6dvm: Difference between revisions

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 ==Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-122==
-<StructureSection load='6dvm' size='340' side='right' caption='[[6dvm]], [[Resolution|resolution]] 1.47&Aring;' scene=''>
+<StructureSection load='6dvm' size='340' side='right'caption='[[6dvm]], [[Resolution|resolution]] 1.47&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6dvm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6dvm]] is a 4 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=6DVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DVM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HBJ:4-(dimethylamino)-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-N-{2-[(4-methylphenyl)amino]-2-oxoethyl}benzamide'>HBJ</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]] 1.47&#8491;</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=6dvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvm OCA], [http://pdbe.org/6dvm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dvm RCSB], [http://www.ebi.ac.uk/pdbsum/6dvm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvm ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HBJ:4-(dimethylamino)-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-N-{2-[(4-methylphenyl)amino]-2-oxoethyl}benzamide'>HBJ</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=6dvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvm OCA], [https://pdbe.org/6dvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dvm RCSB], [https://www.ebi.ac.uk/pdbsum/6dvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvm ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/F8W4B7_DANRE F8W4B7_DANRE]
-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.
-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>
+==See Also==
+*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6dvm" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Christianson, D W]]
+[[Category: Danio rerio]]
-[[Category: Porter, N J]]
+[[Category: Large Structures]]
-[[Category: Histone deacetylaase]]
+[[Category: Christianson DW]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
+[[Category: Porter NJ]]
-[[Category: Metallohydrolase]]