6cym - Revision history

OCA at 09:02, 11 November 2020

OCA — Wed, 11 Nov 2020 09:02:15 GMT

←Older revision		Revision as of 09:02, 11 November 2020
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	==Reversible Covalent Direct Thrombin Inhibitors==		==Reversible Covalent Direct Thrombin Inhibitors==
-	<StructureSection load='6cym' size='340' side='right' caption='[[6cym]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='6cym' size='340' side='right'caption='[[6cym]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cym]] is a 4 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=6CYM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cym]] is a 4 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=6CYM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6CYM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=71F:2-METHOXYBENZOIC+ACID'>71F</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=71F:2-METHOXYBENZOIC+ACID'>71F</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </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=6cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cym OCA], [http://pdbe.org/6cym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cym RCSB], [http://www.ebi.ac.uk/pdbsum/6cym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cym 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=6cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cym OCA], [http://pdbe.org/6cym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cym RCSB], [http://www.ebi.ac.uk/pdbsum/6cym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cym ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
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	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
	[[Category: Thrombin]]		[[Category: Thrombin]]
	[[Category: Sivaraja, M]]		[[Category: Sivaraja, M]]

OCA at 16:37, 15 August 2018

OCA — Wed, 15 Aug 2018 16:37:44 GMT

←Older revision		Revision as of 16:37, 15 August 2018
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.<ref>PMID:2856554</ref>		[[http://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.<ref>PMID:2856554</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	INTRODUCTION: In recent years, the traditional treatments for thrombotic diseases, heparin and warfarin, are increasingly being replaced by novel oral anticoagulants offering convenient dosing regimens, more predictable anticoagulant responses, and less frequent monitoring. However, these drugs can be contraindicated for some patients and, in particular, their bleeding liability remains high. METHODS: We have developed a new class of direct thrombin inhibitors (VE-DTIs) and have utilized kinetics, biochemical, and X-ray structural studies to characterize the mechanism of action and in vitro pharmacology of an exemplary compound from this class, Compound 1. RESULTS: We demonstrate that Compound 1, an exemplary VE-DTI, acts through reversible covalent inhibition. Compound 1 inhibits thrombin by transiently acylating the active site S195 with high potency and significant selectivity over other trypsin-like serine proteases. The compound inhibits the binding of a peptide substrate with both clot-bound and free thrombin with nanomolar potency. Compound 1 is a low micromolar inhibitor of thrombin activity against endogenous substrates such as fibrinogen and a nanomolar inhibitor of the activation of protein C and thrombin-activatable fibrinolysis inhibitor. In the thrombin generation assay, Compound 1 inhibits thrombin generation with low micromolar potency but does not increase the lag time for thrombin formation. In addition, Compound 1 showed weak inhibition of clotting in PT and aPTT assays consistent with its distinctive profile in the thrombin generation assay. CONCLUSION: Compound 1, while maintaining strong potency comparable to the current DTIs, has a distinct mechanism of action which produces a differentiating pharmacological profile. Acting through reversible covalent inhibition, these direct thrombin inhibitors could lead to new anticoagulants with better combined efficacy and bleeding profiles.
		+
		+	Reversible covalent direct thrombin inhibitors.,Sivaraja M, Pozzi N, Rienzo M, Lin K, Shiau TP, Clemens DM, Igoudin L, Zalicki P, Chang SS, Estiarte MA, Short KM, Williams DC, Datta A, Di Cera E, Kita DB PLoS One. 2018 Aug 2;13(8):e0201377. doi: 10.1371/journal.pone.0201377., eCollection 2018. PMID:30071045<ref>PMID:30071045</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6cym" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:19, 9 May 2018

OCA — Wed, 09 May 2018 06:19:22 GMT

←Older revision		Revision as of 06:19, 9 May 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6cym is ~~ON HOLD~~	+	==Reversible Covalent Direct Thrombin Inhibitors==
-		+	<StructureSection load='6cym' size='340' side='right' caption='[[6cym]], [[Resolution\|resolution]] 2.90Å' scene=''>
-	~~Authors~~: ~~Sivaraja~~, M., ~~Williams~~, D.C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6cym]] is a 4 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=6CYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CYM FirstGlance]. <br>
-	~~Description~~: ~~Reversible Covalent Direct~~ Thrombin ~~Inhibitors~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=71F:2-METHOXYBENZOIC+ACID'>71F</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </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=6cym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cym OCA], [http://pdbe.org/6cym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cym RCSB], [http://www.ebi.ac.uk/pdbsum/6cym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cym ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Defects in F2 are the cause of factor II deficiency (FA2D) [MIM:[http://omim.org/entry/613679 613679]]. It is a very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels.<ref>PMID:14962227</ref> <ref>PMID:6405779</ref> <ref>PMID:3771562</ref> <ref>PMID:3567158</ref> <ref>PMID:3801671</ref> <ref>PMID:3242619</ref> <ref>PMID:2719946</ref> <ref>PMID:1354985</ref> <ref>PMID:1421398</ref> <ref>PMID:1349838</ref> <ref>PMID:7865694</ref> <ref>PMID:7792730</ref> Genetic variations in F2 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[http://omim.org/entry/601367 601367]]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref> Defects in F2 are the cause of thrombophilia due to thrombin defect (THPH1) [MIM:[http://omim.org/entry/188050 188050]]. It is a multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis. Defects in F2 are associated with susceptibility to pregnancy loss, recurrent, type 2 (RPRGL2) [MIM:[http://omim.org/entry/614390 614390]]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11506076</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.<ref>PMID:2856554</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Thrombin]]
	[[Category: Sivaraja, M]]		[[Category: Sivaraja, M]]
-	[[Category: Williams, D.C]]	+	[[Category: Williams, D C]]
		+	[[Category: Blood coagulation]]
		+	[[Category: Calcium-binding]]
		+	[[Category: Glycoprotein]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Plasma]]
		+	[[Category: Serine protease]]

OCA: Protected "6cym" [edit=sysop:move=sysop]

OCA — Wed, 18 Apr 2018 04:13:09 GMT

Protected "6cym" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:13, 18 April 2018

OCA: New page: '''Unreleased structure''' The entry 6cym is ON HOLD Authors: Sivaraja, M., Williams, D.C. Description: Reversible Covalent Direct Thrombin Inhibitors [[Category: Unreleased Structures...

OCA — Wed, 18 Apr 2018 04:13:08 GMT

New page: '''Unreleased structure''' The entry 6cym is ON HOLD Authors: Sivaraja, M., Williams, D.C. Description: Reversible Covalent Direct Thrombin Inhibitors [[Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 6cym is ON HOLD

Authors: Sivaraja, M., Williams, D.C.

Description: Reversible Covalent Direct Thrombin Inhibitors
[[Category: Unreleased Structures]]
[[Category: Sivaraja, M]]
[[Category: Williams, D.C]]