› 5vse

X-ray diffraction
1.6Å resolution

Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 17: N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine

Released:
DOI: 10.2210/pdb5vse/pdb
PDB entry 5vse coloured by chain, front view.
PDB entry 5vse coloured by chain, side view.
PDB entry 5vse coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.
Xiong Y, Li F, Babault N, Wu H, Dong A, Zeng H, Chen X, Arrowsmith CH, Brown PJ, Liu J, Vedadi M, Jin J
Bioorg Med Chem 25 4414-4423 (2017)
PMID: 28662962

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(9) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(9)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-188602 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone-lysine N-methyltransferase EHMT2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 275 amino acids
Theoretical weight: 31.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96KQ7 (Residues: 917-1190; Coverage: 23%)
Gene names: BAT8, C6orf30, EHMT2, G9A, KMT1C, NG36
Sequence domains:
Structure domains: SET domain

Ligands and Environments

3 bound ligands:
Ligand ZN 8 x ZN
Ligand SAM 2 x SAM
Ligand 9HG 2 x 9HG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 56.491Å b: 78.691Å c: 72.61Å
α: 90° β: 91.35° γ: 90°
R-values:
R R work R free
0.169 0.168 0.191
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Structure, Activity, and Function of the Protein Lysine Methyltransferase G9a.
Poulard et al. (2021)
6 other articles

3 mentions without citation

Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.
Xiong et al. (2017)
2 more