› 6dq5

X-ray diffraction
1.89Å resolution

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N43 i.e. 3-((6-(4-acryloyl-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid

Released:
DOI: 10.2210/pdb6dq5/pdb
PDB entry 6dq5 coloured by chain, front view.
PDB entry 6dq5 coloured by chain, side view.
PDB entry 6dq5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A.
Horton JR, Woodcock CB, Chen Q, Liu X, Zhang X, Shanks J, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Cyr M, Pohida K, Hu X, Shah P, Xu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Cheng X
J Med Chem 61 10588-10601 (2018)
PMID: 30392349

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(4) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-151436 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 5A Chain: A
Molecule details ›
Chain: A
Length: 330 amino acids
Theoretical weight: 37.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P29375 (Residues: 1-588; Coverage: 19%)
Gene names: JARID1A, KDM5A, RBBP2, RBP2
Sequence domains:
Structure domains: Cupin

Ligands and Environments

2 bound ligands:
Ligand H6G 1 x H6G
Ligand MN 1 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: C2
Unit cell:
a: 116.749Å b: 62.134Å c: 46.601Å
α: 90° β: 92.13° γ: 90°
R-values:
R R work R free
0.228 0.227 0.254
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

The emerging role of KDM5A in human cancer.
Yang et al. (2021)
5 other articles

1 mention without citation

Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A.
Horton et al. (2018)