› 5ngs

X-ray diffraction
1.85Å resolution

Crystal structure of human MTH1 in complex with inhibitor 6-[(2-phenylethyl)sulfanyl]-7H-purin-2-amine

Released:
DOI: 10.2210/pdb5ngs/pdb
PDB entry 5ngs coloured by chain, front view.
PDB entry 5ngs coloured by chain, side view.
PDB entry 5ngs coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space.
Rudling A, Gustafsson R, Almlöf I, Homan E, Scobie M, Warpman Berglund U, Helleday T, Stenmark P, Carlsson J
J Med Chem 60 8160-8169 (2017)
PMID: 28929756

Function and Biology Details

Reaction catalysed: 
2-hydroxy-dATP + H(2)O = 2-hydroxy-dAMP + diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153202 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Oxidized purine nucleoside triphosphate hydrolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 159 amino acids
Theoretical weight: 18.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P36639 (Residues: 1-156; Coverage: 100%)
Gene names: MTH1, NUDT1
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

3 bound ligands:
Ligand 8WW 2 x 8WW
Ligand SO4 9 x SO4
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 60.18Å b: 68.373Å c: 81.121Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.216 0.248
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Key Topics in Molecular Docking for Drug Design.
Torres et al. (2019)
4 more