2y5h: Difference between revisions

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OCA

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-'''Unreleased structure'''
-The entry 2y5h is ON HOLD  until sometime in the future
+==FACTOR XA - CATION INHIBITOR COMPLEX==
+<StructureSection load='2y5h' size='340' side='right'caption='[[2y5h]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2y5h]] 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=2Y5H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y5H 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]] 1.33&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=Y5H:3-[(3AS,4R,5S,8AS,8BR)-4-[2-(5-CHLOROTHIOPHEN-2-YL)-1,3-OXAZOL-4-YL]-1,3-DIOXO-4,6,7,8,8A,8B-HEXAHYDRO-3AH-PYRROLO[3,4-A]PYRROLIZIN-2-YL]PROPYL-TRIMETHYL-AZANIUM'>Y5H</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=2y5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y5h OCA], [https://pdbe.org/2y5h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y5h RCSB], [https://www.ebi.ac.uk/pdbsum/2y5h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y5h ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/FA10_HUMAN FA10_HUMAN] Defects in F10 are the cause of factor X deficiency (FA10D) [MIM:[https://omim.org/entry/227600 227600]. A hemorrhagic disease with variable presentation. Affected individuals can manifest prolonged nasal and mucosal hemorrhage, menorrhagia, hematuria, and occasionally hemarthrosis. Some patients do not have clinical bleeding diathesis.<ref>PMID:2790181</ref> <ref>PMID:1973167</ref> <ref>PMID:1985698</ref> <ref>PMID:7669671</ref> <ref>PMID:8529633</ref> <ref>PMID:7860069</ref> <ref>PMID:8845463</ref> <ref>PMID:8910490</ref> <ref>PMID:10468877</ref> <ref>PMID:10746568</ref> <ref>PMID:10739379</ref> <ref>PMID:11248282</ref> <ref>PMID:11728527</ref> <ref>PMID:12945883</ref> <ref>PMID:15650540</ref> <ref>PMID:17393015</ref> <ref>PMID:19135706</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/FA10_HUMAN FA10_HUMAN] Factor Xa is a vitamin K-dependent glycoprotein that converts prothrombin to thrombin in the presence of factor Va, calcium and phospholipid during blood clotting.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Factor Xa, a serine protease from the blood coagulation cascade, is an ideal enzyme for molecular recognition studies, as its active site is highly shape-persistent and features distinct, concave sub-pockets. We developed a family of non-peptidic, small-molecule inhibitors with a central tricyclic core orienting a neutral heterocyclic substituent into the S1 pocket and a quaternary ammonium ion into the aromatic box in the S4 pocket. The substituents were systematically varied to investigate cation-pi interactions in the S4 pocket, optimal heterocyclic stacking on the flat peptide walls lining the S1 pocket, and potential water replacements in both the S1 and the S4 pockets. Structure-activity relationships were established to reveal and quantify contributions to the binding free enthalpy, resulting from single-atom replacements or positional changes in the ligands. A series of high-affinity ligands with inhibitory constants down to K(i) =2 nM were obtained and their proposed binding geometries confirmed by X-ray co-crystal structures of protein-ligand complexes.
-Authors: BANNER, D.W., SALONEN, L., HOLLAND, M., HAAP, W., BENZ, J., DIEDERICH, F.
+Molecular Recognition at the Active Site of Factor Xa: Cation-pi Interactions, Stacking on Planar Peptide Surfaces, and Replacement of Structural Water.,Salonen LM, Holland MC, Kaib PS, Haap W, Benz J, Mary JL, Kuster O, Schweizer WB, Banner DW, Diederich F Chemistry. 2011 Dec 9. doi: 10.1002/chem.201102571. PMID:22162109<ref>PMID:22162109</ref>
-Description: FACTOR XA -CATION INHIBITOR COMPLEX
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2y5h" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Factor Xa|Factor Xa]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Banner DW]]
+[[Category: Benz J]]
+[[Category: Diederich F]]
+[[Category: Haap W]]
+[[Category: Holland MC]]
+[[Category: Salonen LM]]