ISDA

Deposition Date 2018-06-24

Release Date 2018-08-29

Last Version Date 2024-03-13

Entry Detail

PDB ID:

6DVM

Keywords:

hydrolase/hydrolase inhibitor

Title:

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-122

Biological Source:

Source Organism:

Danio rerio (Taxon ID: 7955)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.47 Å

R-Value Free:

0.16

R-Value Work:

0.14

R-Value Observed:

0.14

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Hdac6 protein
Chain IDs:A, B, C, D
Chain Length:364
Number of Molecules:4
Biological Source:Danio rerio

UniProt ID:F8W4B7 Pfam ID:PF00850

Ligand Molecules

BTB

EDO

HBJ

Primary Citation

Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity.

Porter, N.J, Osko, J.D, Diedrich, D, Kurz, T, Hooker, J.M, Hansen, F.K, Christianson, D.W.Show

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.

Legend

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Disease

Primary Citation of related structures