3wkd: Difference between revisions
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==Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor== | ==Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor== | ||
<StructureSection load='3wkd' size='340' side='right' caption='[[3wkd]], [[Resolution|resolution]] 2.48Å' scene=''> | <StructureSection load='3wkd' size='340' side='right'caption='[[3wkd]], [[Resolution|resolution]] 2.48Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3wkd]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3wkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3wk4|3wk4]], [[3wk5|3wk5]], [[3wk6|3wk6]], [[3wk7|3wk7]], [[3wk8|3wk8]], [[3wk9|3wk9]], [[3wka|3wka]], [[3wkb|3wkb]], [[3wkc|3wkc]], [[3wke|3wke]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wk4|3wk4]], [[3wk5|3wk5]], [[3wk6|3wk6]], [[3wk7|3wk7]], [[3wk8|3wk8]], [[3wk9|3wk9]], [[3wka|3wka]], [[3wkb|3wkb]], [[3wkc|3wkc]], [[3wke|3wke]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EPHX2 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EPHX2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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> | </table> | ||
== Function == | == 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;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[Epoxide hydrolase|Epoxide hydrolase]] | *[[Epoxide hydrolase 3D structures|Epoxide hydrolase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Human]] | [[Category: Human]] | ||
[[Category: Large Structures]] | |||
[[Category: Amano, Y]] | [[Category: Amano, Y]] | ||
[[Category: Tanabe, E]] | [[Category: Tanabe, E]] | ||
Revision as of 08:39, 3 August 2022
Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitorCrystal structure of soluble epoxide hydrolase in complex with fragment inhibitor
Structural highlights
Function[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.[1] [2] Publication Abstract from PubMedSoluble 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. 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[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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