2vh6: Difference between revisions

Revision as of 20:54, 12 April 2023

Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with biaryl P4 motifs

Structural highlights

2vh6 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.
Ligands:	GSV
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

FA10_HUMAN Defects in F10 are the cause of factor X deficiency (FA10D) [MIM: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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17]

Function

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.

Publication Abstract from PubMed

Structure and property based drug design was exploited in the synthesis of sulfonamidopyrrolidin-2-one-based factor Xa (fXa) inhibitors, incorporating biaryl P4 groups, producing highly potent inhibitors with encouraging oral pharmacokinetic profiles and significant but sub-optimal anticoagulant activities.

Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with biaryl P4 motifs.,Young RJ, Borthwick AD, Brown D, Burns-Kurtis CL, Campbell M, Chan C, Charbaut M, Chung CW, Convery MA, Kelly HA, Paul King N, Kleanthous S, Mason AM, Pateman AJ, Patikis AN, Pinto IL, Pollard DR, Senger S, Shah GP, Toomey JR, Watson NS, Weston HE Bioorg Med Chem Lett. 2008 Jan 1;18(1):23-7. Epub 2007 Nov 17. PMID:18054228^[18]

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

References

↑ Reddy SV, Zhou ZQ, Rao KJ, Scott JP, Watzke H, High KA, Jagadeeswaran P. Molecular characterization of human factor XSan Antonio. Blood. 1989 Oct;74(5):1486-90. PMID:2790181
↑ Watzke HH, Lechner K, Roberts HR, Reddy SV, Welsch DJ, Friedman P, Mahr G, Jagadeeswaran P, Monroe DM, High KA. Molecular defect (Gla+14----Lys) and its functional consequences in a hereditary factor X deficiency (factor X "Vorarlberg"). J Biol Chem. 1990 Jul 15;265(20):11982-9. PMID:1973167
↑ James HL, Girolami A, Fair DS. Molecular defect in coagulation factor XFriuli results from a substitution of serine for proline at position 343. Blood. 1991 Jan 15;77(2):317-23. PMID:1985698
↑ Marchetti G, Castaman G, Pinotti M, Lunghi B, Di Iasio MG, Ruggieri M, Rodeghiero F, Bernardi F. Molecular bases of CRM+ factor X deficiency: a frequent mutation (Ser334Pro) in the catalytic domain and a substitution (Glu102Lys) in the second EGF-like domain. Br J Haematol. 1995 Aug;90(4):910-5. PMID:7669671
↑ Bezeaud A, Miyata T, Helley D, Zeng YZ, Kato H, Aillaud MF, Juhan-Vague I, Guillin MC. Functional consequences of the Ser334-->Pro mutation in a human factor X variant (factor XMarseille). Eur J Biochem. 1995 Nov 15;234(1):140-7. PMID:8529633
↑ Kim DJ, Thompson AR, James HL. Factor XKetchikan: a variant molecule in which Gly replaces a Gla residue at position 14 in the light chain. Hum Genet. 1995 Feb;95(2):212-4. PMID:7860069
↑ Messier TL, Wong CY, Bovill EG, Long GL, Church WR. Factor X Stockton: a mild bleeding diathesis associated with an active site mutation in factor X. Blood Coagul Fibrinolysis. 1996 Jan;7(1):5-14. PMID:8845463
↑ Rudolph AE, Mullane MP, Porche-Sorbet R, Tsuda S, Miletich JP. Factor XSt. Louis II. Identification of a glycine substitution at residue 7 and characterization of the recombinant protein. J Biol Chem. 1996 Nov 8;271(45):28601-6. PMID:8910490
↑ Zama T, Murata M, Watanabe R, Yokoyama K, Moriki T, Ambo H, Murakami H, Kikuchi M, Ikeda Y. A family with hereditary factor X deficiency with a point mutation Gla32 to Gln in the Gla domain (factor X Tokyo). Br J Haematol. 1999 Sep;106(3):809-11. PMID:10468877
↑ Millar DS, Elliston L, Deex P, Krawczak M, Wacey AI, Reynaud J, Nieuwenhuis HK, Bolton-Maggs P, Mannucci PM, Reverter JC, Cachia P, Pasi KJ, Layton DM, Cooper DN. Molecular analysis of the genotype-phenotype relationship in factor X deficiency. Hum Genet. 2000 Feb;106(2):249-57. PMID:10746568
↑ Forberg E, Huhmann I, Jimenez-Boj E, Watzke HH. The impact of Glu102Lys on the factor X function in a patient with a doubly homozygous factor X deficiency (Gla14Lys and Glu102Lys). Thromb Haemost. 2000 Feb;83(2):234-8. PMID:10739379
↑ Simioni P, Vianello F, Kalafatis M, Barzon L, Ladogana S, Paolucci P, Carotenuto M, Dal Bello F, Palu G, Girolami A. A dysfunctional factor X (factor X San Giovanni Rotondo) present at homozygous and double heterozygous level: identification of a novel microdeletion (delC556) and missense mutation (Lys(408)-->Asn) in the factor X gene. A study of an Italian family. Thromb Res. 2001 Feb 15;101(4):219-30. PMID:11248282
↑ Vianello F, Lombardi AM, Boldrin C, Luni S, Girolami A. A new factor X defect (factor X Padua 3): a compound heterozygous between true deficiency (Gly(380)-->Arg) and an abnormality (Ser(334)-->Pro). Thromb Res. 2001 Nov 15;104(4):257-64. PMID:11728527
↑ Vianello F, Lombardi AM, Bello FD, Palu G, Zanon E, Girolami A. A novel type I factor X variant (factor X Cys350Phe) due to loss of a disulfide bond in the catalytic domain. Blood Coagul Fibrinolysis. 2003 Jun;14(4):401-5. PMID:12945883
↑ Isshiki I, Favier R, Moriki T, Uchida T, Ishihara H, Van Dreden P, Murata M, Ikeda Y. Genetic analysis of hereditary factor X deficiency in a French patient of Sri Lankan ancestry: in vitro expression study identified Gly366Ser substitution as the molecular basis of the dysfunctional factor X. Blood Coagul Fibrinolysis. 2005 Jan;16(1):9-16. PMID:15650540
↑ Al-Hilali A, Wulff K, Abdel-Razeq H, Saud KA, Al-Gaili F, Herrmann FH. Analysis of the novel factor X gene mutation Glu51Lys in two families with factor X-Riyadh anomaly. Thromb Haemost. 2007 Apr;97(4):542-5. PMID:17393015
↑ Chafa O, Tagzirt M, Tapon-Bretaudiere J, Reghis A, Fischer AM, LeBonniec BF. Characterization of a homozygous Gly11Val mutation in the Gla domain of coagulation factor X. Thromb Res. 2009 May;124(1):144-8. doi: 10.1016/j.thromres.2008.11.018. Epub 2009, Jan 10. PMID:19135706 doi:10.1016/j.thromres.2008.11.018
↑ Young RJ, Borthwick AD, Brown D, Burns-Kurtis CL, Campbell M, Chan C, Charbaut M, Chung CW, Convery MA, Kelly HA, Paul King N, Kleanthous S, Mason AM, Pateman AJ, Patikis AN, Pinto IL, Pollard DR, Senger S, Shah GP, Toomey JR, Watson NS, Weston HE. Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with biaryl P4 motifs. Bioorg Med Chem Lett. 2008 Jan 1;18(1):23-7. Epub 2007 Nov 17. PMID:18054228 doi:S0960-894X(07)01330-3

