Structure of HDAC4 catalytic domain (a double cysteine-to- alanine mutant) bound to a trifluoromethylketone inhbitor

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 13% strand (DSSP).

Ligands and binding sites

• TFG · 2,2,2-trifluoro-1-{5-[(3-phenyl-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl)carbonyl]thiophen-2-yl}ethane-1,1-diol · ligand · 2 copies · chains A, B
• K · Potassium ion · metal · 4 copies · chains A, B
• ZN · Zinc ion · metal · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 3 copies · chains A, 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 · 898 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 2VQQ · Structure of HDAC4 catalytic domain (a double cysteine-to-alanine mutant) bound to a… · the same entry in another collection · chain B against B, TM-score 1.00
• P56524 · AlphaFold monomer V2.0 prediction for histone deacetylase 4 (P56524) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P56524
• Elsewhere: RCSB PDB 2VQQ · PDBe 2VQQ · UniProt P56524