2c4f

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[[Image:2c4f.jpg|left|200px]]<br /><applet load="2c4f" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2c4f, resolution 1.72&Aring;" />
 
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'''CRYSTAL STRUCTURE OF FACTOR VII.STF COMPLEXED WITH PD0297121'''<br />
 
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==Overview==
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==crystal structure of factor VII.stf complexed with pd0297121==
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<StructureSection load='2c4f' size='340' side='right'caption='[[2c4f]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2c4f]] is a 4 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=2C4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C4F FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.72&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GIL:2-{[6-{3-[AMINO(IMINO)METHYL]PHENOXY}-4-(DIISOPROPYLAMINO)-3,5-DIFLUOROPYRIDIN-2-YL]OXY}-5-[(ISOBUTYLAMINO)CARBONYL]BENZOIC+ACID'>GIL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2c4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c4f OCA], [https://pdbe.org/2c4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c4f RCSB], [https://www.ebi.ac.uk/pdbsum/2c4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c4f ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[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>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c4/2c4f_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2c4f ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
The activated factor VII/tissue factor complex (FVIIa/TF) is known to play a key role in the formation of blood clots. Inhibition of this complex may lead to new antithrombotic drugs. A fluoropyridine-based series of FVIIa/TF inhibitors was discovered which utilized a diisopropylamino group for binding in the S2 and S3 binding pockets of the active site of the enzyme complex. In this series, an enhancement in binding affinity was observed by substitution at the 5-position of the hydroxybenzoic acid sidechain. An X-ray crystal structure indicates that amides at this position may increase inhibitor binding affinity through interactions with the S1'/S2' pocket.
The activated factor VII/tissue factor complex (FVIIa/TF) is known to play a key role in the formation of blood clots. Inhibition of this complex may lead to new antithrombotic drugs. A fluoropyridine-based series of FVIIa/TF inhibitors was discovered which utilized a diisopropylamino group for binding in the S2 and S3 binding pockets of the active site of the enzyme complex. In this series, an enhancement in binding affinity was observed by substitution at the 5-position of the hydroxybenzoic acid sidechain. An X-ray crystal structure indicates that amides at this position may increase inhibitor binding affinity through interactions with the S1'/S2' pocket.
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==Disease==
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The discovery of fluoropyridine-based inhibitors of the factor VIIa/TF complex--Part 2.,Kohrt JT, Filipski KJ, Cody WL, Cai C, Dudley DA, Van Huis CA, Willardsen JA, Narasimhan LS, Zhang E, Rapundalo ST, Saiya-Cork K, Leadley RJ, Edmunds JJ Bioorg Med Chem Lett. 2006 Feb 15;16(4):1060-4. Epub 2005 Nov 11. PMID:16289811<ref>PMID:16289811</ref>
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Known diseases associated with this structure: Esophageal squamous cell carcinoma OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=606551 606551]], Factor VII deficiency OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227500 227500]], Myocardial infarction, decreased susceptibility to OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227500 227500]]
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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2C4F is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=GLC:'>GLC</scene>, <scene name='pdbligand=FUC:'>FUC</scene>, <scene name='pdbligand=NAG:'>NAG</scene>, <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=GIL:'>GIL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Site: <scene name='pdbsite=AC1:Nag+Binding+Site+For+Chain+U'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C4F OCA].
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</div>
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<div class="pdbe-citations 2c4f" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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The discovery of fluoropyridine-based inhibitors of the factor VIIa/TF complex--Part 2., Kohrt JT, Filipski KJ, Cody WL, Cai C, Dudley DA, Van Huis CA, Willardsen JA, Narasimhan LS, Zhang E, Rapundalo ST, Saiya-Cork K, Leadley RJ, Edmunds JJ, Bioorg Med Chem Lett. 2006 Feb 15;16(4):1060-4. Epub 2005 Nov 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16289811 16289811]
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*[[Factor VIIa 3D structures|Factor VIIa 3D structures]]
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[[Category: Coagulation factor VIIa]]
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*[[Tissue factor|Tissue factor]]
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[[Category: Protein complex]]
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== References ==
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[[Category: Kohrt, J T.]]
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<references/>
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[[Category: Zhang, E.]]
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__TOC__
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[[Category: CA]]
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</StructureSection>
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[[Category: FUC]]
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[[Category: Homo sapiens]]
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[[Category: GIL]]
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[[Category: Large Structures]]
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[[Category: GLC]]
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[[Category: Kohrt JT]]
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[[Category: NAG]]
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[[Category: Zhang E]]
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[[Category: blood coagulation]]
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[[Category: egf]]
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[[Category: egf-like domain]]
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[[Category: gla]]
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[[Category: glycoprotein]]
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[[Category: hydrolase]]
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[[Category: hydroxylation]]
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[[Category: lipoprotein]]
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[[Category: palmitate]]
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[[Category: protease]]
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[[Category: receptor enzyme]]
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[[Category: serine protease]]
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[[Category: transmembrane]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:44:45 2008''
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Current revision

crystal structure of factor VII.stf complexed with pd0297121

PDB ID 2c4f

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