5k0h - Revision history

OCA at 19:17, 20 September 2023

OCA — Wed, 20 Sep 2023 19:17:03 GMT

←Older revision		Revision as of 19:17, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5k0h' size='340' side='right'caption='[[5k0h]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5k0h' size='340' side='right'caption='[[5k0h]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k0h]] is a 2 chain structure with 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=5K0H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K0H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k0h]] 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=5K0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K0H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6PK:O-BENZYL-N-(BENZYLSULFONYL)-D-SERYL-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]GLYCINAMIDE'>6PK</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.2Å</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_Xa Coagulation factor Xa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.6 3.4.21.6] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6PK:O-BENZYL-N-(BENZYLSULFONYL)-D-SERYL-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]GLYCINAMIDE'>6PK</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=5k0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0h OCA], [~~http~~://pdbe.org/5k0h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k0h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k0h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0h 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=5k0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0h OCA], [https://pdbe.org/5k0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k0h RCSB], [https://www.ebi.ac.uk/pdbsum/5k0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0h ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/FA10_HUMAN FA10_HUMAN]] Defects in F10 are the cause of factor X deficiency (FA10D) [MIM:[~~http~~://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 ==		== Function ==
-	[~~[http~~://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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5k0h" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5k0h" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Factor Xa\|Factor Xa]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Coagulation factor Xa]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Steinmetzer, T]]	+	[[Category: Steinmetzer T]]
-	~~[[Category: Benzamidine inhibitor]]~~	+
-	~~[[Category: Clotting factor]]~~	+
-	~~[[Category: Human factor xa]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibitor complex~~]]	+

OCA at 09:12, 25 June 2020

OCA — Thu, 25 Jun 2020 09:12:45 GMT

←Older revision		Revision as of 09:12, 25 June 2020
Line 1:		Line 1:

	==Human factor Xa in complex with synthetic inhibitor benzylsulfonyl-dSer(Benzyl)-Gly-4-amidinobenzylamide==		==Human factor Xa in complex with synthetic inhibitor benzylsulfonyl-dSer(Benzyl)-Gly-4-amidinobenzylamide==
-	<StructureSection load='5k0h' size='340' side='right' caption='[[5k0h]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5k0h' size='340' side='right'caption='[[5k0h]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k0h]] is a 2 chain structure with 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=5K0H OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K0H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k0h]] is a 2 chain structure with 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=5K0H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K0H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6PK:O-BENZYL-N-(BENZYLSULFONYL)-D-SERYL-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]GLYCINAMIDE'>6PK</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6PK:O-BENZYL-N-(BENZYLSULFONYL)-D-SERYL-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]GLYCINAMIDE'>6PK</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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_Xa Coagulation factor Xa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.6 3.4.21.6] </span></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_Xa Coagulation factor Xa], with EC number [http://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'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5k0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0h OCA], [http://pdbe.org/5k0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k0h RCSB], [http://www.ebi.ac.uk/pdbsum/5k0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0h ProSAT]</span></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=5k0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0h OCA], [http://pdbe.org/5k0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k0h RCSB], [http://www.ebi.ac.uk/pdbsum/5k0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0h ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 27:		Line 27:
	[[Category: Coagulation factor Xa]]		[[Category: Coagulation factor Xa]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
	[[Category: Steinmetzer, T]]		[[Category: Steinmetzer, T]]
	[[Category: Benzamidine inhibitor]]		[[Category: Benzamidine inhibitor]]

OCA at 02:12, 13 July 2016

OCA — Wed, 13 Jul 2016 02:12:56 GMT

←Older revision		Revision as of 02:12, 13 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k0h is ~~ON HOLD~~	+	==Human factor Xa in complex with synthetic inhibitor benzylsulfonyl-dSer(Benzyl)-Gly-4-amidinobenzylamide==
		+	<StructureSection load='5k0h' size='340' side='right' caption='[[5k0h]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k0h]] is a 2 chain structure with 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=5K0H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K0H FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6PK:O-BENZYL-N-(BENZYLSULFONYL)-D-SERYL-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]GLYCINAMIDE'>6PK</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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_Xa Coagulation factor Xa], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5k0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0h OCA], [http://pdbe.org/5k0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k0h RCSB], [http://www.ebi.ac.uk/pdbsum/5k0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0h ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/FA10_HUMAN FA10_HUMAN]] Defects in F10 are the cause of factor X deficiency (FA10D) [MIM:[http://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 ==
		+	[[http://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 ==
		+	The trypsin-like serine protease factor Xa (fXa) is located at the convergence point of the intrinsic and extrinsic coagulation cascade, and therefore has emerged as an attractive target for the design of novel anticoagulants. During the development of substrate-analogue urokinase inhibitors we have found that the protection of the P3-dSer side chain leads to a scaffold of potent fXa inhibitors with the general structure R1-SO2-dSer(R2)-Gly-4-amidinobenzylamide. The first lead (3) with an N-terminal benzylsulfonyl group and dSer(tBu) as P3 residue inhibits human fXa with a Ki of 14 nM. A variety of derivatives with modified P4, P3, and P2 residues have been investigated in terms of inhibition of fXa and related proteases and for their anticoagulant potency and elimination behaviour. Most inhibitors were rapidly cleared from the circulation of rats. However, compound 48 (Ki= 3.5 nM), one of the most potent and selective inhibitors containing a dArg as P3 residue was relatively slowly eliminated (t1/2 approximately 1 h). Inhibitor 48 doubled clotting times in human plasma at 0.32 microM (aPTT) and 0.28 microM (PT), and is approximately 10-fold more potent than the reference fXa inhibitor DX-9065a in the inhibition of the prothrombinase complex. The structures of two inhibitors in complex with human fXa were solved by X-ray crystallography.

-	~~Authors~~: ~~Steinmetzer~~, T.	+	New substrate analogue inhibitors of factor Xa containing 4-amidinobenzylamide as P1 residue: part 1.,Schweinitz A, Sturzebecher A, Sturzebecher U, Schuster O, Sturzebecher J, Steinmetzer T Med Chem. 2006 Jul;2(4):349-61. PMID:16848746<ref>PMID:16848746</ref>

-	~~Description~~: ~~Human~~ factor Xa ~~in complex with synthetic inhibitor benzylsulfonyl-dSer(Benzyl)-Gly-4-amidinobenzylamide~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5k0h" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Coagulation factor Xa]]
		+	[[Category: Homo sapiens]]
	[[Category: Steinmetzer, T]]		[[Category: Steinmetzer, T]]
		+	[[Category: Benzamidine inhibitor]]
		+	[[Category: Clotting factor]]
		+	[[Category: Human factor xa]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibitor complex]]

OCA: Protected "5k0h" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:08:25 GMT

Protected "5k0h" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:08, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k0h is ON HOLD Authors: Steinmetzer, T. Description: Human factor Xa in complex with synthetic inhibitor benzylsulfonyl-dSer(Benzyl)-Gly-4-amidino...

OCA — Wed, 01 Jun 2016 14:08:24 GMT

New page: '''Unreleased structure''' The entry 5k0h is ON HOLD Authors: Steinmetzer, T. Description: Human factor Xa in complex with synthetic inhibitor benzylsulfonyl-dSer(Benzyl)-Gly-4-amidino...

New page

'''Unreleased structure'''

The entry 5k0h is ON HOLD

Authors: Steinmetzer, T.

Description: Human factor Xa in complex with synthetic inhibitor benzylsulfonyl-dSer(Benzyl)-Gly-4-amidinobenzylamide
[[Category: Unreleased Structures]]
[[Category: Steinmetzer, T]]