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Reddy SV, Zhou ZQ, Rao KJ, Scott JP, Watzke H, High KA, Jagadeeswaran P. Molecular characterization of human factor XSan Antonio. Blood. 1989 Oct;74(5):1486-90. PMID:2790181

[2] Watzke HH, Lechner K, Roberts HR, Reddy SV, Welsch DJ, Friedman P, Mahr G, Jagadeeswaran P, Monroe DM, High KA. Molecular defect (Gla+14----Lys) and its functional consequences in a hereditary factor X deficiency (factor X "Vorarlberg"). J Biol Chem. 1990 Jul 15;265(20):11982-9. PMID:1973167

[3] James HL, Girolami A, Fair DS. Molecular defect in coagulation factor XFriuli results from a substitution of serine for proline at position 343. Blood. 1991 Jan 15;77(2):317-23. PMID:1985698

[4] Marchetti G, Castaman G, Pinotti M, Lunghi B, Di Iasio MG, Ruggieri M, Rodeghiero F, Bernardi F. Molecular bases of CRM+ factor X deficiency: a frequent mutation (Ser334Pro) in the catalytic domain and a substitution (Glu102Lys) in the second EGF-like domain. Br J Haematol. 1995 Aug;90(4):910-5. PMID:7669671

[5] Bezeaud A, Miyata T, Helley D, Zeng YZ, Kato H, Aillaud MF, Juhan-Vague I, Guillin MC. Functional consequences of the Ser334-->Pro mutation in a human factor X variant (factor XMarseille). Eur J Biochem. 1995 Nov 15;234(1):140-7. PMID:8529633

[6] Kim DJ, Thompson AR, James HL. Factor XKetchikan: a variant molecule in which Gly replaces a Gla residue at position 14 in the light chain. Hum Genet. 1995 Feb;95(2):212-4. PMID:7860069

