6dvl - Revision history

OCA at 06:14, 11 October 2023

OCA — Wed, 11 Oct 2023 06:14:34 GMT

←Older revision		Revision as of 06:14, 11 October 2023
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	<StructureSection load='6dvl' size='340' side='right'caption='[[6dvl]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6dvl' size='340' side='right'caption='[[6dvl]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dvl]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DVL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dvl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DVL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HBG:N-[2-(cyclohexylamino)-2-oxoethyl]-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-3,5-dimethylbenzamide'>HBG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.1Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hdac6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HBG:N-[2-(cyclohexylamino)-2-oxoethyl]-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-3,5-dimethylbenzamide'>HBG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6dvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvl OCA], [~~http~~://pdbe.org/6dvl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dvl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dvl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvl 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=6dvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvl OCA], [https://pdbe.org/6dvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dvl RCSB], [https://www.ebi.ac.uk/pdbsum/6dvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F8W4B7_DANRE F8W4B7_DANRE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Christianson~~, D W~~]]	+	[[Category: Christianson DW]]
-	[[Category: Porter~~, N J]]~~	+	[[Category: Porter NJ]]
-	~~[[Category: Histone deacetylaase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Metallohydrolase~~]]	+

OCA at 10:14, 18 December 2019

OCA — Wed, 18 Dec 2019 10:14:43 GMT

←Older revision		Revision as of 10:14, 18 December 2019
Line 1:		Line 1:

	==Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-115==		==Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-115==
-	<StructureSection load='6dvl' size='340' side='right' caption='[[6dvl]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='6dvl' size='340' side='right'caption='[[6dvl]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dvl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVL FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dvl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVL FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 6dvl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dvl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone deacetylase 3D structures\|Histone deacetylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Brachidanio rerio]]		[[Category: Brachidanio rerio]]
		+	[[Category: Large Structures]]
	[[Category: Christianson, D W]]		[[Category: Christianson, D W]]
	[[Category: Porter, N J]]		[[Category: Porter, N J]]

OCA at 08:39, 26 September 2018

OCA — Wed, 26 Sep 2018 08:39:55 GMT

←Older revision		Revision as of 08:39, 26 September 2018
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	<StructureSection load='6dvl' size='340' side='right' caption='[[6dvl]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6dvl' size='340' side='right' caption='[[6dvl]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dvl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dvl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HBG:N-[2-(cyclohexylamino)-2-oxoethyl]-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-3,5-dimethylbenzamide'>HBG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HBG:N-[2-(cyclohexylamino)-2-oxoethyl]-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-3,5-dimethylbenzamide'>HBG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hdac6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</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=6dvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvl OCA], [http://pdbe.org/6dvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dvl RCSB], [http://www.ebi.ac.uk/pdbsum/6dvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvl ProSAT]</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=6dvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvl OCA], [http://pdbe.org/6dvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dvl RCSB], [http://www.ebi.ac.uk/pdbsum/6dvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvl ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
	[[Category: Christianson, D W]]		[[Category: Christianson, D W]]
	[[Category: Porter, N J]]		[[Category: Porter, N J]]

OCA at 07:28, 29 August 2018

OCA — Wed, 29 Aug 2018 07:28:43 GMT

←Older revision		Revision as of 07:28, 29 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dvl is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-115==
		+	<StructureSection load='6dvl' size='340' side='right' caption='[[6dvl]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dvl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HBG:N-[2-(cyclohexylamino)-2-oxoethyl]-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-3,5-dimethylbenzamide'>HBG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6dvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvl OCA], [http://pdbe.org/6dvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dvl RCSB], [http://www.ebi.ac.uk/pdbsum/6dvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvl ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Four crystal structures are presented of histone deacetylase 6 (HDAC6) complexes with para-substituted phenylhydromaxamate inhibitors, including bulky peptoids. These structures provide insight regarding the design of capping groups that confer selectivity for binding to HDAC6, specifically with regard to interactions in a pocket formed by the L1 loop. Capping group interactions may also influence hydroxamate-Zn(2+) coordination with monodentate or bidentate geometry.

-	~~Authors: Porter, N.J~~., ~~Christianson~~, D.W.	+	Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity.,Porter NJ, Osko JD, Diedrich D, Kurz T, Hooker JM, Hansen FK, Christianson DW J Med Chem. 2018 Aug 17. doi: 10.1021/acs.jmedchem.8b01013. PMID:30118224<ref>PMID:30118224</ref>

-	~~Description: Crystal structure~~ of ~~Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-115~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Christianson, D.W]]	+	<div class="pdbe-citations 6dvl" style="background-color:#fffaf0;"></div>
-	[[Category: Porter, N.J]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Christianson, D W]]
		+	[[Category: Porter, N J]]
		+	[[Category: Histone deacetylaase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Metallohydrolase]]

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

OCA — Wed, 04 Jul 2018 05:45:04 GMT

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

←Older revision

Revision as of 05:45, 4 July 2018

OCA: New page: '''Unreleased structure''' The entry 6dvl is ON HOLD until Paper Publication Authors: Porter, N.J., Christianson, D.W. Description: Crystal structure of Danio rerio histone deacetylase...

OCA — Wed, 04 Jul 2018 05:45:02 GMT

New page: '''Unreleased structure''' The entry 6dvl is ON HOLD until Paper Publication Authors: Porter, N.J., Christianson, D.W. Description: Crystal structure of Danio rerio histone deacetylase...

New page

'''Unreleased structure'''

The entry 6dvl is ON HOLD until Paper Publication

Authors: Porter, N.J., Christianson, D.W.

Description: Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-115
[[Category: Unreleased Structures]]
[[Category: Christianson, D.W]]
[[Category: Porter, N.J]]