1zom: Difference between revisions

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-[[Image:1zom.gif|left|200px]]
-<!--
+==Crystal Structure of the Catalytic Domain of Coagulation Factor XI in complex with a peptidomimetic Inhibitor==
-The line below this paragraph, containing "STRUCTURE_1zom", creates the "Structure Box" on the page.
+<StructureSection load='1zom' size='340' side='right'caption='[[1zom]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1zom]] 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=1ZOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZOM FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=339:(S)-2-(3-((R)-1-(4-BROMOPHENYL)ETHYL)UREIDO)-N-((S)-1-((S)-5-GUANIDINO-1-OXO-1-(THIAZOL-2-YL)PENTAN-2-YLAMINO)-3-METHYL-1-OXOBUTAN-2-YL)-5-UREIDOPENTANAMIDE'>339</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1zom|  PDB=1zom  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zom OCA], [https://pdbe.org/1zom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zom RCSB], [https://www.ebi.ac.uk/pdbsum/1zom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zom ProSAT]</span></td></tr>
+</table>
-'''Crystal Structure of the Catalytic Domain of Coagulation Factor XI in complex with a peptidomimetic Inhibitor'''
+== Disease ==
+[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Defects in F11 are the cause of factor XI deficiency (FA11D) [MIM:[https://omim.org/entry/612416 612416]; also known as plasma thromboplastin antecedent deficiency or Rosenthal syndrome. It is a hemorrhagic disease characterized by reduced levels and activity of factor XI resulting in moderate bleeding symptoms, usually occurring after trauma or surgery. Patients usually do not present spontaneous bleeding but women can present with menorrhagia. Hemorrhages are usually moderate.<ref>PMID:2813350</ref> <ref>PMID:1547342</ref> <ref>PMID:7888672</ref> <ref>PMID:7669672</ref> <ref>PMID:9401068</ref> <ref>PMID:9787168</ref> <ref>PMID:10027710</ref> <ref>PMID:10606881</ref> <ref>PMID:11895778</ref> <ref>PMID:15026311</ref> <ref>PMID:15180874</ref> <ref>PMID:15953011</ref> <ref>PMID:16607084</ref> <ref>PMID:18005151</ref> <ref>PMID:21668437</ref> <ref>PMID:21457405</ref> <ref>PMID:22016685</ref> <ref>PMID:22322133</ref> <ref>PMID:21999818</ref> <ref>PMID:22159456</ref>
+== Function ==
-==Overview==
+[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zo/1zom_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1zom ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
 Human coagulation factor XIa (FXIa), a serine protease activated by site-specific cleavage of factor XI by thrombin, FXIIa, or autoactivation, is a critical enzyme in the amplification phase of the coagulation cascade. To investigate the potential of FXIa inhibitors as safe anticoagulants, a series of potent, selective peptidomimetic inhibitors of FXIa were designed and synthesized. Some of these inhibitors showed low nanomolar FXIa inhibitory activity with &gt;1000-fold FXa selectivity and &gt;100-fold thrombin selectivity. The X-ray structure of one of these inhibitors, 36, demonstrates its unique binding interactions with FXIa. Compound 32 caused a doubling of the activated partial thromboplastin time in human plasma at 2.4 microM and was efficacious in a rat model of venous thrombosis. These data suggest that factor XIa plays a significant role in venous thrombosis and may be a suitable target for the development of antithrombotic therapy.
-==Disease==
+Design, synthesis, and biological evaluation of peptidomimetic inhibitors of factor XIa as novel anticoagulants.,Lin J, Deng H, Jin L, Pandey P, Quinn J, Cantin S, Rynkiewicz MJ, Gorga JC, Bibbins F, Celatka CA, Nagafuji P, Bannister TD, Meyers HV, Babine RE, Hayward NJ, Weaver D, Benjamin H, Stassen F, Abdel-Meguid SS, Strickler JE J Med Chem. 2006 Dec 28;49(26):7781-91. PMID:17181160<ref>PMID:17181160</ref>
-Known disease associated with this structure: Factor XI deficiency, autosomal dominant OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=264900 264900]], Factor XI deficiency, autosomal recessive OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=264900 264900]]
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-ZOM is a [[Single protein]] structure of 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=1ZOM OCA].
+</div>
+<div class="pdbe-citations 1zom" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Design, synthesis, and biological evaluation of peptidomimetic inhibitors of factor XIa as novel anticoagulants., Lin J, Deng H, Jin L, Pandey P, Quinn J, Cantin S, Rynkiewicz MJ, Gorga JC, Bibbins F, Celatka CA, Nagafuji P, Bannister TD, Meyers HV, Babine RE, Hayward NJ, Weaver D, Benjamin H, Stassen F, Abdel-Meguid SS, Strickler JE, J Med Chem. 2006 Dec 28;49(26):7781-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17181160 17181160]
+*[[Factor XIa 3D structures|Factor XIa 3D structures]]
-[[Category: Coagulation factor XIa]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bibbins, F.]]
+[[Category: Bibbins F]]
-[[Category: Cantin, S.]]
+[[Category: Cantin S]]
-[[Category: Deng, H.]]
+[[Category: Deng H]]
-[[Category: Gorga, J.]]
+[[Category: Gorga J]]
-[[Category: Jin, L.]]
+[[Category: Jin L]]
-[[Category: Lin, J.]]
+[[Category: Lin J]]
-[[Category: Magee, S.]]
+[[Category: Magee S]]
-[[Category: Pandey, P.]]
+[[Category: Pandey P]]
-[[Category: Quinn, J.]]
+[[Category: Quinn J]]
-[[Category: Rynkiewicz, M.]]
+[[Category: Rynkiewicz M]]
-[[Category: Fxia]]
-[[Category: Inhibitor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 17:53:01 2008''