biojs-vis-pdbviewer
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A BioJS 2.0 component to view protein structures
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<span class="h3">PROTOPORPHYRIN IX CONTAINING FE</span>
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<span class="h5">
HEM
is found in <a class="se_searchLink" title="Click to search for entries that have this ligand as a free ligand or as a modified polymeric residue" href="http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=ChemCompIdQuery&chemCompId=HEM&polymericType=Any">3177 entries</a>
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<td class="key perc25"> Name </td>
<td class="value">
PROTOPORPHYRIN IX CONTAINING FE
</td>
</tr>
<tr class="even">
<td class="key perc25">Identifiers </td>
<td class="value">
3,3'-(7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-diyl)dipropanoic acid<br />
3-[(5Z,10Z,14Z,19Z)-18-(2-carboxyethyl)-8,13-bis(ethenyl)-3,7,12,17-tetramethyl-21,23-dihydroporphyrin-2-yl]propanoic acid<br />
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<td class="key perc25">
Synonyms
</td>
<td class="value">
HEME
</td>
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<td class="key perc25">
Formula
</td>
<td class="value">
C<sub>3</sub><sub>4</sub> H<sub>3</sub><sub>2</sub> Fe N<sub>4</sub> O<sub>4</sub>
</td>
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<tr class="odd">
<td class="key perc25">
Molecular Weight
</td>
<td class="value">
616.49 g/mol
</td>
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<td class="key perc25">
Type
</td>
<td class="value">
non-polymer
</td>
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<td class="key perc25">
Isomeric SMILES
</td>
<td class="value">
<textarea class="stringWrapper" readonly="readonly">CC1=C(CCC(O)=O)C2=Cc3c(CCC(O)=O)c(C)c4C=C5C(C)=C(C=C)C6=[N]5[Fe]5([N]2=C1C=c1c(C=C)c(C)c(=C6)n51)n34</textarea>
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<td class="key perc25">
InChI
</td>
<td class="value">
<textarea class="stringWrapper" readonly="readonly">InChI=1S/C34H34N4O4/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25/h7-8,13-16,36-37H,1-2,9-12H2,3-6H3,(H,39,40)(H,41,42)/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-</textarea>
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<td class="key perc25">
InChI key
</td>
<td class="value">
FEDYMSUPMFCVOD-UJJXFSCMSA-N
</td>
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<div style="margin-bottom:10px"> The chemistry of this component is ambiguous (group, ion, metal cluster etc.) </div>
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SMILES_CANONICAL (CACTVS)
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<textarea class="stringWrapper" readonly="readonly">Cc1c2[nH]c(cc3nc(cc4[nH]c(cc5nc(c2)c(C)c5C=C)c(C)c4C=C)c(C)c3CCC(O)=O)c1CCC(O)=O</textarea>
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SMILES (ACDLabs)
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<textarea class="stringWrapper" readonly="readonly">O=C(O)CCc5c(c2nc5cc1nc(C(=C1CCC(=O)O)C)cc4c(c(c(cc3nc(c2)C(=C3\C=C)C)n4)C)\C=C)C</textarea>
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<a class="se_external" href="http://www.bindingdb.org/bind/searchby_smiles.jsp?Similarity=0.90&SearchType=3&submit=Search&smilesStr=CC1%3DC%28CCC%28O%29%3DO%29C2%3DCc3c%28CCC%28O%29%3DO%29c%28C%29c4C%3DC5C%28C%29%3DC%28C%3DC%29C6%3D%5BN%5D5%5BFe%5D5%28%5BN%5D2%3DC1C%3Dc1c%28C%3DC%29c%28C%29c%28%3DC6%29n51%29n34" target="resource_window" style="white-space:nowrap;"> BindingDB <span class="iconSet-main icon-search"> </span></a>
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Searches for more than 90% similar small molecules in BindingDB, a public database of measured binding affinities of drug-like molecules with protein drug-targets
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<td class="key perc25">
<a class="se_external"
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target="resource_window" style="white-space:nowrap;"> ChEBI <span class="iconSet-main icon-search"> </span></a>
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Searches ChEBI, a freely available dictionary of molecular entities that incorporates an ontological classification
