Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 4)

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 13% strand (DSSP).

Ligands and binding sites

• ZLV · (3s,18s,20ar)-18-(6,6-dihydroxyoctyl)-1,5,6,7,8,18,19, 20A-octahydro-4H-14,17-epiminoazeto[1,2-G][1,7,10, 13]benzoxatriazacycloheptadecin-20(2H)-one · 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 · 13 copies · chains A, B, C
• PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–C · 608 Ų buried · 11 hydrogen bonds · protein-protein
• A–B · 547 Ų buried · 14 hydrogen bonds · protein-protein
• B–C · 358 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 7MOS · Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 4) · 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 7MOS · PDBe 7MOS · UniProt Q92769