Linked KDM5A jmj domain bound to the inhibitor N53 I.E. 2-(5-([1,1'- biphenyl]-3-yl)-4-(1-(2-(piperidin-1-YL)ETHOXY)ETHYL)-1H-pyrazol-1- YL)ISONICOTINIC acid

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).

Ligands and binding sites

• H67 · 2-[5-([1,1'-biphenyl]-3-yl)-4-{(1S)-1-[2-(piperidin-1-yl)ethoxy]ethyl}-1H-pyrazol-1-yl]pyridine-4-carboxylic acid · ligand · chains A
• MN · Manganese (II) ion · metal · chains A
• GOL · Glycerol · additive · 2 copies · chains A
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A

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

Pockets

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

Compared structures

• 6DQD · LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N53 i.e.… · the same entry in another collection · chain A against A, TM-score 1.00
• P29375 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5A (P29375) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P29375
• Elsewhere: RCSB PDB 6DQD · PDBe 6DQD · UniProt P29375