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<td class="key perc25">
<a class="se_external" href="http://www.chemspider.com/Search.aspx?q=CC1%3DC%28CCC%28O%29%3DO%29C2%3DCc3c%28CCC%28O%29%3DO%29c%28C%29c4C%3DC5C%28C%29%3DC%28C%3DC%29C6%3D%5BN%5D5%5BFe%5D5%28%5BN%5D2%3DC1C%3Dc1c%28C%3DC%29c%28C%29c%28%3DC6%29n51%29n34" target="resource_window" style="white-space:nowrap;"> ChemSpider <span class="iconSet-main icon-search"> </span></a>
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<td class="value">
Searches ChemSpider, a free access service providing a structure centric community for chemists
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<td class="key perc25">
<a class="se_external" href="http://cactus.nci.nih.gov/cgi-bin/lookup/results?context_all=all&type=smiles&query=CC1%3DC%28CCC%28O%29%3DO%29C2%3DCc3c%28CCC%28O%29%3DO%29c%28C%29c4C%3DC5C%28C%29%3DC%28C%3DC%29C6%3D%5BN%5D5%5BFe%5D5%28%5BN%5D2%3DC1C%3Dc1c%28C%3DC%29c%28C%29c%28%3DC6%29n51%29n34" target="resource_window" style="white-space:nowrap;"> CSLS <span class="iconSet-main icon-search"> </span></a>
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Searches the Chemical Structure Lookup Service (CSLS), meant to work as an address book for chemical structures
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<td class="key perc25">
<a class="se_external" href="http://www.emolecules.com/cgi-bin/search?t=ex&q=CC1%3DC%28CCC%28O%29%3DO%29C2%3DCc3c%28CCC%28O%29%3DO%29c%28C%29c4C%3DC5C%28C%29%3DC%28C%3DC%29C6%3D%5BN%5D5%5BFe%5D5%28%5BN%5D2%3DC1C%3Dc1c%28C%3DC%29c%28C%29c%28%3DC6%29n51%29n34" target="resource_window" style="white-space:nowrap;"> eMolecules <span class="iconSet-main icon-search"> </span></a>
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Searches eMolecules providing suppliers and information for chemicals
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<td class="key perc25">
<a class="se_external" href="http://xray.bmc.uu.se/hicup/HEM/index.html" target="resource_window" style="white-space:nowrap;"> HIC-Up</a>
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<td class="value">
A freely accessible resource for structural biologists who are dealing dealing with hetero-compounds ("small molecules")
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<td class="key perc25">
<a class="se_external" href="http://www.genome.jp/tools-bin/strsearch_view_compound?PROGRAM=SUBCOMP&DATABASE=compound&opt_search=-m all&smiles=CC1%3DC%28CCC%28O%29%3DO%29C2%3DCc3c%28CCC%28O%29%3DO%29c%28C%29c4C%3DC5C%28C%29%3DC%28C%3DC%29C6%3D%5BN%5D5%5BFe%5D5%28%5BN%5D2%3DC1C%3Dc1c%28C%3DC%29c%28C%29c%28%3DC6%29n51%29n34&compute_btn=Compute" target="resource_window" style="white-space:nowrap;"> KEGG COMPOUND <span class="iconSet-main icon-search"> </span></a>
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<td class="value">
Searches KEGG COMPOUND for chemical substances and reactions that are relevant to life
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<td class="key perc25">
<a class="se_external" href="http://ligand-expo.rcsb.org/reports/H/HEM/index.html" target="resource_window" style="white-space:nowrap;">Ligand Expo</a>
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<td class="value">
An RCSB PDB resource for searching, exploring, and downloading information and coordinates about the chemical components found in the PDB
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<td class="key perc25">
<a class="se_external" href="http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?FUNCTION=getByCode&CODE=HEM" target="resource_window" style="white-space:nowrap;"> PDBeChem</a>
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<td class="value">
Dictionary of chemical components in the PDB
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<tr class="odd">
<td class="key perc25">
<a class="se_external"
href="http://pubchem.ncbi.nlm.nih.gov/search/search.cgi?cmd=search&q_type=dt&simp_schtp=fs&q_data=CC1%3DC%28CCC%28O%29%3DO%29C2%3DCc3c%28CCC%28O%29%3DO%29c%28C%29c4C%3DC5C%28C%29%3DC%28C%3DC%29C6%3D%5BN%5D5%5BFe%5D5%28%5BN%5D2%3DC1C%3Dc1c%28C%3DC%29c%28C%29c%28%3DC6%29n51%29n34"
