7JOM image
Entry Detail
PDB ID:
7JOM
Title:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with TO-317
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2020-08-06
Release Date:
2021-06-16
Method Details:
Experimental Method:
Resolution:
1.84 Å
R-Value Free:
0.20
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Hdac6 protein
Chain IDs:A, B
Chain Length:364
Number of Molecules:2
Biological Source:Danio rerio
Primary Citation
Unique Molecular Interaction with the Histone Deacetylase 6 Catalytic Tunnel: Crystallographic and Biological Characterization of a Model Chemotype.
J.Med.Chem. 64 2691 2704 (2021)
PMID: 33576627 DOI: 10.1021/acs.jmedchem.0c01922

Abstact

Histone deacetylase 6 (HDAC6) is involved in multiple regulatory processes, ranging from cellular stress to intracellular transport. Inhibition of aberrant HDAC6 activity in several cancers and neurological diseases has been shown to be efficacious in both preclinical and clinical studies. While selective HDAC6 targeting has been pursued as an alternative to pan-HDAC drugs, identifying truly selective molecular templates has not been trivial. Herein, we report a structure-activity relationship study yielding TO-317, which potently binds HDAC6 catalytic domain 2 (Ki = 0.7 nM) and inhibits the enzyme function (IC50 = 2 nM). TO-317 exhibits 158-fold selectivity for HDAC6 over other HDAC isozymes by binding the catalytic Zn2+ and, uniquely, making a never seen before direct hydrogen bond with the Zn2+ coordinating residue, His614. This novel structural motif targeting the second-sphere His614 interaction, observed in a 1.84 Å resolution crystal structure with drHDAC6 from zebrafish, can provide new pharmacophores for identifying enthalpically driven, high-affinity, HDAC6-selective inhibitors.

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