› 6bgz

X-ray diffraction
1.69Å resolution

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(1-methyl-1H-imidazol-2-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N47)

Released:
DOI: 10.2210/pdb6bgz/pdb
PDB entry 6bgz coloured by chain, front view.
PDB entry 6bgz coloured by chain, side view.
PDB entry 6bgz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.
Horton JR, Liu X, Wu L, Zhang K, Shanks J, Zhang X, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Pohida K, Fang Y, Hu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Yan Q, Cheng X
J Med Chem 61 3193-3208 (2018)
PMID: 29537847

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

Assembly composition:
monomeric (preferred)
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

3 bound ligands:
Ligand DNV 1 x DNV
Ligand MN 1 x MN
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 116.963Å b: 62.198Å c: 46.779Å
α: 90° β: 92.26° γ: 90°
R-values:
R R work R free
0.187 0.186 0.197
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 citation in other articles

KDM5 histone demethylases repress immune response via suppression of STING.
Wu et al. (2018)
3 more

1 mention without citation

Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.
Horton et al. (2018)