Crystal structure of fragment 3-(3-benzyl-2-oxo-2H-[1,2,4]TRIAZINO[2, 3-C]QUINAZOLIN-6-YL)PROPANOIC acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 17% strand (DSSP).

Ligands and binding sites

• 9ZV · 3-(3-benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid · ligand · chains A
• ZN · Zinc ion · metal · 3 copies · chains A
• UNX · Unknown atom or ion · ion · 8 copies · chains A
• CL · Chloride ion · ion · chains A
• FMT · Formic acid · additive · 3 copies · chains A
• ACT · Acetate ion · additive · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Compared structures

• 5WBN · Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)p… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9UBN7 · AlphaFold monomer V2.0 prediction for histone deacetylase 6 (Q9UBN7) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

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• Every structure of UniProt Q9UBN7
• Elsewhere: RCSB PDB 5WBN · PDBe 5WBN · UniProt Q9UBN7