3wkd: Difference between revisions

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-{{STRUCTURE_3wkd|  PDB=3wkd  |  SCENE=  }}
-===Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor===
-{{ABSTRACT_PUBMED_24656800}}
-==Function==
+==Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor==
-[[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>
+<StructureSection load='3wkd' size='340' side='right'caption='[[3wkd]], [[Resolution|resolution]] 2.48&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3wkd]] is a 1 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=3WKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WKD FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.48&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=S0K:N-[2-(MORPHOLIN-4-YL)PHENYL]THIOPHENE-3-CARBOXAMIDE'>S0K</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3wkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wkd OCA], [https://pdbe.org/3wkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wkd RCSB], [https://www.ebi.ac.uk/pdbsum/3wkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wkd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Soluble epoxide hydrolase (sEH) is a component of the arachidonic acid cascade and is a candidate target for therapies for hypertension or inflammation. Although many sEH inhibitors are available, their scaffolds are not structurally diverse, and knowledge of their specific interactions with sEH is limited. To obtain detailed structural information about protein-ligand interactions, we conducted fragment screening of sEH, analyzed the fragments using high-throughput X-ray crystallography, and determined 126 fragment-bound structures at high resolution. Aminothiazole and benzimidazole derivatives were identified as novel scaffolds that bind to the catalytic triad of sEH with good ligand efficiency. We further identified fragment hits that bound to subpockets of sEH called the short and long branches. The water molecule conserved in the structure plays an important role in binding to the long branch, whereas Asp496 and the main chain of Phe497 form hydrogen bonds with fragment hits in the short branch. Fragment hits and their crystal structures provide structural insights into ligand binding to sEH that will facilitate the discovery of novel and potent inhibitors of sEH.
-==About this Structure==
+Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography.,Amano Y, Yamaguchi T, Tanabe E Bioorg Med Chem. 2014 Apr 15;22(8):2427-34. doi: 10.1016/j.bmc.2014.03.001. Epub , 2014 Mar 12. PMID:24656800<ref>PMID:24656800</ref>
-[[3wkd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WKD OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:024656800</ref><references group="xtra"/><references/>
+</div>
-[[Category: Amano, Y.]]
+<div class="pdbe-citations 3wkd" style="background-color:#fffaf0;"></div>
-[[Category: Tanabe, E.]]
-[[Category: Yamaguchi, T.]]
+==See Also==
-[[Category: Hydrolase]]
+*[[Epoxide hydrolase 3D structures|Epoxide hydrolase 3D structures]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Amano Y]]
+[[Category: Tanabe E]]
+[[Category: Yamaguchi T]]