5u6j

From Proteopedia

(Difference between revisions)

Current revision

Factor VIIa in complex with the inhibitor 3-{[(2R)-17-ethyl-4-methyl-3,12-dioxo-7-[(propan-2-yl)sulfonyl]-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaen-2-yl]amino}benzamide

Structural highlights

5u6j is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

FA7_HUMAN Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM: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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18] ^[19] ^[20] ^[21] ^[22] ^[23] ^[24]

Function

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.

Publication Abstract from PubMed

Factor VIIa (FVIIa) inhibitors have shown strong antithrombotic efficacy in preclinical thrombosis models with limited bleeding liabilities. Discovery of potent, orally active FVIIa inhibitors has been largely unsuccessful due to the requirement of a basic P1 group to interact with Asp189 in the S1 binding pocket, limiting their membrane permeability. We have combined recently reported neutral P1 binding substituents with a highly optimized macrocyclic chemotype to produce FVIIa inhibitors with low nanomolar potency and enhanced permeability.

Neutral macrocyclic factor VIIa inhibitors.,Wurtz NR, Parkhurst BL, DeLucca I, Glunz PW, Jiang W, Zhang X, Cheney DL, Bozarth JM, Rendina AR, Wei A, Harper T, Luettgen JM, Wu Y, Wong PC, Seiffert DA, Wexler RR, Priestley ES Bioorg Med Chem Lett. 2017 Apr 19. pii: S0960-894X(17)30372-4. doi:, 10.1016/j.bmcl.2017.04.008. PMID:28460818^[25]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bernardi F, Liney DL, Patracchini P, Gemmati D, Legnani C, Arcieri P, Pinotti M, Redaelli R, Ballerini G, Pemberton S, et al.. Molecular defects in CRM+ factor VII deficiencies: modelling of missense mutations in the catalytic domain of FVII. Br J Haematol. 1994 Mar;86(3):610-8. PMID:8043443
↑ O'Brien DP, Gale KM, Anderson JS, McVey JH, Miller GJ, Meade TW, Tuddenham EG. Purification and characterization of factor VII 304-Gln: a variant molecule with reduced activity isolated from a clinically unaffected male. Blood. 1991 Jul 1;78(1):132-40. PMID:2070047
↑ Marchetti G, Patracchini P, Gemmati D, DeRosa V, Pinotti M, Rodorigo G, Casonato A, Girolami A, Bernardi F. Detection of two missense mutations and characterization of a repeat polymorphism in the factor VII gene (F7). Hum Genet. 1992 Jul;89(5):497-502. PMID:1634227
↑ Marchetti G, Ferrati M, Patracchini P, Redaelli R, Bernardi F. A missense mutation (178Cys-->Tyr) and two neutral dimorphisms (115His and 333Ser) in the human coagulation factor VII gene. Hum Mol Genet. 1993 Jul;2(7):1055-6. PMID:8364544
↑ Chaing S, Clarke B, Sridhara S, Chu K, Friedman P, VanDusen W, Roberts HR, Blajchman M, Monroe DM, High KA. Severe factor VII deficiency caused by mutations abolishing the cleavage site for activation and altering binding to tissue factor. Blood. 1994 Jun 15;83(12):3524-35. PMID:8204879
↑ Bernardi F, Castaman G, Redaelli R, Pinotti M, Lunghi B, Rodeghiero F, Marchetti G. Topologically equivalent mutations causing dysfunctional coagulation factors VII (294Ala-->Val) and X (334Ser-->Pro). Hum Mol Genet. 1994 Jul;3(7):1175-7. PMID:7981691
↑ Ohiwa M, Hayashi T, Wada H, Minamikawa K, Shirakawa S, Suzuki K. Factor VII Mie: homozygous asymptomatic type I deficiency caused by an amino acid substitution of His (CAC) for Arg(247) (CGC) in the catalytic domain. Thromb Haemost. 1994 Jun;71(6):773-7. PMID:7974346
↑ Arbini AA, Mannucci M, Bauer KA. A Thr359Met mutation in factor VII of a patient with a hereditary deficiency causes defective secretion of the molecule. Blood. 1996 Jun 15;87(12):5085-94. PMID:8652821
↑ Bernardi F, Castaman G, Pinotti M, Ferraresi P, Di Iasio MG, Lunghi B, Rodeghiero F, Marchetti G. Mutation pattern in clinically asymptomatic coagulation factor VII deficiency. Hum Mutat. 1996;8(2):108-15. PMID:8844208 doi:<108::AID-HUMU2>3.0.CO;2-7 10.1002/(SICI)1098-1004(1996)8:2<108::AID-HUMU2>3.0.CO;2-7
↑ Bharadwaj D, Iino M, Kontoyianni M, Smith KJ, Foster DC, Kisiel W. Factor VII central. A novel mutation in the catalytic domain that reduces tissue factor binding, impairs activation by factor Xa, and abolishes amidolytic and coagulant activity. J Biol Chem. 1996 Nov 29;271(48):30685-91. PMID:8940045
