus, exploring the location of ligand binding and understanding a ligand’s interactions can help you understand the mechanism of biomolecular functions. It can also help you design or customize these interactions for specific purposes - e.g., to regulate the protein or nucleic acid function to treat or prevent a disease.</p> <a class="content-anchor" id="what-are-ligands-of-interest"></a> <h3>What are ligands of interest?</h3> <p>While there may be many different ligands interacting with the biological macromolecules in a structure, only those having an impact on the function(s) of the molecules in the structure are examined closely and validated. Note that at this time only X-ray structures that have experimental data and complete validation information are validated to assess goodness of fit for ligands. Learn more about <a href="/docs/general-help/ligand-structure-quality-in-pdb-structures" target="_blank">Ligand Validation</a>.</p> <a class="content-anchor" id="documentation"></a> <h2>Documentation</h2> <a class="content-anchor" id="the-interface"></a> <h3>The Interface</h3> <p>The Ligands tab displays the following plots and table for all validated non-polymer ligands, and indicate whether they are the ligands of interest (LOI). LOI is a functional ligand in macromolecular complexes designated as focus of research in the experiment by structure authors or by RCSB PDB under the criteria of: (1) Formula Weight > 150 Da, and (2) Not in an exclusion list of likely non-functional ligands, as described in <a href="/docs/general-help/ligand-structure-quality-in-pdb-structures" target="_blank">Ligand Validation</a>.</p> <table><tr><td><a href="https://cdn.rcsb.org/rcsb-pdb/content/6182731a04fb9835c6ae1898/lig-figure1-jan24.png" data-toggle="lightbox" data-title="Figure 1: A 2D plot of the quality of the ligand HEM’s goodness of fit for the best instance in the structure (green diamond) for the PDB entry 7lad (as of December 2023)"><img class="img-responsive" src="https://cdn.rcsb.org/rcsb-pdb/content/6182731a04fb9835c6ae1898/lig-figure1-jan24.png" alt="Figure 1: A 2D plot of the quality of the ligand HEM’s goodness of fit for the best instance in the structure (green diamond) for the PDB entry 7lad (as of December 2023)"> </a></td></tr><tr><td class="content-img-caption" style="width:1314px;">Figure 1: A 2D plot of the quality of the ligand HEM’s goodness of fit for the best instance in the structure (green diamond) for the PDB entry 7lad (as of December 2023)</td></tr></table><div style="height: 20px;"></div><p>In the Figure 1 (for the PDB ID 7lad) the</p> <ul style="list-style-type:disc;"> <li>Top half of the page has 2D plots showing </li> <ul style="list-style-type:disc;"> <li>quality of all instances of the ligand (HEM) in the entry (left plot).</li> <li>a comparison of the ligand quality in structures where the same ligand is bound to the same target (middle plot, yellow circles) or other targets (right plot, blue circles).</li> </ul> <li>Bottom half presents measures of ligand quality in instances of the ligand displayed in the 2D plots.</li> <li>Note for this structure there is no validation data available for the ligand XRD.</li> </ul> <div style="height: 20px;"></div><a class="content-anchor" id="learning-about-the-structure"></a> <h3>Learning about the Structure</h3> <p>The experimental data fitting vs geometry 2D plot in the left presents ligand quality for all instances of the ligand in the structure. The best instance is shown as a green diamond, while all other instances are shown as green circles. All other data on the ligands tab compares the quality of the ligand in the entry of interest in other structures.</p> <a class="content-anchor" id="exploring-other-structures"></a> <h3>Exploring other structures</h3> <p>The experimental data fitting vs geometry 2D plot in the left presents ligand quality for all instances of the ligand in the structure. The best instance is shown as a green diamond, while all other instances are shown as green circles. All other data on the ligands tab compares the quality of the ligand in the entry of interest in other structures.</p> <p>Various measures of fit to electron density and geometry of the ligand in other entries are presented in 2D plots and tabular format. This analysis allows you to compare the ligand of interest in these structures to the same ligand in other structures (either bound to the same or different targets) and select the best instance(s) for visualization, analysis, and hypothesis development. Learn more about the <a href="/docs/general-help/ligand-structure-quality-in-pdb-structures" target="_blank">ligand validation process and measures</a>. <br /><br />All instances of the ligand of interest in the archive can be found from the Ligand Definition and Summary page by clicking on the button on the top right corner of the page.