› 4p5e

X-ray diffraction
1.35Å resolution

CRYSTAL STRUCTURE OF HUMAN DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIBOSIDE-MONOPHOSPHATE

Released:
DOI: 10.2210/pdb4p5e/pdb
PDB entry 4p5e coloured by chain, front view.
PDB entry 4p5e coloured by chain, side view.
PDB entry 4p5e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: synthesis, structural studies and cytotoxic activities.
Amiable C, Paoletti J, Haouz A, Padilla A, Labesse G, Kaminski PA, Pochet S
Eur J Med Chem 85 418-37 (2014)
PMID: 25108359

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129016 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5-hydroxymethyl-dUMP N-hydrolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 152 amino acids
Theoretical weight: 17.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43598 (Residues: 20-162; Coverage: 82%)
Gene names: C6orf108, DNPH1, RCL
Sequence domains: Nucleoside 2-deoxyribosyltransferase
Structure domains: Rossmann fold

Ligands and Environments

2 bound ligands:
Ligand N6P 2 x N6P
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P21
Unit cell:
a: 48.974Å b: 52.284Å c: 54.454Å
α: 90° β: 104.77° γ: 90°
R-values:
R R work R free
0.156 0.155 0.18
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides.
Shaughnessy KH. (2015)
1 more

1 mention without citation

Human 2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1: Mechanism of 2'-Deoxyuridine 5'-Monophosphate Hydrolysis.
Devi et al. (2023)