› 6au2

X-ray diffraction
1.63Å resolution

Crystal structure of SETDB1 Tudor domain with aryl triazole fragments

Released:
DOI: 10.2210/pdb6au2/pdb
PDB entry 6au2 coloured by chain, front view.
PDB entry 6au2 coloured by chain, side view.
PDB entry 6au2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification and characterization of the first fragment hits for SETDB1 Tudor domain.
Mader P, Mendoza-Sanchez R, Iqbal A, Dong A, Dobrovetsky E, Corless VB, Liew SK, Houliston SR, De Freitas RF, Smil D, Sena CCD, Kennedy S, Diaz DB, Wu H, Dombrovski L, Allali-Hassani A, Min J, Schapira M, Vedadi M, Brown PJ, Santhakumar V, Yudin AK, Arrowsmith CH
Bioorg Med Chem 27 3866-3878 (2019)
PMID: 31327677

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) = S-adenosyl-L-homocysteine + a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(9)
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-172172 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone-lysine N-methyltransferase SETDB1 Chain: A
Molecule details ›
Chain: A
Length: 213 amino acids
Theoretical weight: 24.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15047 (Residues: 196-402; Coverage: 16%)
Gene names: ESET, KIAA0067, KMT1E, SETDB1
Sequence domains:
Structure domains: SH3 type barrels.

Ligands and Environments

5 bound ligands:
Ligand CGJ 1 x CGJ
Ligand BME 2 x BME
Ligand SO4 5 x SO4
Ligand EDO 6 x EDO
Ligand UNX 13 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 55.202Å b: 63.273Å c: 69.859Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.188 0.208
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Chemical tools targeting readers of lysine methylation.
Ortiz et al. (2023)
2 more

2 mentions without citation

Improvement of Cell Permeability of Human Neuronal Nitric Oxide Synthase Inhibitors Using Potent and Selective 2-Aminopyridine-Based Scaffolds with a Fluorobenzene Linker.
Do et al. (2017)
1 more