↑ Tamary H, Fromovich Y, Shalmon L, Reich Z, Dym O, Lanir N, Brenner B, Paz M, Luder AS, Blau O, Korostishevsky M, Zaizov R, Seligsohn U. Ala244Val is a common, probably ancient mutation causing factor VII deficiency in Moroccan and Iranian Jews. Thromb Haemost. 1996 Sep;76(3):283-91. PMID:8883260
↑ Leonard BJ, Chen Q, Blajchman MA, Ofosu FA, Sridhara S, Yang D, Clarke BJ. Factor VII deficiency caused by a structural variant N57D of the first epidermal growth factor domain. Blood. 1998 Jan 1;91(1):142-8. PMID:9414278
↑ Ozawa T, Takikawa Y, Niiya K, Ejiri N, Suzuki K, Sato S, Sakuragawa N. Factor VII Morioka (FVII L-26P): a homozygous missense mutation in the signal sequence identified in a patient with factor VII deficiency. Br J Haematol. 1998 Apr;101(1):47-9. PMID:9576180
↑ Alshinawi C, Scerri C, Galdies R, Aquilina A, Felice AE. Two new missense mutations (P134T and A244V) in the coagulation factor VII gene. Hum Mutat. 1998;Suppl 1:S189-91. PMID:9452082
↑ Au WY, Lam CC, Chan EC, Kwong YL. Two novel factor VII gene mutations in a Chinese family with factor VII deficiency. Br J Haematol. 2000 Oct;111(1):143-5. PMID:11091194
↑ Millar DS, Kemball-Cook G, McVey JH, Tuddenham EG, Mumford AD, Attock GB, Reverter JC, Lanir N, Parapia LA, Reynaud J, Meili E, von Felton A, Martinowitz U, Prangnell DR, Krawczak M, Cooper DN. Molecular analysis of the genotype-phenotype relationship in factor VII deficiency. Hum Genet. 2000 Oct;107(4):327-42. PMID:11129332
↑ Wulff K, Herrmann FH. Twenty two novel mutations of the factor VII gene in factor VII deficiency. Hum Mutat. 2000;15(6):489-96. PMID:10862079 doi:<489::AID-HUMU1>3.0.CO;2-J 10.1002/1098-1004(200006)15:6<489::AID-HUMU1>3.0.CO;2-J
↑ Nagaizumi K, Inaba H, Suzuki T, Hatta Y, Hagiwara T, Amano K, Arai M, Fukutake K. Two double heterozygous mutations in the F7 gene show different manifestations. Br J Haematol. 2002 Dec;119(4):1052-8. PMID:12472587
↑ Takamiya O, Hino K. A patient homozygous for a Gly354Cys mutation in factor VII that results in severely impaired secretion of the molecule, but not complete deficiency. Br J Haematol. 2004 Feb;124(3):336-42. PMID:14717781
↑ Mota L, Shetty S, Idicula-Thomas S, Ghosh K. Phenotypic and genotypic characterization of Factor VII deficiency patients from Western India. Clin Chim Acta. 2009 Nov;409(1-2):106-11. doi: 10.1016/j.cca.2009.09.007. Epub, 2009 Sep 13. PMID:19751712 doi:10.1016/j.cca.2009.09.007
↑ Herrmann FH, Wulff K, Auerswald G, Schulman S, Astermark J, Batorova A, Kreuz W, Pollmann H, Ruiz-Saez A, De Bosch N, Salazar-Sanchez L. Factor VII deficiency: clinical manifestation of 717 subjects from Europe and Latin America with mutations in the factor 7 gene. Haemophilia. 2009 Jan;15(1):267-80. doi: 10.1111/j.1365-2516.2008.01910.x. Epub, 2008 Oct 30. PMID:18976247 doi:10.1111/j.1365-2516.2008.01910.x
↑ Landau D, Rosenberg N, Zivelin A, Staretz-Chacham O, Kapelushnik J. Familial factor VII deficiency with foetal and neonatal fatal cerebral haemorrhage associated with homozygosis to Gly180Arg mutation. Haemophilia. 2009 May;15(3):774-8. doi: 10.1111/j.1365-2516.2009.02004.x. PMID:19432927 doi:10.1111/j.1365-2516.2009.02004.x
↑ Kwon MJ, Yoo KY, Lee KO, Kim SH, Kim HJ. Recurrent mutations and genotype-phenotype correlations in hereditary factor VII deficiency in Korea. Blood Coagul Fibrinolysis. 2011 Mar;22(2):102-5. doi:, 10.1097/MBC.0b013e328343641a. PMID:21206266 doi:10.1097/MBC.0b013e328343641a
↑ Jiang M, Wang Z, Yu Z, Bai X, Su J, Cao L, Zhang W, Ruan C. A novel missense mutation close to the charge-stabilizing system in a patient with congenital factor VII deficiency. Blood Coagul Fibrinolysis. 2011 Jun;22(4):264-70. doi:, 10.1097/MBC.0b013e3283447388. PMID:21372693 doi:10.1097/MBC.0b013e3283447388
↑ Wurtz NR, Parkhurst BL, DeLucca I, Glunz PW, Jiang W, Zhang X, Cheney DL, Bozarth JM, Rendina AR, Wei A, Harper T, Luettgen JM, Wu Y, Wong PC, Seiffert DA, Wexler RR, Priestley ES. Neutral macrocyclic factor VIIa inhibitors. Bioorg Med Chem Lett. 2017 Apr 19. pii: S0960-894X(17)30372-4. doi:, 10.1016/j.bmcl.2017.04.008. PMID:28460818 doi:http://dx.doi.org/10.1016/j.bmcl.2017.04.008

