4cqf - Revision history

OCA at 12:14, 20 December 2023

OCA — Wed, 20 Dec 2023 12:14:47 GMT

←Older revision		Revision as of 12:14, 20 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4cqf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Schistosoma_mansoni Schistosoma mansoni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CQF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4cqf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Schistosoma_mansoni Schistosoma mansoni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CQF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9Z8:6-(2-MERCAPTOACETYLAMINO)-N-PHENYLHEXANAMIDE'>9Z8</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9Z8:6-(2-MERCAPTOACETYLAMINO)-N-PHENYLHEXANAMIDE'>9Z8</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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'>[https://proteopedia.org/fgij/fg.htm?mol=4cqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cqf OCA], [https://pdbe.org/4cqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cqf RCSB], [https://www.ebi.ac.uk/pdbsum/4cqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cqf 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=4cqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cqf OCA], [https://pdbe.org/4cqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cqf RCSB], [https://www.ebi.ac.uk/pdbsum/4cqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cqf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A5H660_SCHMA A5H660_SCHMA]]	+	[https://www.uniprot.org/uniprot/A5H660_SCHMA A5H660_SCHMA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:27, 14 September 2022

OCA — Wed, 14 Sep 2022 07:27:32 GMT

←Older revision		Revision as of 07:27, 14 September 2022
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	<StructureSection load='4cqf' size='340' side='right'caption='[[4cqf]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4cqf' size='340' side='right'caption='[[4cqf]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4cqf]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Blood_fluke Blood fluke~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CQF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4CQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4cqf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Schistosoma_mansoni Schistosoma mansoni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CQF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9Z8:6-(2-MERCAPTOACETYLAMINO)-N-PHENYLHEXANAMIDE'>9Z8</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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" id="ligandDat"><scene name='pdbligand=9Z8:6-(2-MERCAPTOACETYLAMINO)-N-PHENYLHEXANAMIDE'>9Z8</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4cqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cqf OCA], [~~http~~://pdbe.org/4cqf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4cqf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4cqf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4cqf 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=4cqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cqf OCA], [https://pdbe.org/4cqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cqf RCSB], [https://www.ebi.ac.uk/pdbsum/4cqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cqf ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A5H660_SCHMA A5H660_SCHMA]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 20:

	==See Also==		==See Also==
-	*[[Histone deacetylase\|Histone deacetylase]]	+	*[[Histone deacetylase 3D structures\|Histone deacetylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Blood fluke]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Marek, M~~]]	+	[[Category: Schistosoma mansoni]]
-	[[Category: ~~Romier, C~~]]	+	[[Category: Marek M]]
-	[[Category: ~~Epigenetic]]~~	+	[[Category: Romier C]]
-	~~[[Category: Eukaryote]]~~	+
-	~~[[Category: Histone deacetylase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibition]]~~	+
-	~~[[Category: Platyhelminth]]~~	+
-	~~[[Category: Structural protein~~]]	+

OCA at 09:46, 20 March 2019

OCA — Wed, 20 Mar 2019 09:46:25 GMT

←Older revision		Revision as of 09:46, 20 March 2019
Line 1:		Line 1:

	==Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor==		==Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor==
-	<StructureSection load='4cqf' size='340' side='right' caption='[[4cqf]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4cqf' size='340' side='right'caption='[[4cqf]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4cqf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Blood_fluke Blood fluke]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CQF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4cqf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Blood_fluke Blood fluke]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CQF FirstGlance]. <br>
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Blood fluke]]		[[Category: Blood fluke]]
		+	[[Category: Large Structures]]
	[[Category: Marek, M]]		[[Category: Marek, M]]
	[[Category: Romier, C]]		[[Category: Romier, C]]

OCA at 16:35, 11 August 2016

OCA — Thu, 11 Aug 2016 16:35:52 GMT

←Older revision		Revision as of 16:35, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor==		==Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor==
	<StructureSection load='4cqf' size='340' side='right' caption='[[4cqf]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4cqf' size='340' side='right' caption='[[4cqf]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4cqf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Blood_fluke Blood fluke]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CQF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4cqf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Blood_fluke Blood fluke]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CQF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9Z8:6-(2-MERCAPTOACETYLAMINO)-N-PHENYLHEXANAMIDE'>9Z8</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=9Z8:6-(2-MERCAPTOACETYLAMINO)-N-PHENYLHEXANAMIDE'>9Z8</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4cqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cqf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cqf RCSB], [http://www.ebi.ac.uk/pdbsum/4cqf 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=4cqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cqf OCA], [http://pdbe.org/4cqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4cqf RCSB], [http://www.ebi.ac.uk/pdbsum/4cqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4cqf 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 4cqf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone deacetylase\|Histone deacetylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:48, 20 January 2015

