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<li ><a href='http://mmcif.wwpdb.org' target='_blank' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> PDBx/mmCIF</a></li> <li class='active'><a href='/data/ccd' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Chemical Component Dictionary</a></li> <li ><a href='/data/bird' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Biologically Interesting Molecule Reference Dictionary (BIRD)</a></li> </ul> </div> <div class="col-md-9"> <div class="wwpdb-content">  <style> td.code { font-family: monospace; } table.ccd { margin-bottom:20px; } </style> <script src="/js/jquery-2.1.0.min.js"></script> <script> function toggleTable(num) { var div = $("#div_table" + num); var tableDiv = $("#table" + num); if (div.css("height") == "0px") { div.animate({height: tableDiv.height() + 10}); } else { div.animate({height: 0}); } $("#table_icon_" + num).toggleClass("glyphicon-chevron-down"); $("#table_icon_" + num).toggleClass("glyphicon-chevron-up"); } </script> <h1>Chemical Component Dictionary</h1> <p>The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in PDB entries. This dictionary contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, chemical descriptors (SMILES & InChI), systematic chemical names, and idealized coordinates (generated using Molecular Networks' Corina, and if there are issues, OpenEye's OMEGA).</p> <p>The dictionary is organized by the 3-character alphanumeric code that PDB assigns to each chemical component. New chemical component definitions appear in the dictionary as the entries in which they are observed are released in the PDB archive; consequently, the dictionary is updated with each weekly PDB release. The dictionary is regularly reviewed and remediated. Any obsoleted components remain in the dictionary marked with status OBS.</p> <p>Users can search and browse the Chemical Component Dictionary using resources such as <a href="#pdbechem">PDBeChem</a> and <a href="#ligandExpo">Ligand Expo.</a></p> <p>The entire Chemical Component Dictionary and the companion dictionary of amino acid protonation variants can be downloaded from the wwPDB ftp site:</p> <p> Chemical Component Dictionary: <a href="https://files.wwpdb.org/pub/pdb/data/monomers/components.cif">mmCIF (plain text)</a> | <a href="https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz">mmCIF (gz)</a> | <a href="https://files.wwpdb.org/pub/pdb/data/monomers/components-pub.sdf.gz">SDF/MOL (gz)</a><br> Protonation Variants Companion Dictionary: <a href="https://files.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif">mmCIF (plain text)</a> | <a href="https://files.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif.gz">mmCIF (gz)</a><br> Chemical Component Model data file: <a href="https://files.wwpdb.org/pub/pdb/data/component-models/complete/chem_comp_model.cif">mmCIF (plain text)</a> | <a href="https://files.wwpdb.org/pub/pdb/data/component-models/complete/chem_comp_model.cif.gz">mmCIF (gz)</a><br> <small>Please note that these files are large, and may take a while to download. You may wish to right-click on the "plain text" link to save the file.</small></p> <p>The dictionary of protonation variants provides additional nomenclature information for the protonation states of standard amino acids in N-terminal, C-terminal, and free forms, and includes common side chain protonation states. The identifiers used in this extension dictionary longer identifier codes to distinguish the various protonation forms of the standard amino acids. For instance, an identifier code <em>ARG_LFOH_DHH12</em> is used to identify the arginine variant with a neutral peptide unit and side chain protonated at NH1. The extended identifier codes are not compatible with the 3-character format restrictions for the residue identifier in the PDB format, so these codes do not currently appear in PDB files. In PDB entries, protonated residues are identified by the 3-character code of their parent amino acid; however, the atom nomenclature for protonated forms will be taken from the variant dictionary definitions.