› 4wuy

X-ray diffraction
1.63Å resolution

Crystal Structure of Protein Lysine Methyltransferase SMYD2 in complex with LLY-507, a Cell-Active, Potent and Selective Inhibitor

Released:
DOI: 10.2210/pdb4wuy/pdb
PDB entry 4wuy coloured by chain, front view.
PDB entry 4wuy coloured by chain, side view.
PDB entry 4wuy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
LLY-507, a Cell-active, Potent, and Selective Inhibitor of Protein-lysine Methyltransferase SMYD2.
Nguyen H, Allali-Hassani A, Antonysamy S, Chang S, Chen LH, Curtis C, Emtage S, Fan L, Gheyi T, Li F, Liu S, Martin JR, Mendel D, Olsen JB, Pelletier L, Shatseva T, Wu S, Zhang FF, Arrowsmith CH, Brown PJ, Campbell RM, Garcia BA, Barsyte-Lovejoy D, Mader M, Vedadi M
J Biol Chem 290 13641-53 (2015)
PMID: 25825497

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: 441 amino acids
Theoretical weight: 50.78 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

4 bound ligands:
Ligand 3UJ 1 x 3UJ
Ligand SAH 1 x SAH
Ligand GOL 3 x GOL
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21212
Unit cell:
a: 89.025Å b: 99.92Å c: 60.297Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.151 0.2
Expression system: Spodoptera frugiperda

Quick links

Citations

23 review citations

Marked for death: targeting epigenetic changes in cancer.
Pfister et al. (2017)
22 more

5 mentions without citation

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