OCA — Tue, 20 Jan 2015 10:48:13 GMT

←Older revision		Revision as of 10:48, 20 January 2015
Line 19:		Line 19:
	</StructureSection>		</StructureSection>
	[[Category: Blood fluke]]		[[Category: Blood fluke]]
-	[[Category: Marek, M.]]	+	[[Category: Marek, M]]
-	[[Category: Romier, C.]]	+	[[Category: Romier, C]]
	[[Category: Epigenetic]]		[[Category: Epigenetic]]
	[[Category: Eukaryote]]		[[Category: Eukaryote]]

OCA at 05:29, 8 October 2014

OCA — Wed, 08 Oct 2014 05:29:36 GMT

←Older revision		Revision as of 05:29, 8 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4cqf\| PDB=4cqf \| SCENE= }}~~	+	==Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor==
-	===Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor===	+	<StructureSection load='4cqf' size='340' side='right' caption='[[4cqf]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24657767}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4cqf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Blood_fluke Blood fluke]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CQF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9Z8:6-(2-MERCAPTOACETYLAMINO)-N-PHENYLHEXANAMIDE'>9Z8</scene>, <scene name='pdbligand=DMF:DIMETHYLFORMAMIDE'>DMF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4cqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cqf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cqf RCSB], [http://www.ebi.ac.uk/pdbsum/4cqf PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Schistosomiasis, caused by the parasitic flatworm Schistosoma mansoni and related species, is a tropical disease that affects over 200 million people worldwide. A new approach for targeting eukaryotic parasites is to tackle their dynamic epigenetic machinery that is necessary for the extensive phenotypic changes during the life cycle of the parasite. Recently, we identified S. mansoni histone deacetylase 8 (smHDAC8) as a potential target for anti-parasitic therapy. Here we present results on the investigations of a focused set of HDAC inhibitors on smHDAC8. Besides several active hydroxamates, we identified a thiol based inhibitor that inhibited smHDAC8 activity in the micromolar range with unexpected selectivity over the human isotype, which has not been observed so far. The crystal structure of smHDAC8 complexed with the thiol derivative revealed that the inhibitor is accommodated in the catalytic pocket, where it interacts with both the catalytic zinc ion and the essential catalytic tyrosine (Y341) residue via its mercaptoacetamide warhead. To our knowledge, this is the first complex crystal structure of any HDAC inhibited by a mercaptoacetamide inhibitor, and therefore this finding offers a rationale for further improvement. Finally, an ester prodrug of the thiol HDAC inhibitor exhibited anti-parasitic activity on cultured schistosomes in a dose-dependent manner.

-	~~==About this Structure==~~	+	Molecular basis for the anti-parasitic activity of a mercaptoacetamide derivative that inhibits histone deacetylase 8 (HDAC8) from the human pathogen Schistosoma mansoni.,Stolfa DA, Marek M, Lancelot J, Hauser AT, Walter A, Leproult E, Melesina J, Rumpf T, Wurtz JM, Cavarelli J, Sippl W, Pierce RJ, Romier C, Jung M J Mol Biol. 2014 Mar 20. pii: S0022-2836(14)00131-4. doi:, 10.1016/j.jmb.2014.03.007. PMID:24657767<ref>PMID:24657767</ref>
-	~~[[4cqf]] is~~ a 4 ~~chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4CQF OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024657767</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Blood fluke]]
	[[Category: Marek, M.]]		[[Category: Marek, M.]]
	[[Category: Romier, C.]]		[[Category: Romier, C.]]

OCA at 09:03, 2 April 2014

OCA — Wed, 02 Apr 2014 09:03:38 GMT

←Older revision		Revision as of 09:03, 2 April 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4cqf\| PDB=4cqf \| SCENE= }}
		+	===Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor===
		+	{{ABSTRACT_PUBMED_24657767}}

-	~~The entry~~ 4cqf is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4cqf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CQF OCA].

-	~~Authors~~: Marek, M., Romier, C.	+	==Reference==
-		+	<ref group="xtra">PMID:024657767</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor~~	+	[[Category: Marek, M.]]
		+	[[Category: Romier, C.]]
		+	[[Category: Epigenetic]]
		+	[[Category: Eukaryote]]
		+	[[Category: Histone deacetylase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibition]]
		+	[[Category: Platyhelminth]]
		+	[[Category: Structural protein]]

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

OCA — Mon, 03 Mar 2014 16:17:19 GMT

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

←Older revision

Revision as of 16:17, 3 March 2014

OCA: New page: '''Unreleased structure''' The entry 4cqf is ON HOLD until Paper Publication Authors: Marek, M., Romier, C. Description: Crystal structure of Schistosoma mansoni HDAC8 complexed with a...

OCA — Mon, 03 Mar 2014 16:17:18 GMT

New page: '''Unreleased structure''' The entry 4cqf is ON HOLD until Paper Publication Authors: Marek, M., Romier, C. Description: Crystal structure of Schistosoma mansoni HDAC8 complexed with a...

New page

'''Unreleased structure'''

The entry 4cqf is ON HOLD until Paper Publication

Authors: Marek, M., Romier, C.

Description: Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor