Linked KDM5A jmj domain bound to the inhibitor N19 [2-(5-((4-chloro-2- METHYLBENZYL)OXY)-1H-pyrazol-1-YL)ISONICOTINIC acid]

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).

Ligands and binding sites

• 6EP · 2-{5-[(4-chloro-2-methylphenyl)methoxy]-1H-pyrazol-1-yl}pyridine-4-carboxylic acid · ligand · chains A
• AKG · 2-oxoglutaric acid · ligand · chains A
• MN · Manganese (II) ion · metal · chains A
• EDO · 1,2-ethanediol · additive · 2 copies · chains A
• GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

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

Compared structures

• 5IW0 · Linked KDM5A Jmj Domain Bound to the Inhibitor N19… · 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 5IW0 · PDBe 5IW0 · UniProt P29375