target="resource_window" style="white-space:nowrap;"> PubChem <span class="iconSet-main icon-search"> </span></a>
</td>
<td class="value">
Searches PubChem, a component of NIH's Molecular Libraries Roadmap Initiative with information on the biological activities of small molecules
</td>
</tr>
<tr class="even">
<td class="key perc25">
<a class="se_external" href="http://bioinf-tomcat.charite.de/superligands/resultHET.faces?hetid=HEM" target="resource_window" style="white-space:nowrap;"> SuperLigands </a>
</td>
<td class="value">
An encyclopedia dedicated to a ligand oriented view that integrates different information about drug-likeness or binding properties
</td>
</tr>
<tr class="odd">
<td class="key perc25">
<a class="se_external" href="http://bioinformatics.charite.de/superhapten/hapten_similarity_marvin.php?hetero=HEM" target="resource_window" style="white-space:nowrap;"> SuperHapten <span class="iconSet-main icon-search"> </span></a>
</td>
<td class="value">
Searches for similar small molecules in SuperHapten, an immunogenic compound database
</td>
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<div class="box_header">
<b>Ligand Image</b>
</div>
</div>
<div class="w_body3">
<div class="box_contentWrapperNoPad">
<div class="middleCell" id="ligStatic">
<a rel="lightbox" href="http://www.rcsb.org/pdb/images/HEM_600.gif" >
<img src="http://www.rcsb.org/pdb/images/HEM_270.gif" />
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<div style="display:none;margin-bottom:5px;text-align:center" id="jmol_options">
<span style="display:none" id="jmol_box_resize_tip">Drag the right-bottom corner to resize.<br/></span>
<b>Toggle</b> <input type='checkbox' id='toggleHydrogens' checked='checked' onclick='toggleHydrogens()'>Hydrogens
<input type='checkbox' id='toggleLabels' checked='checked' onclick='toggleLabels()'>Labels
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<a rel="lightbox" href="http://www.rcsb.org/pdb/images/HEM_620.gif" >Large image</a> -
<a rel="lightbox" href="http://www.rcsb.org/pdb/images/HEM_600.gif" >View atom labels</a>
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<div class="button" id="jmolDiv">
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<a title="Jmol (Applet) requires Java plugin" id="jmol" name="jmol">
<span class="iconSet-main icon-3d"> </span> View in Jmol
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<ul id="lig_widgets_right" class="widget_list">
<!-- ============================================================================================================================================================================================================================== -->
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<table class="perc100"><tr>
<td class="leftCell" style="cursor:move;">
<span class="webDisplay iconSet-int icon-move" title="Click and Drag Section" > </span>
<b>Instances in PDB Entries</b>
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Hide
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<div class="lb_body3">
<div class="box_contentWrapper">
In polymers:
<a class="se_searchLink" title="Click to search for entries that have this ligand as a modified polymeric resiude" href="http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=ChemCompIdQuery&chemCompId=HEM&polymericType=Polymeric">
1 entries
</a>
<blockquote>
Ex: <a title="Click to view structure 3TNK" href="http://www.rcsb.org/pdb/explore.do?structureId=3TNK">3TNK</a>
</blockquote>
</div>
</div>
<div class="w_body3">
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As free ligands:
<a class="se_searchLink" title="Click to search for entries that have this ligand as a free ligand" href="http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=ChemCompIdQuery&chemCompId=HEM&polymericType=Free">
3177 entries
</a>
<blockquote>
Ex: <a title="Click to view structure 101M" href="http://www.rcsb.org/pdb/explore.do?structureId=101M">101M</a>, <a title="Click to view structure 102M" href="http://www.rcsb.org/pdb/explore.do?structureId=102M">102M</a>, <a title="Click to view structure 103M" href="http://www.rcsb.org/pdb/explore.do?structureId=103M">103M</a>...
