3pdc

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{{STRUCTURE_3pdc| PDB=3pdc | SCENE= }}
 
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===Crystal structure of hydrolase domain of human soluble epoxide hydrolase complexed with a benzoxazole inhibitor===
 
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{{ABSTRACT_PUBMED_21302953}}
 
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==Function==
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==Crystal structure of hydrolase domain of human soluble epoxide hydrolase complexed with a benzoxazole inhibitor==
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[[http://www.uniprot.org/uniprot/HYES_HUMAN HYES_HUMAN]] Bifunctional enzyme. The C-terminal domain has epoxide hydrolase activity and acts on epoxides (alkene oxides, oxiranes) and arene oxides. Plays a role in xenobiotic metabolism by degrading potentially toxic epoxides. Also determines steady-state levels of physiological mediators. The N-terminal domain has lipid phosphatase activity, with the highest activity towards threo-9,10-phosphonooxy-hydroxy-octadecanoic acid, followed by erythro-9,10-phosphonooxy-hydroxy-octadecanoic acid, 12-phosphonooxy-octadec-9Z-enoic acid, 12-phosphonooxy-octadec-9E-enoic acid, and p-nitrophenyl phospate.<ref>PMID:12574508</ref> <ref>PMID:12574510</ref>
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<StructureSection load='3pdc' size='340' side='right'caption='[[3pdc]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3pdc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PDC FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZYI:N-(5-CHLORO-1,3-BENZOXAZOL-2-YL)-2-CYCLOPENTYLACETAMIDE'>ZYI</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pdc OCA], [https://pdbe.org/3pdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pdc RCSB], [https://www.ebi.ac.uk/pdbsum/3pdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pdc ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/HYES_HUMAN HYES_HUMAN] Bifunctional enzyme. The C-terminal domain has epoxide hydrolase activity and acts on epoxides (alkene oxides, oxiranes) and arene oxides. Plays a role in xenobiotic metabolism by degrading potentially toxic epoxides. Also determines steady-state levels of physiological mediators. The N-terminal domain has lipid phosphatase activity, with the highest activity towards threo-9,10-phosphonooxy-hydroxy-octadecanoic acid, followed by erythro-9,10-phosphonooxy-hydroxy-octadecanoic acid, 12-phosphonooxy-octadec-9Z-enoic acid, 12-phosphonooxy-octadec-9E-enoic acid, and p-nitrophenyl phospate.<ref>PMID:12574508</ref> <ref>PMID:12574510</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Structure-based virtual screening was applied to design combinatorial libraries to discover novel and potent soluble epoxide hydrolase (sEH) inhibitors. X-ray crystal structures revealed unique interactions for a benzoxazole template in addition to the conserved hydrogen bonds with the catalytic machinery of sEH. By exploitation of the favorable binding elements, two iterations of library design based on amide coupling were employed, guided principally by the docking results of the enumerated virtual products. Biological screening of the libraries demonstrated as high as 90% hit rate, of which over two dozen compounds were single digit nanomolar sEH inhibitors by IC(50) determination. In total the library design and synthesis produced more than 300 submicromolar sEH inhibitors. In cellular systems consistent activities were demonstrated with biochemical measurements. The SAR understanding of the benzoxazole template provides valuable insights into discovery of novel sEH inhibitors as therapeutic agents.
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==About this Structure==
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Discovery of potent inhibitors of soluble epoxide hydrolase by combinatorial library design and structure-based virtual screening.,Xing L, McDonald JJ, Kolodziej SA, Kurumbail RG, Williams JM, Warren CJ, O'Neal JM, Skepner JE, Roberds SL J Med Chem. 2011 Mar 10;54(5):1211-22. Epub 2011 Feb 8. PMID:21302953<ref>PMID:21302953</ref>
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[[3pdc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PDC OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<ref group="xtra">PMID:021302953</ref><references group="xtra"/><references/>
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</div>
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<div class="pdbe-citations 3pdc" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Epoxide hydrolase 3D structures|Epoxide hydrolase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Soluble epoxide hydrolase]]
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[[Category: Large Structures]]
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[[Category: Kurumbail, R G.]]
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[[Category: Kurumbail RG]]
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[[Category: Williams, J M.]]
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[[Category: Williams JM]]
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[[Category: Acetylation of lysine]]
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[[Category: Alpha/beta hydrolase fold]]
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[[Category: Beta barrel]]
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[[Category: Binds mg2+]]
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[[Category: Cytoplasm]]
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[[Category: Epoxide hydrolase]]
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[[Category: Epoxide hydrolase fold]]
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[[Category: Hydrolase]]
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[[Category: Hydrolase-hydrolase inhibitor complex]]
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[[Category: Hypertension]]
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[[Category: Peroxisome]]
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Current revision

Crystal structure of hydrolase domain of human soluble epoxide hydrolase complexed with a benzoxazole inhibitor

PDB ID 3pdc

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