› 3sx0

X-ray diffraction
2.28Å resolution

Crystal structure of Dot1l in complex with a brominated SAH analog

Released:
DOI: 10.2210/pdb3sx0/pdb
PDB entry 3sx0 coloured by chain, front view.
PDB entry 3sx0 coloured by chain, side view.
PDB entry 3sx0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Bromo-deaza-SAH: a potent and selective DOT1L inhibitor.
Yu W, Smil D, Li F, Tempel W, Fedorov O, Nguyen KT, Bolshan Y, Al-Awar R, Knapp S, Arrowsmith CH, Vedadi M, Brown PJ, Schapira M
Bioorg Med Chem 21 1787-1794 (2013)
PMID: 23433670

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(79) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(79)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186244 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone-lysine N-methyltransferase, H3 lysine-79 specific Chain: A
Molecule details ›
Chain: A
Length: 421 amino acids
Theoretical weight: 47.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q8TEK3 (Residues: 1-420; Coverage: 27%)
Gene names: DOT1L, KIAA1814, KMT4
Sequence domains: Histone methylation protein DOT1
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SX0 1 x SX0
Ligand SO4 1 x SO4
Ligand UNX 20 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P65
Unit cell:
a: 152.917Å b: 152.917Å c: 50.964Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.21 0.21 0.228
Expression system: Escherichia coli BL21

Quick links

Citations

25 review citations

Chromatin proteins and modifications as drug targets.
Helin et al. (2013)
24 more

3 mentions without citation

Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives.
Andreoli et al. (2013)
2 more