Crystal structure of HDAC8-inhibitor complex

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 13% strand (DSSP).

Ligands and binding sites

• V5X · (2R)-N~8~-hydroxy-2-{[(5-methoxy-2-methyl-1H-indol-3-yl)acetyl]amino}-N~1~-[2-(2-phenyl-1H-indol-3-yl)ethyl]octanediamide · ligand · 2 copies · chains A, B
• K · Potassium ion · metal · 4 copies · chains A, B
• ZN · Zinc ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 636 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 2V5X · Crystal structure of HDAC8-inhibitor complex · the same entry in another collection · chain A against A, TM-score 1.00
• Q9BY41 · AlphaFold monomer V2.0 prediction for histone deacetylase 8 (Q9BY41) · a predicted model of the same protein · chain B against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9BY41
• Elsewhere: RCSB PDB 2V5X · PDBe 2V5X · UniProt Q9BY41