ISDA

Deposition Date 2016-06-14

Release Date 2016-07-27

Last Version Date 2023-09-27

Entry Detail

PDB ID:

5KH3

Keywords:

HYDROLASE

Title:

Crystal structure of fragment (3-(5-Chloro-1,3-benzothiazol-2-yl)propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.60 Å

R-Value Free:

0.19

R-Value Work:

0.15

R-Value Observed:

0.15

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone deacetylase 6
Gene (Uniprot):HDAC6
Chain IDs:A
Chain Length:107
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9UBN7 Pfam ID:PF02148 EC:3.5.1.98

Ligand Molecules

6U6

UNX

Primary Citation

Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin.

Harding, R.J, Ferreira de Freitas, R, Collins, P, Franzoni, I, Ravichandran, M, Ouyang, H, Juarez-Ornelas, K.A, Lautens, M, Schapira, M, von Delft, F, Santhakumar, V, Arrowsmith, C.H.Show

J. Med. Chem. 60 9090 9096 (2017)

PMID: 29019676 DOI: 10.1021/acs.jmedchem.7b00933

Abstact

Inhibitors of HDAC6 have attractive potential in numerous cancers. HDAC6 inhibitors to date target the catalytic domains, but targeting the unique zinc-finger ubiquitin-binding domain (Zf-UBD) of HDAC6 may be an attractive alternative strategy. We developed X-ray crystallography and biophysical assays to identify and characterize small molecules capable of binding to the Zf-UBD and competing with ubiquitin binding. Our results revealed two adjacent ligand-able pockets of HDAC6 Zf-UBD and the first functional ligands for this domain.

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Primary Citation of related structures