A degradation product of pd 404182 (P2742) bound to histone deacetylase-like amidohydrolase

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 14% strand (DSSP).

Ligands and binding sites

• F0Z · 2-(1,4,5,6-tetrahydropyrimidin-2-yl)benzenethiol · ligand · 4 copies · chains A, B
• MLT · D-malate · ligand · chains A, B
• K · Potassium ion · metal · 4 copies · chains A, B
• ZN · Zinc ion · metal · 2 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
• 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
• ACT · Acetate ion · additive · 2 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, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 386 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 6GJK · A degradation product of PD 404182 (P2742) bound to Histone Deacetylase-like… · the same entry in another collection · chain A against A, TM-score 1.00
• Q70I53 · AlphaFold monomer V2.0 prediction for histone deacetylase-like amidohydrolase (Q70I53) · a predicted model of the same protein · chain A 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 Q70I53
• Elsewhere: RCSB PDB 6GJK · PDBe 6GJK · UniProt Q70I53