</blockquote>
</div>
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<div class="box_contentWrapper">
Found in
<a class="se_searchLink" title="Click to search for entries that have this ligand as a free ligand or as a modified polymeric residue" href="http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=ChemCompIdQuery&chemCompId=HEM&polymericType=Any">3177 entries</a>
total.
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<b>Related Ligands in the PDB</b>
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Find <a class="se_searchLink tooltip" title="Find stereoisomers" href="http://www.rcsb.org/pdb/search/smart.do?smartSearchSubtype_0=ChemSmilesQuery&smiles_0=CC1%3DC%28CCC%28O%29%3DO%29C2%3DCc3c%28CCC%28O%29%3DO%29c%28C%29c4C%3DC5C%28C%29%3DC%28C%3DC%29C6%3D%5BN%5D5%5BFe%5D5%28%5BN%5D2%3DC1C%3Dc1c%28C%3DC%29c%28C%29c%28%3DC6%29n51%29n34&searchType_0=Exact&polymericType_0=Any&smartComparator=and&target=Ligand">stereoisomers</a>
</div>
</div>
<div class="w_body3">
<div class="box_contentWrapper">
Find <a class="se_searchLink tooltip" title="Find related ligands" href="http://www.rcsb.org/pdb/search/smart.do?smartSearchSubtype_0=ChemSmilesQuery&smiles_0=CC1%3DC%28CCC%28O%29%3DO%29C2%3DCc3c%28CCC%28O%29%3DO%29c%28C%29c4C%3DC5C%28C%29%3DC%28C%3DC%29C6%3D%5BN%5D5%5BFe%5D5%28%5BN%5D2%3DC1C%3Dc1c%28C%3DC%29c%28C%29c%28%3DC6%29n51%29n34&searchType_0=Similar&similarity_0=0.8&polymericType_0=Any&smartComparator=and&target=Ligand">similar ligands</a>
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<div class="lb_body3">
<div class="box_contentWrapper">
Use HEM for a <a class="se_searchLink tooltip" title="Use HEM for a Chemical Structure Search" href="chemAdvSearch.do?chemCompId=HEM">chemical structure search</a>
</div>
</div>
</div>
<div class="lb_foot3">
</div>
</div>
</li>
<li id="widget_lig_chemDetails" class="widget_on" >
<div>
<div class="db_head3">
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<table class="perc100"><tr>
<td class="leftCell" style="cursor:move;">
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<b>Chemical Details</b>
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Hide
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<div id="lig_chemDetails" >
<div class="w_body3">
<div class="box_contentWrapperNoPad">
<table class="plain">
<tr class="even">
<td class="key perc50">
Formal Charge
</td>
<td class="value perc50 middleCell">
0
</td>
</tr>
<tr class="odd">
<td class="key perc50">
Atom Count
</td>
<td class="value perc50 middleCell">
75
</td>
</tr>
<tr class="even">
<td class="key perc50">
Chiral Atom Count
</td>
<td class="value perc50 middleCell">
1
</td>
</tr>
<tr class="odd">
<td class="key perc50">
Chiral Atoms
</td>
<td class="value perc50 middleCell">
FE
</td>
</tr>
<tr class="even">
<td class="key perc50">
Bond Count
</td>
<td class="value perc50 middleCell">
82
</td>
</tr>
<tr class="odd">
<td class="key perc50">
Aromatic Bond Count
</td>
<td class="value perc50 middleCell">
28
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="lb_foot3">
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