› 5ngr

X-ray diffraction
2.2Å resolution

Crystal structure of human MTH1 in complex with fragment inhibitor 8-(methylsulfanyl)-7H-purin-6-amine

Released:
DOI: 10.2210/pdb5ngr/pdb
PDB entry 5ngr coloured by chain, front view.
PDB entry 5ngr coloured by chain, side view.
PDB entry 5ngr 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

2 bound ligands:
Ligand 8WT 2 x 8WT
Ligand SO4 6 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 59.902Å b: 67.842Å c: 82.131Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.21 0.254
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