Structure of human HDAC2 in complex with an inhibitor lacking a zinc binding group (compound 19)

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).

Ligands and binding sites

• YEV · (2R)-2-(5-hydroxy-2-methyl-1H-indol-3-yl)-N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}propanamide · ligand · 3 copies · chains A, B, C
• CA · Calcium ion · metal · 6 copies · chains A, B, C
• ZN · Zinc ion · metal · 3 copies · chains A, B, C
• SO4 · Sulfate ion · ion · 12 copies · chains A, B, C
• PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C
• ACT · Acetate ion · additive · 3 copies · chains A, B, C

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–C · 644 Ų buried · 12 hydrogen bonds · protein-protein
• A–B · 566 Ų buried · 14 hydrogen bonds · protein-protein
• B–C · 362 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 7LTL · Structure of human HDAC2 in complex with an inhibitor lacking a zinc binding group… · the same entry in another collection · chain A against A, TM-score 1.00
• Q92769 · AlphaFold monomer V2.0 prediction for histone deacetylase 2 (Q92769) · 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 Q92769
• Elsewhere: RCSB PDB 7LTL · PDBe 7LTL · UniProt Q92769