</p> <p>The <a href="https://files.wwpdb.org/pub/pdb/data/component-models/complete/chem_comp_model.cif.gz">Chemical Component Model data file</a> contains the matching chemical structures in the Chemical Component Dictionary and the Cambridge Structural Database (CSD) archive. This reference file includes accession code correspondences, Cartesian coordinates and R-value, data-collection temperature and a disorder flag, SMILES and InChI descriptors, and a Digital Object Identifier (DOI) for the citation associated with the CSD entry.</p> <p>Prior to development of the Chemical Component Dictionary, PDB chemical information was solely in the form of connection tables. This older representation, called the PDB HET dictionary, is still made available on the wwPDB ftp site (<a href="https://files.wwpdb.org/pub/pdb/data/monomers/het_dictionary.txt">download</a>). PDB HET format dictionary entries for individual components are available at <a href="https://files.wwpdb.org/pub/pdb/data/monomers/">https://files.wwpdb.org/pub/pdb/data/monomers/</a>.</p> <p>The Chemical Component Dictionary was formerly called the HET Group Dictionary.</p> <p>Descriptions of chemical components in <a href="#mmcifFormat">mmCIF</a> and <a href="#pdbFormat">PDB</a> formats are provided below.</p> <p>J.D. Westbrook, C. Shao, Z. Feng, M. Zhuravleva, S. Velankar, J. Young (2014) The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank Bioinformatics doi: <a href="http://dx.doi.org/10.1093/bioinformatics/btu789" target="_blank">10.1093/bioinformatics/btu789</a></p> <a class="anchor" name="pdbechem"></a> <h3>PDBeChem</h3> <p><a href="https://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl" target="_blank">PDBeChem</a><sup><a href="#Article1">1</a></sup> offers a wide range of possibilities for searching and exploring the dictionary:</p> <ul> <li>Search for a particular 3-letter code</li> <li>Search using part of the name</li> <li>Search for a formula range</li> <li>Search for a substructure</li> <li>Search for a fragment expression</li> </ul> <p>Users can also search by references in macromolecules, molecule classification, and atom energy type.</p> <p>A generic browsing interface lets users follow links that are available from every record in order to navigate through the relationships of the dictionary. For example, a relationship link can be followed to view the atoms of a ligand and then for a particular atom, its bonds and energy types and so on.</p> <p>For more information, please see<br><a href="https://www.ebi.ac.uk/msd-srv/msdchem/ligand/help.htm" target="_blank">https://www.ebi.ac.uk/msd-srv/msdchem/ligand/help.htm</a></p> <a class="anchor" name="ligandExpo"></a> <h3>Ligand Expo</h3> <p><a href="http://ligand-expo.rcsb.org/index.html" target="_blank">Ligand Expo</a>, formerly the Ligand Depot<sup><a href="#Article2">2</a></sup>, can be used to navigate the Chemical Component Dictionary. It integrates databases, services, tools and methods related to small molecules, and allows users to:</p> <ul> <li>Search for a chemical component</li> <li>Browse tables of components that contain</li> <ul> <li>modified amino acids and nucleotides</li> <li>popular drugs (trade and generic names)</li> <li>common ring systems</li> </ul> <li>Review related information in chemical dictionaries and resource files (chemistry, geometry, atom nomenclature, and more)</li> <li>Download model and ideal chemical component coordinates</li> <li>View all instances of a component in released PDB entries</li> </ul> <p>Ligand Expo provides information in Chemical Component Dictionary and individual chemical components within PDB entries for download in a variety of formats and packaging at <a href="http://ligand-expo.rcsb.org/ld-download.html" target="_blank">http://ligand-expo.rcsb.org/ld-download.html</a>.</p> <a class="anchor" name="mmcifFormat"></a> <h3>Chemical Components in mmCIF Format</h3> <p>The mmCIF format combines collections of related data items (tokens) into categories. A category is essentially a table in which each token represents a row in the table. The question mark (?) is used to mark an item value as missing. A period (.) may be used to identify that there is no appropriate value for the item or that a value has been intentionally omitted.</p> <p>Vectors and tables of data may be encoded in mmCIF using a loop_ directive. To build a table, the data item names corresponding to the table columns are preceded by the loop_ directive, and followed by the corresponding rows of data.