4ygv - Revision history

OCA at 10:55, 10 January 2024

2024-01-10T10:55:07Z

←Older revision		Revision as of 10:55, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ygv]] 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=4YGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YGV FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ygv]] 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=4YGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YGV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.76Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=4ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ygv OCA], [https://pdbe.org/4ygv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ygv RCSB], [https://www.ebi.ac.uk/pdbsum/4ygv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ygv 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=4ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ygv OCA], [https://pdbe.org/4ygv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ygv RCSB], [https://www.ebi.ac.uk/pdbsum/4ygv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ygv ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:13, 3 May 2023

2023-05-03T08:13:46Z

←Older revision		Revision as of 08:13, 3 May 2023
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	<StructureSection load='4ygv' size='340' side='right'caption='[[4ygv]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='4ygv' size='340' side='right'caption='[[4ygv]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ygv]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YGV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YGV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ygv]] 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=4YGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YGV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=4ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ygv OCA], [~~http~~://pdbe.org/4ygv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ygv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ygv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ygv 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=4ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ygv OCA], [https://pdbe.org/4ygv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ygv RCSB], [https://www.ebi.ac.uk/pdbsum/4ygv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ygv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Nar, H]]	+	[[Category: Nar H]]
-	[[Category: Schiele, F]]	+	[[Category: Schiele F]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Antidote]]~~	+
-	~~[[Category: Dabigatran]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Pradaxa]]~~	+
-	~~[[Category: Reversal agent~~]]	+

OCA at 06:51, 12 June 2019

2019-06-12T06:51:34Z

←Older revision		Revision as of 06:51, 12 June 2019
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		+
	==Reversal Agent for Dabigatran==		==Reversal Agent for Dabigatran==
-	<StructureSection load='4ygv' size='340' side='right' caption='[[4ygv]], [[Resolution\|resolution]] 1.76Å' scene=''>	+	<StructureSection load='4ygv' size='340' side='right'caption='[[4ygv]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ygv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YGV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YGV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ygv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YGV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YGV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=4ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ygv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ygv RCSB], [http://www.ebi.ac.uk/pdbsum/4ygv PDBsum]</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=4ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ygv OCA], [http://pdbe.org/4ygv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ygv RCSB], [http://www.ebi.ac.uk/pdbsum/4ygv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ygv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4ygv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Nar, H]]		[[Category: Nar, H]]
	[[Category: Schiele, F]]		[[Category: Schiele, F]]

OCA at 15:10, 17 June 2015

2015-06-17T15:10:32Z

←Older revision		Revision as of 15:10, 17 June 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Reversal Agent for Dabigatran==
		+	<StructureSection load='4ygv' size='340' side='right' caption='[[4ygv]], [[Resolution\|resolution]] 1.76Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ygv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YGV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YGV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=4ygv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ygv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ygv RCSB], [http://www.ebi.ac.uk/pdbsum/4ygv PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Novel oral anticoagulants are effective and safe alternatives to vitamin-K antagonists for anticoagulation therapy. However, anticoagulation therapy in general is associated with an elevated risk of bleeding. Idarucizumab is a reversal agent for the direct thrombin inhibitor, dabigatran etexilate (Pradaxa(R)) and is currently in Phase 3 studies. Here, we report data on the antibody fragment aDabi-Fab2, a putative backup molecule for idarucizumab. Although aDabi-Fab2 completely reversed effects of dabigatran in a rat model in vivo, we observed significantly reduced duration of action compared to idarucizumab. Rational protein engineering, based on the X-ray structure of aDabi-Fab2, led to the identification of mutant Y103W. The mutant had optimized shape complementarity to dabigatran while maintaining an energetically favored hydrogen bond. It displayed increased affinity for dabigatran, mainly driven by a slower off-rate. Interestingly, the increased residence time translated into longer duration of action in vivo. It was thus possible to further enhance the efficacy of aDabi-Fab2 based on rational design, giving it the potential to serve as a back-up candidate for idarucizumab.

-	~~The entry 4ygv is ON HOLD until Paper Publication~~	+	Structure-guided residence time optimization of a dabigatran reversal agent.,Schiele F, van Ryn J, Litzenburger T, Ritter M, Seeliger D, Nar H MAbs. 2015 Jun 5:0. PMID:26047352<ref>PMID:26047352</ref>

-	~~Authors: Schiele~~, F.~~, Nar, H~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Reversal Agent for Dabigatran~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Nar, H]]		[[Category: Nar, H]]
	[[Category: Schiele, F]]		[[Category: Schiele, F]]
		+	[[Category: Antibody]]
		+	[[Category: Antidote]]
		+	[[Category: Dabigatran]]
		+	[[Category: Immune system]]
		+	[[Category: Pradaxa]]
		+	[[Category: Reversal agent]]

OCA at 10:36, 11 March 2015

2015-03-11T10:36:09Z

←Older revision		Revision as of 10:36, 11 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ygv is ON HOLD	+	The entry 4ygv is ON HOLD until Paper Publication

	Authors: Schiele, F., Nar, H.		Authors: Schiele, F., Nar, H.

OCA: Protected "4ygv" [edit=sysop:move=sysop]

2015-03-04T10:28:23Z

Protected "4ygv" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:28, 4 March 2015

OCA: New page: '''Unreleased structure''' The entry 4ygv is ON HOLD Authors: Schiele, F., Nar, H. Description: Reversal Agent for Dabigatran Category: Unreleased Structures Category: Nar, H [...

2015-03-04T10:28:22Z

New page: '''Unreleased structure''' The entry 4ygv is ON HOLD Authors: Schiele, F., Nar, H. Description: Reversal Agent for Dabigatran Category: Unreleased Structures Category: Nar, H [...

New page

'''Unreleased structure'''

The entry 4ygv is ON HOLD

Authors: Schiele, F., Nar, H.

Description: Reversal Agent for Dabigatran
[[Category: Unreleased Structures]]
[[Category: Nar, H]]
[[Category: Schiele, F]]