› 6xue

X-ray diffraction
1.94Å resolution

Human Ecto-5'-nucleotidase (CD73) in complex with A2396 (compound 74 in publication) in the closed form in crystal form IV

Released:
DOI: 10.2210/pdb6xue/pdb
PDB entry 6xue coloured by chain, front view.
PDB entry 6xue coloured by chain, side view.
PDB entry 6xue coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of Potent and Selective Non-Nucleotide Small Molecule Inhibitors of CD73.
Beatty JW, Lindsey EA, Thomas-Tran R, Debien L, Mandal D, Jeffrey JL, Tran AT, Fournier J, Jacob SD, Yan X, Drew SL, Ginn E, Chen A, Pham AT, Zhao S, Jin L, Young SW, Walker NP, Leleti MR, Moschütz S, Sträter N, Powers JP, Lawson KV
J Med Chem 63 3935-3955 (2020)
PMID: 32212732

Function and Biology Details

Reactions catalysed: 
Thymidylate + H(2)O = thymidine + phosphate
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
CMP + H(2)O = cytidine + phosphate
IMP + H(2)O = inosine + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149316 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5'-nucleotidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 538 amino acids
Theoretical weight: 59.44 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P21589 (Residues: 27-549; Coverage: 95%)
Gene names: NT5, NT5E, NTE
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand ZN 4 x ZN
Ligand CA 2 x CA
Ligand PO4 2 x PO4
Ligand O1H 2 x O1H
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21212
Unit cell:
a: 94.019Å b: 232.175Å c: 54.83Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.19 0.219
Expression system: Homo sapiens

Quick links

Citations

3 review citations

The elegant complexity of mammalian ecto-5'-nucleotidase (CD73).
Alcedo et al. (2021)
2 more

1 mention without citation

Generation of Non-Nucleotide CD73 Inhibitors Using a Molecular Docking and 3D-QSAR Approach.
Bhujbal et al. (2021)