</p> <p>A detailed description of the <a href="http://mmcif.pdb.org/" target="_blank">mmCIF</a> syntax and logic structure is available.</p> <p>In the Chemical Component Dictionary, each chemical component is defined by sets of tokens in the five categories. Click on a category link to see the dictionary definitions of the category contents (with examples).</p> <div onclick="toggleTable(1);" class="wwpdb-table-link"> chem_comp  <i id="table_icon_1" class='glyphicon glyphicon-chevron-down' style='color:#ccc; float:right;'></i> </div> <div id="div_table1" class="wwpdb-table-toggle"> <div id="table1" style="padding:0px 10px 10px;"> <table class="table table-striped table-bordered ccd"> <tr> <th class="success">Token</th> <th class="success">Definition</th> <th class="success">Example</th> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.id.html" target="_blank">_chem_comp.id</a></td> <td>The alphanumeric code for the chemical component.</td> <td class="code">HYP</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.name.html" target="_blank">_chem_comp.name</a></td> <td>The name of the chemical component.</td> <td class="code">4-HYDROXYPROLINE</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.type.html" target="_blank">_chem_comp.type</a></td> <td>The type of monomer.</td> <td class="code">L-peptide linking</td> </tr> <tr> <td valign="top"><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_type.html" target="_blank">_chem_comp.pdbx_type</a></td> <td>A preliminary internal classification used by PDB.</td> <td class="code">ATOMP</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.formula.html" target="_blank">_chem_comp.formula</a></td> <td>The chemical formula of the chemical component.</td> <td class="code">C5 H9 N1 O3'</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.mon_nstd_parent_comp_id.html" target="_blank">_chem_comp.mon_nstd_parent_comp_id</a></td> <td>The identifier for the parent component of the nonstandard component. May be a comma-separated list if this component is derived from multiple components.</td> <td class="code">PRO</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_synonyms.html" target="_blank">_chem_comp.pdbx_synonyms</a></td> <td>Synonym list for the non-standard residue.</td> <td class="code">HYDROXYPROLINE</td> </tr>  <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_formal_charge.html" target="_blank">_chem_comp.pdbx_formal_charge</a></td> <td>The formal charge on the chemical component.</td> <td class="code">+1</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_initial_date.html" target="_blank">_chem_comp.pdbx_initial_date</a></td> <td>Date the chemical component was added to the database.</td> <td class="code">yyyy-mm-dd</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_modified_date.html" target="_blank">_chem_comp.pdbx_modified_date</a></td> <td>Date that the component was last modified.</td> <td class="code">yyyy-mm-dd</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_ambiguous_flag.html" target="_blank">_chem_comp.pdbx_ambiguous_flag</a></td> <td>For ligands with unconventional bonding (i.e. ligands with transition metal complexes).</td> <td class="code">code</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_release_status.html" target="_blank">_chem_comp.pdbx_release status</a></td> <td>Status of ligand (released, hold, obsoleted).</td> <td class="code">yyyy-mm-dd</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_replaced_by.html" target="_blank">_chem_comp.pdbx_replaced_by</a></td> <td>Identifies the _chem_comp.id of the new component that has replaced this component.</td> <td class="code">3-letter identifier</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_replaces.html" target="_blank">_chem_comp.pdbx_replaces</a></td> <td>Identifies the _chem_comp.id of the component this entry replaces. Converse of _replaced_by.</td> <td class="code">3-letter identifier</td> </tr> <tr> <td valign="top"><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.formula_weight.html" target="_blank">_chem_comp.formula_weight</a></td> <td> Formula mass of the chemical component in Daltons.</td> <td class="code">131.131</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.one_letter_code.html" target="_blank">_chem_comp.one_letter_code</a></td> <td>Reports the one-letter code of the component, if applicable.