Crystal structure of a human HDAC8 L6 loop mutant complexed with Quisinostat

Structure

x-ray diffraction · resolution 2.096 · 1 distinct chain · 41% helix, 13% strand (DSSP).

Ligands and binding sites

• GOK · 2-[4-[[(1-methylindol-3-yl) methylamino]methyl]piperidin-1-yl]-~{N}-oxidanyl-pyrimidine-5-carboxamide · 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

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 278 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 6HSK · Crystal structure of a human HDAC8 L6 loop mutant complexed with quisinostat · 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 6HSK · PDBe 6HSK · UniProt Q9BY41