Crystal structure of a low occupancy fragment candidate (N-(4-methyl- 1,3-thiazol-2-YL)PROPANAMIDE) bound adjacent to the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 18% strand (DSSP).

Ligands and binding sites

• 6T4 · ~{N}-(4-methyl-1,3-thiazol-2-yl)ethanamide · ligand · chains A
• ZN · Zinc ion · metal · 3 copies · chains A
• NA · Sodium ion · metal · chains A
• UNX · Unknown atom or ion · ion · 36 copies · chains A
• FMT · Formic acid · 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

• 5B8D · Crystal structure of a low occupancy fragment candidate… · 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 0.99

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 Q9UBN7
• Elsewhere: RCSB PDB 5B8D · PDBe 5B8D · UniProt Q9UBN7