Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with ddk-122

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).

Ligands and binding sites

• HBJ · 4-(dimethylamino)-N-{[4-(hydroxycarbamoyl) phenyl]methyl}-N-{2-[(4-methylphenyl)amino]-2-oxoethyl}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 · 13 copies · chains A, B, C, D
• BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains C

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–B · 641 Ų buried · 4 hydrogen bonds · protein-protein
• B–C · 368 Ų buried · 8 hydrogen bonds · protein-protein
• A–C · 344 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 278 Ų buried · 6 hydrogen bonds · protein-protein
• A–D · 167 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 6DVM · 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 6DVM · PDBe 6DVM · UniProt A7YT55