</td> <td class="code">one-letter identifier</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.three_letter_code.html" target="_blank">_chem_comp.three_letter_code</a></td> <td>Reports the three-letter code of the component, if applicable.</td> <td class="code">ATP</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_model_coordinates_details.html" target="_blank">_chem_comp.pdbx_model_coordinates_details</a></td> <td>Provides additional details about the model coordinates in the component definition.</td> <td class="code">text</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_model_coordinates_missing_flag.html" target="_blank">_chem_comp.pdbx_model_coordinates_missing_flag</a></td> <td>This data item identifies if model coordinates are missing in this definition</td> <td class="code">Y or N</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_ideal_coordinates_details.html" target="_blank">_chem_comp.pdbx_ideal_coordinates_details</a></td> <td>Identifies the source of the ideal coordinates in the component definition.</td> <td class="code">text</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_ideal_coordinates_missing_flag.html" target="_blank">_chem_comp.pdbx_ideal_coordinates_missing_flag</a></td> <td>Identifies if ideal coordinates are missing in this definition.</td> <td class="code">Y or N</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_model_coordinates_db_code.html" target="_blank">_chem_comp.pdbx_model_coordinates_db_code</a></td> <td>Identifies the PDB database code from which the heavy atom model coordinates were obtained.</td> <td class="code">PDB entry id</td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_processing_site.html" target="_blank">_chem_comp.pdbx_processing_site</a></td> <td>Identifies the deposition site that processed this chemical component defintion.</td> <td class="code">RCSB PDB, PDBj, PDBe</td> </tr> </table> </div> </div> <div onclick="toggleTable(2);" class="wwpdb-table-link"> chem_comp_atom  <i id="table_icon_2" class='glyphicon glyphicon-chevron-down' style='color:#ccc; float:right;'></i> </div> <div id="div_table2" class="wwpdb-table-toggle"> <div id="table2" style="padding:0px 10px 10px;"> <p>Tokens in this section are looped through for each atom in the chemical component</p> <table class="table table-striped table-bordered ccd"> <tr> <th class="success">Token</th> <th class="success">Definition</th> <th class="success">Example</th> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.comp_id.html" target="_blank">_chem_comp_atom.comp_id</a></td> <td>Same as _chem_comp.id</td> <td class="code"> HYP </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.atom_id.html" target="_blank">_chem_comp_atom.atom_id</a></td> <td>Identifier for each atom in the chemical component - new format</td> <td class="code"> CA </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.alt_atom_id.html" target="_blank">_chem_comp_atom.alt_atom_id</a></td> <td>Previous format of identifier for each atom in the chemical component.</td> <td class="code"> CA </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.type_symbol.html" target="_blank">_chem_comp_atom.type_symbol</a></td> <td>The element type for each atom in the chemical component.</td> <td class="code"> C O N, etc. </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.charge.html" target="_blank">_chem_comp_atom.charge</a></td> <td>The formal charge assigned to each atom in the chemical component.</td> <td class="code"> 0 </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.pdbx_align.html" target="_blank">_chem_comp_atom.pdbx_align</a></td> <td>Determines which column the atom name appears within the PDB coordinate files. The possible values are 0 or 1.</td> <td class="code"> 0 or 1 </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.pdbx_aromatic_flag.html" target="_blank">_chem_comp_atom.pdbx_aromatic_flag</a></td> <td>Defines atoms in an aromatic moiety.</td> <td class="code"> Y or N </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.pdbx_leaving_atom_flag.html" target="_blank">_chem_comp_atom.pdbx_leaving_atom_flag</a></td> <td>Flags atoms with "leaving" capability.