6DVL image
Deposition Date 2018-06-24
Release Date 2018-08-29
Last Version Date 2023-10-11
Entry Detail
PDB ID:
6DVL
Keywords:
hydrolase/hydrolase inhibitor
Title:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-115
Biological Source:
Source Organism:
Danio rerio (Taxon ID: 7955)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.10 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 1 21 1
6DVL validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Hdac6 protein
Chain IDs:A, B
Chain Length:364
Number of Molecules:2
Biological Source:Danio rerio
UniProt ID:F8W4B7 Pfam ID:PF00850
Ligand Molecules
HBG
K
ZN
Primary Citation
Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity.
J. Med. Chem. 61 8054 8060 (2018)
PMID: 30118224 DOI: 10.1021/acs.jmedchem.8b01013

Abstact

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-Zn2+ coordination with monodentate or bidentate geometry.

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Disease

Primary Citation of related structures
6DVL