</p> </div></div><br><hr><div class="item-info"><div>Please report any encountered broken links to <a href='mailto:info@rcsb.org'>info@rcsb.org</a></div><div>Last updated: 1/8/2024</div></div></div></div></div></div><div data-elastic-exclude><div class="hidden-print" id="footer_main"><div class="container" style="padding:0"><div class="row"><div class="col-md-6 col-sm-12" style="padding-left:0"> <div class="row"><div class="col-sm-4"><ul><li><span class="row_header">About</span></li><li><a href="/pages/about-us/index">About Us</a></li><li><a href="/pages/policies#References">Citing Us</a></li><li><a href="/pages/publications">Publications</a></li><li><a href="/pages/team">Team</a></li><li><a href="/pages/jobs">Careers</a></li><li><a href="/pages/policies">Usage & Privacy</a></li></ul></div><div class="col-sm-4" style="padding-left:0"><ul><li><span class="row_header">Support</span></li><li><a href="/pages/contactus">Contact Us</a></li><li><a href="/help">Help</a></li><li><a href="/docs/general-help/website-faq">Website FAQ</a></li><li><a href="/docs/general-help/glossary">Glossary</a></li><li><a href="https://status.rcsb.org/" target="_blank">Service Status</a></li></ul></div><div class="col-md-4 hidden-sm"></div></div></div><div class="col-md-6 col-sm-12" style="padding-left:5px"> <div class="row"><div class="col-sm-4"><p class="row_header">RCSB PDB is hosted by</p><div class="footerLogos"><hr><a href="http://www.rutgers.edu/"><img class="Rutgerslogo" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/Logo_Rutgers-2024.png" alt="Rutgers University logo"></a><hr><a href="https://ucsd.edu/"><img class="UCSDlogo" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/Logo_UCSD-navy.png" alt="Uiversity of California San Diego logo"></a><a href="https://www.sdsc.edu/"><img class="SDSClogo" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/Logo_SDSC-black.png" alt="San Diego Supercomputer Center logo"></a><hr><a href="https://www.ucsf.edu/"><img class="UCSFlogo" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/Logo_UCSF.png" alt="University of California San Francisco Logo"></a></div></div><div class="col-sm-4"><p class="row_header">RCSB PDB is a member of the</p><div class="footerLogos"><span id="pdbmembers_footer"><hr><a href="https://www.wwpdb.org" target="_blank" rel="noopener"><img class="wwpdblogo" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/Logo_wwpdb.png" alt="wwPDB"></a><hr><a href="https://www.emdataresource.org" target="_blank" rel="noopener"><img id="emdatabanklogo_footer" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/EMDataResourcelogo.png" alt="EMDataResource"></a></span></div></div><div class="col-sm-4"><ul><li><span class="row_header">RCSB Partners</span></li><li><a href="https://nakb.org/" target="_blank" rel="noopener">Nucleic Acid Knowledgebase</a></li></ul><ul><li><span class="row_header"><a href="https://www.wwpdb.org/" target="_blank" rel="noopener" style="text-decoration: none; color: black">wwPDB Partners</a></span></li><li><a href="/">RCSB PDB</a></li><li><a href="https://www.ebi.ac.uk/pdbe/" target="_blank" rel="noopener">PDBe</a></li><li><a href="https://www.pdbj.org/" target="_blank" rel="noopener">PDBj</a></li><li><a href="https://bmrb.io/" target="_blank" rel="noopener">BMRB</a></li><li><a href="https://emdb-empiar.org/" target="_blank" rel="noopener">EMDB</a></li></ul></div></div></div></div></div></div><div id="footer_grant"><div class="container"><div class="row"><p>RCSB PDB Core Operations are funded by the <a href="http://www.nsf.gov/" target="_blank" rel="noopener">U.S. National Science Foundation</a> (DBI-2321666), the <a href="http://science.energy.gov/" target="_blank" rel="noopener">US Department of Energy</a> (DE-SC0019749), and the <a href="http://www.cancer.gov/" target="_blank" rel="noopener">National Cancer Institute</a>, <a href="http://www.niaid.nih.gov/" target="_blank" rel="noopener">National Institute of Allergy and Infectious Diseases</a>, and <a href="http://www.nigms.nih.gov/" target="_blank" rel="noopener">National Institute of General Medical Sciences</a> of the <a href="http://www.nih.gov/" target="_blank" rel="noopener">National Institutes of Health</a> under grant R01GM157729.</p></div></div></div><div id="jira-fdbck"></div></div></div></body></html>