</td> <td class="code"> Y or N </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.pdbx_stereo_config.html" target="_blank">_chem_comp_atom.pdbx_stereo_config</a></td> <td>Defines the stereochemical configuration of the chiral center atom.</td> <td class="code"> R or S or N </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.model_Cartn_x.html" target="_blank">_chem_comp_atom.model_Cartn_x</a></td> <td>The x component of the coordinates for each atom specified as orthogonal angstroms.</td> <td class="code"> 26.056 </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.model_Cartn_y.html" target="_blank">_chem_comp_atom.model_Cartn_y</a></td> <td>The y component of the coordinates for each atom specified as orthogonal angstroms.</td> <td class="code"> 5.609 </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.model_Cartn_z.html" target="_blank">_chem_comp_atom.model_Cartn_z</a></td> <td>The z component of the coordinates for each atom specified as orthogonal angstroms.</td> <td class="code"> 5.594 </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.pdbx_model_Cartn_x_ideal.html" target="_blank">_chem_comp_atom.pdbx_model_Cartn_x_ideal</a></td> <td>Computed idealized coordinates, x component of the vector (in Angstroms)</td> <td class="code"> number </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.pdbx_model_Cartn_y_ideal.html" target="_blank">_chem_comp_atom.pdbx_model_Cartn_y_ideal</a></td> <td>Computed idealized coordinates, y component of the vector (in Angstroms)</td> <td class="code"> number </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.pdbx_model_Cartn_z_ideal.html" target="_blank">_chem_comp_atom.pdbx_model_Cartn_z_ideal</a></td> <td>Computed idealized coordinates, z component of the vector (in Angstroms)</td> <td class="code"> number </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_atom.pdbx_ordinal.html" target="_blank">_chem_comp_atom.pdbx_ordinal</a></td> <td>Ordinal index for the chemical component atom list. </td> <td class="code"> 1 (integer) </td> </tr> </table> </div> </div> <div onclick="toggleTable(3);" class="wwpdb-table-link"> chem_comp_bond  <i id="table_icon_3" class='glyphicon glyphicon-chevron-down' style='color:#ccc; float:right;'></i> </div> <div id="div_table3" class="wwpdb-table-toggle"> <div id="table3" style="padding:0px 10px 10px;"> <p>Tokens in this section are looped through for each bond in the chemical component</p> <table class="table table-striped table-bordered ccd"> <tr> <th class="success">Token</th> <th class="success">Definition</th> <th class="success">Example</th> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_bond.comp_id.html" target="_blank">_chem_comp_bond.comp_id</a></td> <td>Same as _chem_comp.id</td> <td class="code"> HYP </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_bond.atom_id_1.html" target="_blank">_chem_comp_bond.atom_id_1</a></td> <td>The ID of the first of the two atoms that define the bond.</td> <td class="code"> N </td> </tr> <tr> <td>_<a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_bond.atom_id_2.html" target="_blank">chem_comp_bond.atom_id_2</a></td> <td>The ID of the second of the two atoms that define the bond.</td> <td class="code"> CA </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_bond.value_order.html" target="_blank">_chem_comp_bond.value_order</a></td> <td>The bond order of the chemical bond associated with the specified atoms.</td> <td class="code"> SING </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_bond.pdbx_aromatic_flag.html" target="_blank">_chem_comp_bond.pdbx_aromatic_flag</a></td> <td>Defines aromatic bonds. </td> <td class="code"> Y or N </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_bond.pdbx_stereo_config.html" target="_blank">_chem_comp_bond.pdbx_stereo_config</a></td> <td>Defines stereochemical bonds.</td> <td class="code"> Y or N </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp_bond.pdbx_ordinal.html" target="_blank">_chem_comp_bond.pdbx_ordinal</a></td> <td>Ordinal index for the component bond list. </td> <td class="code"> 1 (integer) </td> </tr> </table> </div> </div> <div onclick="toggleTable(4);" class="wwpdb-table-link"> pdbx_chem_comp_descriptor  <i id="table_icon_4" class='glyphicon glyphicon-chevron-down' style='color:#ccc; float:right;'></i> </div> <div id="div_table4" class="wwpdb-table-toggle"> <div id="table4" style="padding:0px 10px 10px;"> <table class="table table-striped table-bordered ccd"> <tr> <th class="success">Token</th> <th class="success">Definition</th> <th class="success">Example</th> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_descriptor.comp_id.html" target="_blank">_pdbx_chem_comp_descriptor.comp_id</a></td> <td>This data item is a pointer to _chem_comp.id in the CHEM_COMP category.