Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with ITF3756

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).

Ligands and binding sites

• UZW · ~{N}-oxidanyl-4-[(5-thiophen-2-yl-1,2,3,4-tetrazol-1-yl)methyl]benzamide · ligand · 2 copies · chains A, B
• K · Potassium ion · metal · 4 copies · chains A, B
• ZN · Zinc ion · metal · 2 copies · chains A, B
• IOD · Iodide ion · ion · 4 copies · chains A, B
• GOL · Glycerol · additive · 5 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
• B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 645 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 7O2P · 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 F8W4B7
• Elsewhere: RCSB PDB 7O2P · PDBe 7O2P · UniProt F8W4B7