6mr5: Difference between revisions

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<StructureSection load='6mr5' size='340' side='right'caption='[[6mr5]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
<StructureSection load='6mr5' size='340' side='right'caption='[[6mr5]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6mr5]] 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=6MR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MR5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6mr5]] 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=6MR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MR5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=W45:N-[5-(5,6-dichloro-1H-indol-1-yl)pentyl]-2-sulfanylacetamide'>W45</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]] 1.85&#8491;</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=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=W45:N-[5-(5,6-dichloro-1H-indol-1-yl)pentyl]-2-sulfanylacetamide'>W45</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=6mr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mr5 OCA], [http://pdbe.org/6mr5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mr5 RCSB], [http://www.ebi.ac.uk/pdbsum/6mr5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mr5 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=6mr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mr5 OCA], [https://pdbe.org/6mr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mr5 RCSB], [https://www.ebi.ac.uk/pdbsum/6mr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mr5 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/F8W4B7_DANRE F8W4B7_DANRE]
Mercaptoacetamide histone deacetylase inhibitors are neuroprotective agents that do not exhibit the genotoxicity associated with more commonly used hydroxamate inhibitors. Here, we present the crystal structure of a selective mercaptoacetamide complexed with the C-terminal catalytic domain of HDAC6. When compared with the structure of a mercaptoacetamide bound to the class I isozyme HDAC8, different interactions are observed with the conserved tandem histidine pair in the active site. These differences likely contribute to the selectivity for inhibition of HDAC6, an important target for cancer chemotherapy and the treatment of neurodegenerative disease.
 
Molecular Basis for the Selective Inhibition of Histone Deacetylase 6 by a Mercaptoacetamide Inhibitor.,Porter NJ, Shen S, Barinka C, Kozikowski AP, Christianson DW ACS Med Chem Lett. 2018 Nov 21;9(12):1301-1305. doi:, 10.1021/acsmedchemlett.8b00487. eCollection 2018 Dec 13. PMID:30613344<ref>PMID:30613344</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6mr5" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
== References ==
<references/>
__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 deacetylase]]
[[Category: Hydrolase-hydrolase inhibitor complex]]
[[Category: Zinc hydrolase]]

Latest revision as of 17:44, 13 March 2024

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with a mercaptoacetamide-based inhibitorCrystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with a mercaptoacetamide-based inhibitor

Structural highlights

6mr5 is a 2 chain structure with sequence from Danio rerio. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.85Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

F8W4B7_DANRE

See Also

6mr5, resolution 1.85Å

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OCA
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