</td> <td class="code"> text </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_descriptor.type.html" target="_blank">_pdbx_chem_comp_descriptor.type</a></td> <td>The type of the program or library used to compute the descriptor.</td> <td class="code"> text </td> </tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_descriptor.program.html" target="_blank">_pdbx_chem_comp_descriptor.program</a></td> <td>The name of the program or library used to compute the descriptor.</td> <td class="code"> text </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_descriptor.program_version.html" target="_blank">_pdbx_chem_comp_descriptor.program_version</a></td> <td>The version of the program or library used to compute the descriptor.</td> <td class="code"> version number </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_descriptor.descriptor.html" target="_blank">_pdbx_chem_comp_descriptor.descriptor</a></td> <td>The chemical descriptor value for this component.</td> <td class="code"> code </td> </tr> </table> </div> </div> <div onclick="toggleTable(5);" class="wwpdb-table-link"> pdbx_chem_comp_identifier  <i id="table_icon_5" class='glyphicon glyphicon-chevron-down' style='color:#ccc; float:right;'></i> </div> <div id="div_table5" class="wwpdb-table-toggle"> <div id="table5" style="padding:0px 10px 10px;"> <table class="table table-striped table-bordered ccd"> <tr> <th class="success">Token</th> <th class="success">Definition</th> <th class="success">Example</th> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_identifier.comp_id.html" target="_blank">_pdbx_chem_comp_identifier.comp_id</a></td> <td>This data item is a pointer to _chem_comp.id in the CHEM_COMP category.</td> <td class="code"> text </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_identifier.type.html" target="_blank">_pdbx_chem_comp_identifier.type</a></td> <td>Contains the identifier type.</td> <td class="code"> CAS Reg No. or PUBCHEM, etc. </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_identifier.program.html" target="_blank">_pdbx_chem_comp_identifier.program</a></td> <td>The name of the program or library used to compute the identifier.</td> <td class="code"> OpenEye OECHEM program, etc. </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_identifier.program_version.html" target="_blank">_pdbx_chem_comp_identifier.program_version</a></td> <td>The version of the program or library used to compute the identifier.</td> <td class="code"> v1.2 (numbers) </td> </tr> <tr> <td><a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_identifier.identifier.html" target="_blank">_pdbx_chem_comp_identifier.identifier</a></td> <td>Contains the identifier value for this chemical component..</td> <td class="code"> text </td> </tr> </table> </div> </div> <br /> <p>In a PDB entry, the mmCIF category chem_comp is used to describe the chemical components in the file. The chemical name is described in chem_comp.name, chemical formula in chem_comp.formula, and molecular weight in chem_comp.formula_weight.</p> <p>For example, the mmCIF file for PDB entry 1t5d contains the ligand 4-Chloro-benzoic Acid (ID code: 174):</p> <div class="bg-lightgrey"> <pre class="cite"> data_174 # _chem_comp.id 174 _chem_comp.name "4-CHLORO-BENZOIC ACID" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C7 H5 Cl O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-05-07 _chem_comp.pdbx_modified_date 2008-04-29 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 156.566 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 174 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code Â 1T5D _chem_comp.pdbx_processing_site RCSB </pre> </div> <p>Further information describing this residue (174) is then provided in the Chemical Component Dictionary (See the <a href="#mmcifExample">example</a> below).