6pye - Revision history

OCA at 07:38, 11 October 2023

OCA — Wed, 11 Oct 2023 07:38:07 GMT

←Older revision		Revision as of 07:38, 11 October 2023
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	<StructureSection load='6pye' size='340' side='right'caption='[[6pye]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='6pye' size='340' side='right'caption='[[6pye]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pye]] 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=6PYE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PYE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pye]] 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=6PYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PYE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=P5Y:N-[(1-benzyl-1H-tetrazol-5-yl)methyl]-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-2-(trifluoromethyl)benzamide'>P5Y</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]] 1.480003Å</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=P5Y:N-[(1-benzyl-1H-tetrazol-5-yl)methyl]-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-2-(trifluoromethyl)benzamide'>P5Y</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~~://proteopedia.org/fgij/fg.htm?mol=6pye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pye OCA], [~~http~~://pdbe.org/6pye PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pye RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pye PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pye 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=6pye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pye OCA], [https://pdbe.org/6pye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pye RCSB], [https://www.ebi.ac.uk/pdbsum/6pye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pye 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: Osko~~, J D]]~~	+	[[Category: Osko JD]]
-	~~[[Category: Histone deacetylase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metallohydrolase~~]]	+

OCA at 07:24, 30 September 2020

OCA — Wed, 30 Sep 2020 07:24:45 GMT

←Older revision		Revision as of 07:24, 30 September 2020
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	==Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with NR160==		==Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with NR160==
-	<StructureSection load='6pye' size='340' side='right'caption='[[6pye]]' scene=''>	+	<StructureSection load='6pye' size='340' side='right'caption='[[6pye]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PYE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PYE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pye]] 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=6PYE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PYE FirstGlance]. <br>
-	</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=6pye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pye OCA], [http://pdbe.org/6pye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pye RCSB], [http://www.ebi.ac.uk/pdbsum/6pye PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pye ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=P5Y:N-[(1-benzyl-1H-tetrazol-5-yl)methyl]-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-2-(trifluoromethyl)benzamide'>P5Y</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://proteopedia.org/fgij/fg.htm?mol=6pye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pye OCA], [http://pdbe.org/6pye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pye RCSB], [http://www.ebi.ac.uk/pdbsum/6pye PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pye ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Histone deacetylase 6 (HDAC6) is an emerging target for the treatment of cancer, neurodegenerative diseases, inflammation, and other diseases. Here, we present the multicomponent synthesis and structure-activity relationship of a series of tetrazole-based HDAC6 inhibitors. We discovered the hit compound NR-160 by investigating the inhibition of recombinant HDAC enzymes and protein acetylation. A cocrystal structure of HDAC6 complexed with NR-160 disclosed that the steric complementarity of the bifurcated capping group of NR-160 to the L1 and L2 loop pockets may be responsible for its HDAC6-selective inhibition. While NR-160 displayed only low cytotoxicity as a single agent against leukemia cell lines, it augmented the apoptosis induction of the proteasome inhibitor bortezomib in combination experiments significantly. Furthermore, a combinatorial high-throughput drug screen revealed significantly enhanced cytotoxicity when NR-160 was used in combination with epirubicin and daunorubicin. The synergistic effect in combination with bortezomib and anthracyclines highlights the potential of NR-160 in combination therapies.
		+
		+	Multicomponent Synthesis, Binding Mode, and Structure-Activity Relationship of Selective Histone Deacetylase 6 (HDAC6) Inhibitors with Bifurcated Capping Groups.,Ressing N, Sonnichsen M, Osko JD, Scholer A, Schliehe-Diecks J, Skerhut A, Borkhardt A, Hauer J, Kassack MU, Christianson DW, Bhatia S, Hansen FK J Med Chem. 2020 Sep 24;63(18):10339-10351. doi: 10.1021/acs.jmedchem.9b01888., Epub 2020 Sep 1. PMID:32803970<ref>PMID:32803970</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6pye" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone deacetylase 3D structures\|Histone deacetylase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Christianson DW]]	+	[[Category: Christianson, D W]]
-	[[Category: Osko JD]]	+	[[Category: Osko, J D]]
		+	[[Category: Histone deacetylase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metallohydrolase]]

OCA at 11:08, 29 July 2020

OCA — Wed, 29 Jul 2020 11:08:02 GMT

←Older revision		Revision as of 11:08, 29 July 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6pye ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with NR160==
-		+	<StructureSection load='6pye' size='340' side='right'caption='[[6pye]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PYE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PYE FirstGlance]. <br>
-	~~Description~~:	+	</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=6pye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pye OCA], [http://pdbe.org/6pye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pye RCSB], [http://www.ebi.ac.uk/pdbsum/6pye PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pye ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Christianson DW]]
		+	[[Category: Osko JD]]

OCA at 13:47, 28 August 2019

OCA — Wed, 28 Aug 2019 13:47:20 GMT

←Older revision		Revision as of 13:47, 28 August 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6pye is ON HOLD	+	The entry 6pye is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 07 Aug 2019 04:20:11 GMT

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

←Older revision

Revision as of 04:20, 7 August 2019

OCA: New page: '''Unreleased structure''' The entry 6pye is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 07 Aug 2019 04:20:10 GMT

New page: '''Unreleased structure''' The entry 6pye is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6pye is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]