Crystal structure of human HDAC2 in complex with (R)-6-[3,4-dioxo-2- (4-trifluoromethoxy-phenylamino)-cyclobut-1-enylamino]-heptanoic acid hydroxyamide

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 13% strand (DSSP).

Ligands and binding sites

• EL8 · (6~{R})-6-[[3,4-bis(oxidanylidene)-2-[[4-(trifluoromethyloxy)phenyl]amino]cyclobuten-1-yl]amino]-~{N}-oxidanyl-heptanamide · ligand · 3 copies · chains A, B, C
• ZN · Zinc ion · metal · 3 copies · chains A, B, C
• CA · Calcium ion · metal · 3 copies · chains A, B, C
• NA · Sodium ion · metal · 3 copies · chains A, B, C
• SO4 · Sulfate ion · ion · 2 copies · chains B, A, C
• 1PE · Pentaethylene glycol · additive · chains B, C
• PG4 · Tetraethylene glycol · 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, 3 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 652 Ų buried · 7 hydrogen bonds · protein-protein
• A–B · 556 Ų buried · 13 hydrogen bonds · protein-protein
• B–C · 398 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 6G3O · Crystal structure of human HDAC2 in complex with… · 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 6G3O · PDBe 6G3O · UniProt Q92769