</p> <a class="anchor" name="pdbFormat"></a> <h3>Chemical Components in PDB Format</h3> <p>The heterogen section of a PDB coordinate file describes ligands in the entry. The chemical name of the ligand is given in the HETNAM record and the chemical formula is given in the FORMUL record. Any synonyms for the chemical name are given in the HETSYN records.</p> <p>For example, the PDB format file for PDB entry 1t5d contains the ligand 4-Chloro-benzoic Acid (ID code: 174):</p> <div class="bg-light-grey"> <pre class="cite"> HET 174 15 HETNAM 174 4-CHLORO-BENZOIC ACID FORMUL 174 C7 H5 CL O2 </pre> </div> <p>Further information describing this residue (174) is then provided in the Chemical Component Dictionary (See the <a href="#pdbExample">example</a> below).</p> <p>Please refer to the <a href="../documentation/file-format.php">PDB File Format Guide</a> for further description.</p> <a class="anchor" name="mmcifExample"></a> <h3>Examples</h3> <p><h4>Chemical Component Dictionary (mmCIF Format)</h4></p> <div class="bg-lightgrey"> <pre class="cite"> data_174 # _chem_comp.id 174 _chem_comp.name "4-CHLORO-BENZOIC ACID" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C7 H5 Cl O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-05-07 _chem_comp.pdbx_modified_date 2008-04-29 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 156.566 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 174 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1T5D _chem_comp.pdbx_processing_site RCSB # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_ordinal 174 CL4 CL4 CL 0 0 N N N -19.787 95.862 18.541 0.032 -0.000 -3.376 1 174 C4 C4 C 0 1 Y N N -19.932 94.201 19.219 0.005 -0.000 -1.640 2 174 C5 C5 C 0 1 Y N N -18.817 93.715 19.901 -1.205 0.000 -0.969 3 174 C6 C6 C 0 1 Y N N -18.847 92.452 20.466 -1.233 0.000 0.409 4 174 C3 C3 C 0 1 Y N N -21.099 93.428 19.089 1.196 -0.000 -0.932 5 174 C2 C2 C 0 1 Y N N -21.127 92.158 19.664 1.182 0.004 0.446 6 174 C1 C1 C 0 1 Y N N -19.996 91.681 20.342 -0.036 -0.000 1.128 7 174 C C C 0 1 N N N -19.962 90.330 20.989 -0.059 -0.000 2.605 8 174 O1 O1 O 0 1 N N N -20.968 89.592 20.924 1.097 -0.001 3.296 9 174 O2 O2 O 0 1 N N N -18.919 89.991 21.597 -1.120 0.000 3.196 10 174 H5 H5 H 0 1 N N N -17.907 94.332 19.994 -2.130 0.001 -1.526 11 174 H6 H6 H 0 1 N N N -17.967 92.065 21.008 -2.178 0.000 0.931 12 174 H3 H3 H 0 1 N N N -21.978 93.812 18.545 2.138 -0.001 -1.461 13 174 H2 H2 H 0 1 N N N -22.035 91.537 19.583 2.110 0.003 0.997 14 174 HO1 HO1 H 0 1 N N N -20.946 88.735 21.334 1.082 -0.001 4.263 15 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 174 CL4 C4 SING N N 1 174 C4 C5 DOUB Y N 2 174 C4 C3 SING Y N 3 174 C5 C6 SING Y N 4 174 C5 H5 SING N N 5 174 C6 C1 DOUB Y N 6 174 C6 H6 SING N N 7 174 C3 C2 DOUB Y N 8 174 C3 H3 SING N N 9 174 C2 C1 SING Y N 10 174 C2 H2 SING N N 11 174 C1 C SING N N 12 174 C O1 SING N N 13 174 C O2 DOUB N N 14 174 O1 HO1 SING N N 15 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor 174 SMILES ACDLabs 10.04 O=C(O)c1ccc(Cl)cc1 174 SMILES_CANONICAL CACTVS 3.341 OC(=O)c1ccc(Cl)cc1 174 SMILES CACTVS 3.341 OC(=O)c1ccc(Cl)cc1 174 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cc(ccc1C(=O)O)Cl 174 SMILES "OpenEye OEToolkits" 1.5.0 c1cc(ccc1C(=O)O)Cl 174 InChI InChI 1.02b InChI=1/C7H5ClO2/c8-6- 3-1-5(2-4-6)7(9)10/h1-4H,(H,9,10)/f/h9H 174 InChIKey InChI 1.02b XRHGYUZYPHTUJZ-BGGKNDAXCA # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier 174 "SYSTEMATIC NAME" ACDLabs 10.04 "4-chlorobenzoic acid" 174 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "4-chlorobenzoic acid" # </pre> </div> <a class="anchor" name="pdbExample"></a> <p><h4>Heterogen List (PDB Format)</h4></p> <div class="bg-lightgrey"> <pre class="cite"> RESIDUE 174 15 CONECT CL4 1 C4 CONECT C4 3 CL4 C5 C3 CONECT C5 3 C4 C6 H5 CONECT C6 3 C5 C1 H6 CONECT C3 3 C4 C2 H3 CONECT C2 3 C3 C1 H2 CONECT C1 3 C6 C2 C CONECT C 3 C1 O1 O2 CONECT O1 2 C HO1 CONECT O2 1 C CONECT H5 1 C5 CONECT H6 1 C6 CONECT H3 1 C3 CONECT H2 1 C2 CONECT HO1 1 O1 END HET 174 15 HETNAM 174 4-CHLORO-BENZOIC ACID FORMUL 174 7 H5 Cl1 O2 </pre> </div> <br> <small> <ol> <li><a class="anchor" name="Article1"></a>D. Dimitropoulos, J. Ionides, K. Henrick (2006) UNIT 14.3: Using MSDchem to search the PDB ligand dictionary In Current Protocols in Bioinformatics (A.D. Baxevanis, R.D.M. Page, G.A. Petsko, L.D. Stein, and G.D. Stormo, eds.) pp 14.3.1-14.3.3 John Wiley & Sons, Hoboken, NJ.