› 3u78

X-ray diffraction
2.69Å resolution

E67-2 selectively inhibits KIAA1718, a human histone H3 lysine 9 Jumonji demethylase

Released:
DOI: 10.2210/pdb3u78/pdb
PDB entry 3u78 coloured by chain, front view.
PDB entry 3u78 coloured by chain, side view.
PDB entry 3u78 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
An analog of BIX-01294 selectively inhibits a family of histone H3 lysine 9 Jumonji demethylases.
Upadhyay AK, Rotili D, Han JW, Hu R, Chang Y, Labella D, Zhang X, Yoon YS, Mai A, Cheng X
J Mol Biol 416 319-27 (2012)
PMID: 22227394

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) + 2-oxoglutarate + O(2) = a [histone H3]-N(6)-methyl-L-lysine(9) + 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-180579 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase 7A Chain: A
Molecule details ›
Chain: A
Length: 397 amino acids
Theoretical weight: 46.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6ZMT4 (Residues: 92-488; Coverage: 42%)
Gene names: JHDM1D, KDM7, KDM7A, KIAA1718
Sequence domains:
Structure domains:

Ligands and Environments

6 bound ligands:
Ligand AKG 1 x AKG
Ligand NI 1 x NI
Ligand CL 1 x CL
Ligand SO4 1 x SO4
Ligand EDO 2 x EDO
Ligand E67 1 x E67
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P6122
Unit cell:
a: 77.429Å b: 77.429Å c: 289.685Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.205 0.198 0.264
Expression system: Escherichia coli

Quick links

Citations

8 review citations

The cancer driver genes IDH1/2, JARID1C/ KDM5C, and UTX/ KDM6A: crosstalk between histone demethylation and hypoxic reprogramming in cancer metabolism.
Chang et al. (2019)
7 more

5 mentions without citation

Targeting histone lysine demethylases - progress, challenges, and the future.
Thinnes et al. (2014)
4 more