[7] Messier TL, Wong CY, Bovill EG, Long GL, Church WR. Factor X Stockton: a mild bleeding diathesis associated with an active site mutation in factor X. Blood Coagul Fibrinolysis. 1996 Jan;7(1):5-14. PMID:8845463

[8] Rudolph AE, Mullane MP, Porche-Sorbet R, Tsuda S, Miletich JP. Factor XSt. Louis II. Identification of a glycine substitution at residue 7 and characterization of the recombinant protein. J Biol Chem. 1996 Nov 8;271(45):28601-6. PMID:8910490

[9] Zama T, Murata M, Watanabe R, Yokoyama K, Moriki T, Ambo H, Murakami H, Kikuchi M, Ikeda Y. A family with hereditary factor X deficiency with a point mutation Gla32 to Gln in the Gla domain (factor X Tokyo). Br J Haematol. 1999 Sep;106(3):809-11. PMID:10468877

[10] Millar DS, Elliston L, Deex P, Krawczak M, Wacey AI, Reynaud J, Nieuwenhuis HK, Bolton-Maggs P, Mannucci PM, Reverter JC, Cachia P, Pasi KJ, Layton DM, Cooper DN. Molecular analysis of the genotype-phenotype relationship in factor X deficiency. Hum Genet. 2000 Feb;106(2):249-57. PMID:10746568

[11] Forberg E, Huhmann I, Jimenez-Boj E, Watzke HH. The impact of Glu102Lys on the factor X function in a patient with a doubly homozygous factor X deficiency (Gla14Lys and Glu102Lys). Thromb Haemost. 2000 Feb;83(2):234-8. PMID:10739379

[12] Simioni P, Vianello F, Kalafatis M, Barzon L, Ladogana S, Paolucci P, Carotenuto M, Dal Bello F, Palu G, Girolami A. A dysfunctional factor X (factor X San Giovanni Rotondo) present at homozygous and double heterozygous level: identification of a novel microdeletion (delC556) and missense mutation (Lys(408)-->Asn) in the factor X gene. A study of an Italian family. Thromb Res. 2001 Feb 15;101(4):219-30. PMID:11248282

[13] Vianello F, Lombardi AM, Boldrin C, Luni S, Girolami A. A new factor X defect (factor X Padua 3): a compound heterozygous between true deficiency (Gly(380)-->Arg) and an abnormality (Ser(334)-->Pro). Thromb Res. 2001 Nov 15;104(4):257-64. PMID:11728527

[14] Vianello F, Lombardi AM, Bello FD, Palu G, Zanon E, Girolami A. A novel type I factor X variant (factor X Cys350Phe) due to loss of a disulfide bond in the catalytic domain. Blood Coagul Fibrinolysis. 2003 Jun;14(4):401-5. PMID:12945883

[15] Isshiki I, Favier R, Moriki T, Uchida T, Ishihara H, Van Dreden P, Murata M, Ikeda Y. Genetic analysis of hereditary factor X deficiency in a French patient of Sri Lankan ancestry: in vitro expression study identified Gly366Ser substitution as the molecular basis of the dysfunctional factor X. Blood Coagul Fibrinolysis. 2005 Jan;16(1):9-16. PMID:15650540

[16] Al-Hilali A, Wulff K, Abdel-Razeq H, Saud KA, Al-Gaili F, Herrmann FH. Analysis of the novel factor X gene mutation Glu51Lys in two families with factor X-Riyadh anomaly. Thromb Haemost. 2007 Apr;97(4):542-5. PMID:17393015

[17] Chafa O, Tagzirt M, Tapon-Bretaudiere J, Reghis A, Fischer AM, LeBonniec BF. Characterization of a homozygous Gly11Val mutation in the Gla domain of coagulation factor X. Thromb Res. 2009 May;124(1):144-8. doi: 10.1016/j.thromres.2008.11.018. Epub 2009, Jan 10. PMID:19135706 doi:10.1016/j.thromres.2008.11.018

[18] Young RJ, Borthwick AD, Brown D, Burns-Kurtis CL, Campbell M, Chan C, Charbaut M, Chung CW, Convery MA, Kelly HA, Paul King N, Kleanthous S, Mason AM, Pateman AJ, Patikis AN, Pinto IL, Pollard DR, Senger S, Shah GP, Toomey JR, Watson NS, Weston HE. Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with biaryl P4 motifs. Bioorg Med Chem Lett. 2008 Jan 1;18(1):23-7. Epub 2007 Nov 17. PMID:18054228 doi:S0960-894X(07)01330-3

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[5]

