9MQP image
Deposition Date 2025-01-04
Release Date 2025-03-05
Last Version Date 2025-03-12
Entry Detail
PDB ID:
9MQP
Keywords:
Title:
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with SelSA
Biological Source:
Source Organism:
Danio rerio (Taxon ID: 7955)
Method Details:
Experimental Method:
Resolution:
2.15 Å
R-Value Free:
0.24
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Hdac6 protein
Chain IDs:A, B
Chain Length:364
Number of Molecules:2
Biological Source:Danio rerio
Primary Citation
Mechanism-Based Inhibition of Histone Deacetylase 6 by a Selenocyanate Is Subject to Redox Modulation.
J.Am.Chem.Soc. 147 6373 6377 (2025)
PMID: 39957581 DOI: 10.1021/jacs.5c00157

Abstact

Organoselenocyanates have attracted considerable attention in recent years due to their therapeutic potential and versatility in medicinal chemistry. Here, we report on the mechanism of inhibition by 5-phenylcarbamoylpentyl selenocyanide (SelSA-2), an analogue of the well-characterized histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA, a.k.a. Vorinostat). We show that histone deacetylases 6 and 10 promote selenocyanate hydrolysis to generate a selenolate anion, and we explore the redox chemistry of selenium as it modulates inhibitory activity through reversible formation of the diselenide. The 2.15 Å-resolution crystal structure of histone deacetylase 6 cocrystallized with SelSA-2 conclusively demonstrates that it is not the selenocyanate, but instead a zinc-bound selenolate anion, that is the active pharmacophore responsible for enzyme inhibition.

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