Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with ddk-137

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 13% strand (DSSP).

Ligands and binding sites

• HB7 · N-[2-(benzylamino)-2-oxoethyl]-4-(dimethylamino)-N-{[4-(hydroxycarbamoyl)phenyl]methyl}benzamide · ligand · 4 copies · chains A, B, C, D
• K · Potassium ion · metal · 8 copies · chains A, B, C, D
• ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• B–C · 410 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 337 Ų buried · 5 hydrogen bonds · protein-protein
• C–D · 264 Ų buried · 2 hydrogen bonds · protein-protein
• A–B · 211 Ų buried · 2 hydrogen bonds · protein-protein
• A–D · 210 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 6DVN · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with… · the same entry in another collection · chain A 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 A7YT55
• Elsewhere: RCSB PDB 6DVN · PDBe 6DVN · UniProt A7YT55