</li> <li><a class="anchor" name="Article2"></a>Z. Feng, L. Chen, H. Maddula, O. Akcan, R. Oughtred, H.M. Berman, J. Westbrook. (2004) Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics 20(13):2153-2155.</li> </ol> </small>  </div> </div> </div> <br> <footer class="footer"> <div class="container-fluid hidden-print" style="position: relative;"> <div class="row topFooter tinyPad"> <div class="ScreenLimitFooter"> <div class="col-sm-4"> <div class="smallMarginTop"> <a href="https://www.facebook.com/pages/Worldwide-PDB/223648640998643" target="_blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/facebook.png" width="24" height="24"></a> <a href="https://www.youtube.com/channel/UCgM7zpapumhWHDMV11FIz0Q" target="_blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/youtube-logo.png" width="24" height="24"></a> <a href="#"><img alt="RSS Feed for the Latest News" src="https://cdn.rcsb.org/wwpdb/img/core/rss.png" width="24" height="24"></a> <a href="mailto: info@wwpdb.org"><img src="https://cdn.rcsb.org/wwpdb/img/core/mail.png" width="24" height="24"></a> </div> <div class="smallMarginTop"> <a href="/news/news.php"> <p><a href="/news/news.php">News & Announcements</a></p> </a> </div> <div> <p><a href="https://lists.wwpdb.org/list/pdb-l.lists.wwpdb.org">Community Bulletin Board</a></p> </div> <div><a class='brand hidden-desktop' href='http://foundation.wwpdb.org/' target='_blank'><img src="https://cdn.rcsb.org/wwpdb/img/core/wwpdb-foundation-logo.png" class="logoLimit smallMarginTop"></a></div> </div> <div class="col-sm-4"> <div class="tinyMarginTop"> <h4><a class="h4-link" href="/download/downloads.php">Download Archive</a></h4> </div> <div class="smallMarginTop"> <a href="https://files.wwpdb.org/pub/pdb/">RCSB PDB</a> | <a href="https://ftp.ebi.ac.uk/pub/databases/pdb/">PDBe</a> | <a href="https://ftp.pdbj.org/pub/pdb/">PDBj</a> <br> <a href="/download/downloads.php">Instructions</a> </div> <div class="row"> <div class="col-sm-4"> <div class="tinyMarginTop"> <h4>Archive Snapshots</h4> </div> <div class="smallMarginTop"> <a href="https://s3snapshots.rcsb.org">RCSB PDB (https)</a> | <a href="ftp://snapshots.pdbj.org/">PDBj</a> </div> </div>  </div> </div> <div class="col-sm-3"> <h4> Cite wwPDB: </h4> <div class="smallMarginTop"> <em>Nature Structural Biology</em> <strong>10</strong>, 980 (2003)<br> <a href="http://dx.doi.org/10.1038/nsb1203-980" target="_blank">doi: 10.1038/nsb1203-980</a> <p class="tinyMarginTop"><a href="/about/publications.php">More publications</a></p> </div> </div> <div class="row" style="padding: 40px 0px 10px 10px"> <div class="col-sm-7"> <div class="tinyPad"> <h4>wwPDB Members:</h4> </div> <div class="col-sm-2 tinyPad"><a href="https://www.pdbj.org/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/pdbj.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.rcsb.org/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/rcsb-pdb.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.ebi.ac.uk/pdbe/emdb/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/emdb.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="http://bmrb.io/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/bmrb.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.ebi.ac.uk/pdbe/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/pdbe.png" class="logoLimit img-responsive"></a></div> </div> <div class="col-sm-1"><br></br></div> <div class="col-sm-4"> <div class="row"> <div class="col-xs-6"> <a href='http://www.CoreTrustSeal.org' target='_blank'><img src="https://cdn.rcsb.org/wwpdb/img/homepage/CoreTrustSeal-logo-transparent-small.png" class='img-responsive seal' style="border-right: 1px solid #666; padding-right: 50px"/></a> </div> <div class="col-xs-6"> <a href='https://globalbiodata.org/' target='_blank'><img src="https://cdn.rcsb.org/wwpdb/img/homepage/GCBR-Logo-RGB.png" class='img-responsive seal'/></a> </div> </div> </div> </div> </div> <div class="row bottomFooter"> © wwPDB </div> </div> </footer>  <script type="text/javascript" src="/js/jquery-2.1.0.min.js"></script> <script type="text/javascript" src="/js/bootstrap-3.1.1.min.js"></script> <script type="text/javascript" src="/js/NavbarControl.js?v2"></script> <script> (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-62256915-1', 'auto'); ga('send', 'pageview'); </script> </body> </html>