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@@ Line 5: / Line 5: @@
 <table><tr><td colspan='2'>[[2vh6]] 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=2VH6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VH6 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GSV:2-(5-CHLOROTHIOPHEN-2-YL)-N-{(3S)-1-[3-FLUORO-2-(METHYLSULFONYL)BIPHENYL-4-YL]-2-OXOPYRROLIDIN-3-YL}ETHANESULFONAMIDE'>GSV</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2j34|2j34]], [[1wu1|1wu1]], [[2bq7|2bq7]], [[1ioe|1ioe]], [[1f0s|1f0s]], [[1nfw|1nfw]], [[1xka|1xka]], [[2gd4|2gd4]], [[1f0r|1f0r]], [[1msx|1msx]], [[1lpg|1lpg]], [[1p0s|1p0s]], [[2g00|2g00]], [[2bmg|2bmg]], [[1mq5|1mq5]], [[1iqn|1iqn]], [[1mq6|1mq6]], [[1xkb|1xkb]], [[2bqw|2bqw]], [[1iqm|1iqm]], [[1ezq|1ezq]], [[1iqe|1iqe]], [[1g2m|1g2m]], [[1fjs|1fjs]], [[2vh0|2vh0]], [[1lpk|1lpk]], [[2j4i|2j4i]], [[1nfy|1nfy]], [[2uwl|2uwl]], [[2bok|2bok]], [[1nfx|1nfx]], [[1lpz|1lpz]], [[1hcg|1hcg]], [[2j94|2j94]], [[1iqj|1iqj]], [[1z6e|1z6e]], [[2uwp|2uwp]], [[2j95|2j95]], [[2cji|2cji]], [[2j38|2j38]], [[2boh|2boh]], [[1g2l|1g2l]], [[1nfu|1nfu]], [[1iqi|1iqi]], [[2bq6|2bq6]], [[1fax|1fax]], [[1iqf|1iqf]], [[1nl8|1nl8]], [[1kye|1kye]], [[1iqg|1iqg]], [[1iqk|1iqk]], [[1iqh|1iqh]], [[1v3x|1v3x]], [[1lqd|1lqd]], [[2fzz|2fzz]], [[2j2u|2j2u]], [[2uwo|2uwo]], [[1ksn|1ksn]], [[1c5m|1c5m]], [[1iql|1iql]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Coagulation_factor_Xa Coagulation factor Xa], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.6 3.4.21.6] </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=2vh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vh6 OCA], [https://pdbe.org/2vh6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vh6 RCSB], [https://www.ebi.ac.uk/pdbsum/2vh6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vh6 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>
+[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.
+[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 ==
@@ Line 29: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Coagulation factor Xa]]
 [[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Borthwick, A D]]
+[[Category: Borthwick AD]]
-[[Category: Brown, D]]
+[[Category: Brown D]]
-[[Category: Burns-Kurtis, C L]]
+[[Category: Burns-Kurtis CL]]
-[[Category: Campbell, M]]
+[[Category: Campbell M]]
-[[Category: Chan, C]]
+[[Category: Chan C]]
-[[Category: Charbaut, M]]
+[[Category: Charbaut M]]
-[[Category: Chung, C W]]
+[[Category: Chung CW]]
-[[Category: Convery, M A]]
+[[Category: Convery MA]]
-[[Category: Kelly, H A]]
+[[Category: Kelly HA]]
-[[Category: King, N P]]
+[[Category: King NP]]
-[[Category: Kleanthous, S]]
+[[Category: Kleanthous S]]
-[[Category: Mason, A M]]
+[[Category: Mason AM]]
-[[Category: Pateman, A J]]
+[[Category: Pateman AJ]]
-[[Category: Patikis, A N]]
+[[Category: Patikis AN]]
-[[Category: Pinto, I L]]
+[[Category: Pinto IL]]
-[[Category: Pollard, D R]]
+[[Category: Pollard DR]]
-[[Category: Senger, S]]
+[[Category: Senger S]]
-[[Category: Shah, G P]]
+[[Category: Shah GP]]
-[[Category: Toomey, J R]]
+[[Category: Toomey JR]]
-[[Category: Watson, N S]]
+[[Category: Watson NS]]
-[[Category: Weston, H E]]
+[[Category: Weston HE]]
-[[Category: Young, R J]]
+[[Category: Young RJ]]
-[[Category: Blood coagulation]]
-[[Category: Calcium]]
-[[Category: Cleavage on pair of basic residue]]
-[[Category: Complex]]
-[[Category: Egf-like domain]]
-[[Category: Gamma-carboxyglutamic acid]]
-[[Category: Glycoprotein]]
-[[Category: Hydrolase]]
-[[Category: Hydroxylation]]
-[[Category: Polymorphism]]
-[[Category: Protease]]
-[[Category: Serine protease]]
-[[Category: Zymogen]]

2vh6: Difference between revisions

Revision as of 20:54, 12 April 2023

Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with biaryl P4 motifs

Structural highlights

Disease

Function

Publication Abstract from PubMed

See Also

References

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