Linked KDM5A jmj domain bound to the inhibitor 2-((2-chlorophenyl) (PROPOXY)METHYL)-1H-PYRROLO[3,2-B]PYRIDINE (compound N9)

Structure

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

Ligands and binding sites

• DKP · 2-[(R)-(2-chlorophenyl)(propoxy)methyl]-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid · ligand · chains A
• MN · Manganese (II) ion · metal · chains A
• SO4 · Sulfate ion · ion · chains A
• EDO · 1,2-ethanediol · additive · 4 copies · chains A
• GOL · Glycerol · additive · 2 copies · chains A
• DMS · Dimethyl sulfoxide · additive · 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

• 6BGU · LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR… · 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 6BGU · PDBe 6BGU · UniProt P29375