1 Structural highlights
2 Disease
3 Function
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5u6j"

Categories: Homo sapiens | Large Structures | Wei A

@@ Line 3: / Line 3: @@
 <StructureSection load='5u6j' size='340' side='right'caption='[[5u6j]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5u6j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U6J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5U6J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5u6j]] 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=5U6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U6J FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=82J:3-{[(2R)-17-ETHYL-4-METHYL-3,12-DIOXO-7-[(PROPAN-2-YL)SULFONYL]-13-OXA-4,11-DIAZATRICYCLO[14.2.2.1~6,10~]HENICOSA-1(18),6(21),7,9,16,19-HEXAEN-2-YL]AMINO}BENZAMIDE'>82J</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=82J:3-{[(2R)-17-ETHYL-4-METHYL-3,12-DIOXO-7-[(PROPAN-2-YL)SULFONYL]-13-OXA-4,11-DIAZATRICYCLO[14.2.2.1~6,10~]HENICOSA-1(18),6(21),7,9,16,19-HEXAEN-2-YL]AMINO}BENZAMIDE'>82J</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5u6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6j OCA], [http://pdbe.org/5u6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u6j RCSB], [http://www.ebi.ac.uk/pdbsum/5u6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6j ProSAT]</span></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=5u6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6j OCA], [https://pdbe.org/5u6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u6j RCSB], [https://www.ebi.ac.uk/pdbsum/5u6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6j ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[http://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>
+[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 ==
-[[http://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.
+[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.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 21: @@
 </div>
 <div class="pdbe-citations 5u6j" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Factor VIIa 3D structures|Factor VIIa 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Coagulation factor VIIa]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Wei, A]]
+[[Category: Wei A]]
-[[Category: Blood coagulation factor]]
-[[Category: Calcium- binding]]
-[[Category: Glycoprotein]]
-[[Category: Hydrolase]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
-[[Category: Plasma]]
-[[Category: Protein inhibitor complex]]
-[[Category: Serine protease]]

5u6j

From Proteopedia

Current revision

Factor VIIa in complex with the inhibitor 3-{[(2R)-17-ethyl-4-methyl-3,12-dioxo-7-[(propan-2-yl)sulfonyl]-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaen-2-yl]amino}benzamide

Structural highlights

Disease

Function

Publication Abstract from PubMed

See Also

References

Contents

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