Structure of hdac like protein from bordetella alcaligenes bound the photoswitchable pyrazole inhibitor CEW395

Structure

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

Ligands and binding sites

• 9RB · (2E)-N-hydroxy-3-{4-[(E)-(1,3,5-trimethyl-1H-pyrazol-4-yl)diazenyl]phenyl}prop-2-enamide · ligand · 2 copies · 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 · 7 copies · chains A, B
• 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 403 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 5G1C · Structure of HDAC like protein from Bordetella Alcaligenes bound the photoswitchable… · 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 5G1C · PDBe 5G1C · UniProt Q70I53