1w2k: Difference between revisions

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-[[Image:1w2k.gif|left|200px]]
- {{Structure
+==tf7a_4380 complex==
-|PDB= 1w2k |SIZE=350|CAPTION= <scene name='initialview01'>1w2k</scene>, resolution 3.00&Aring;
+<StructureSection load='1w2k' size='340' side='right'caption='[[1w2k]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Bgc+Binding+Site+For+Chain+L'>AC1</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=380:(2R)-2-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO)-N-BENZYL-2-(3,4-DIMETHOXYPHENYL)ACETAMIDE'>380</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>
+<table><tr><td colspan='2'>[[1w2k]] is a 3 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=1W2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W2K FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Coagulation_factor_VIIa Coagulation factor VIIa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.21 3.4.21.21] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=380:(2R)-2-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO)-N-BENZYL-2-(3,4-DIMETHOXYPHENYL)ACETAMIDE'>380</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1w2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w2k OCA], [https://pdbe.org/1w2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w2k RCSB], [https://www.ebi.ac.uk/pdbsum/1w2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w2k ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1w2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w2k OCA], [http://www.ebi.ac.uk/pdbsum/1w2k PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1w2k RCSB]</span>
+== Disease ==
-}}
+[https://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[https://omim.org/entry/227500 227500]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.<ref>PMID:8043443</ref> <ref>PMID:2070047</ref> <ref>PMID:1634227</ref> <ref>PMID:8364544</ref> <ref>PMID:8204879</ref> <ref>PMID:7981691</ref> <ref>PMID:7974346</ref> <ref>PMID:8652821</ref> <ref>PMID:8844208</ref> <ref>PMID:8940045</ref> <ref>PMID:8883260</ref> <ref>PMID:9414278</ref> <ref>PMID:9576180</ref> <ref>PMID:9452082</ref> <ref>PMID:11091194</ref> <ref>PMID:11129332</ref> <ref>PMID:10862079</ref> <ref>PMID:12472587</ref> <ref>PMID:14717781</ref> <ref>PMID:19751712</ref> <ref>PMID:18976247</ref> <ref>PMID:19432927</ref> <ref>PMID:21206266</ref> <ref>PMID:21372693</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN] Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium.
+== 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/w2/1w2k_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1w2k ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Proof of concept experiments have shown that tissue factor/factor VIIa inhibitors have antithrombotic activity without enhancing bleeding propensity. Starting from lead compounds generated by a biased combinatorial approach, phenylglycine amide tissue factor/factor VIIa inhibitors with low nanomolar affinity and good selectivity against other serine proteases of the coagulation cascade were designed, using the guidance of X-ray structural analysis and molecular modelling.
-'''TF7A_4380 COMPLEX'''
+Design of selective phenylglycine amide tissue factor/factor VIIa inhibitors.,Groebke Zbinden K, Banner DW, Ackermann J, D'Arcy A, Kirchhofer D, Ji YH, Tschopp TB, Wallbaum S, Weber L Bioorg Med Chem Lett. 2005 Feb 1;15(3):817-22. PMID:15664864<ref>PMID:15664864</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1w2k" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Proof of concept experiments have shown that tissue factor/factor VIIa inhibitors have antithrombotic activity without enhancing bleeding propensity. Starting from lead compounds generated by a biased combinatorial approach, phenylglycine amide tissue factor/factor VIIa inhibitors with low nanomolar affinity and good selectivity against other serine proteases of the coagulation cascade were designed, using the guidance of X-ray structural analysis and molecular modelling.
+*[[Factor VIIa 3D structures|Factor VIIa 3D structures]]
+*[[Tissue factor|Tissue factor]]
-==About this Structure==
+== References ==
-W2K is a [[Protein complex]] structure of sequences 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=1W2K OCA].
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-Design of selective phenylglycine amide tissue factor/factor VIIa inhibitors., Groebke Zbinden K, Banner DW, Ackermann J, D'Arcy A, Kirchhofer D, Ji YH, Tschopp TB, Wallbaum S, Weber L, Bioorg Med Chem Lett. 2005 Feb 1;15(3):817-22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15664864 15664864]
-[[Category: Coagulation factor VIIa]]
 [[Category: Homo sapiens]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Ackermann, J.]]
+[[Category: Ackermann J]]
-[[Category: Arcy, A D.]]
+[[Category: Banner DW]]
-[[Category: Banner, D W.]]
+[[Category: D'Arcy A]]
-[[Category: Groebke-Zbinden, K.]]
+[[Category: Groebke-Zbinden K]]
-[[Category: Ji, Y.]]
+[[Category: Ji Y-H]]
-[[Category: Kirchhofer, D.]]
+[[Category: Kirchhofer D]]
-[[Category: Tschopp, T B.]]
+[[Category: Tschopp TB]]
-[[Category: Wallbaum, S.]]
+[[Category: Wallbaum S]]
-[[Category: Weber, L.]]
+[[Category: Weber L]]
-[[Category: blood coagulation]]
-[[Category: calcium-binding]]
-[[Category: co-factor]]
-[[Category: coagulation]]
-[[Category: enzyme complex]]
-[[Category: gamma-carboxyglutamic acid]]
-[[Category: glycoprotein]]
-[[Category: hydrolase]]
-[[Category: plasma]]
-[[Category: serine protease]]
-[[Category: vitamin k]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:30:16 2008''