› 6fiu

X-ray diffraction
2.5Å resolution

Human cytosolic 5'-nucleotidase II soaked with 10mM 2-(6-([1,1'-Biphenyl]-3-carboxamido)-9H-purin-9-yl)acetic acid

Released:
DOI: 10.2210/pdb6fiu/pdb
PDB entry 6fiu coloured by chain, front view.
PDB entry 6fiu coloured by chain, side view.
PDB entry 6fiu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Lead optimization and biological evaluation of fragment-based cN-II inhibitors.
Guillon R, Rahimova R, Egron D, Rouanet S, Dumontet C, Aghajari N, Jordheim LP, Chaloin L, Peyrottes S
Eur J Med Chem 168 28-44 (2019)
PMID: 30798051

Function and Biology Details

Reactions catalysed: 
A nucleotide + a 2'-deoxynriboucleoside = a nucleoside + a 2'-deoxyribonucleoside 5'-phosphate
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate
IMP + H(2)O = inosine + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156074 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytosolic purine 5'-nucleotidase Chain: A
Molecule details ›
Chain: A
Length: 536 amino acids
Theoretical weight: 62.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P49902 (Residues: 1-536; Coverage: 96%)
Gene names: NT5B, NT5C2, NT5CP, PNT5
Sequence domains: 5' nucleotidase family

Ligands and Environments

3 bound ligands:
Ligand SO4 7 x SO4
Ligand GOL 6 x GOL
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: I222
Unit cell:
a: 90.69Å b: 128.18Å c: 129.64Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.176 0.238
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Concepts and Core Principles of Fragment-Based Drug Design.
Kirsch et al. (2019)
3 other articles