› 4ynd

X-ray diffraction
2.79Å resolution

The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2

Released:
DOI: 10.2210/pdb4ynd/pdb
PDB entry 4ynd coloured by chain, front view.
PDB entry 4ynd coloured by chain, side view.
PDB entry 4ynd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2.
Sweis RF, Wang Z, Algire M, Arrowsmith CH, Brown PJ, Chiang GG, Guo J, Jakob CG, Kennedy S, Li F, Maag D, Shaw B, Soni NB, Vedadi M, Pappano WN
ACS Med Chem Lett 6 695-700 (2015)
PMID: 26101576

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192559 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-lysine methyltransferase SMYD2 Chain: A
Molecule details ›
Chain: A
Length: 461 amino acids
Theoretical weight: 53.21 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9NRG4 (Residues: 1-433; Coverage: 100%)
Gene names: KMT3C, SMYD2
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 3 x ZN
Ligand 4GQ 1 x 4GQ
Ligand SAM 1 x SAM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 52.796Å b: 71.301Å c: 118.93Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.253
Expression system: Spodoptera frugiperda

Quick links

Citations

14 review citations

Epigenetics in cancer: Fundamentals and Beyond.
Biswas et al. (2017)
13 more

4 mentions without citation

Inhibitors of Protein Methyltransferases and Demethylases.
Kaniskan et al. (2018)
3 more