SMTL ID : 9hjg.1 (1 other biounit)

Crystal structure of human CD73 (ecto-5'-nucleotidase) in complex with an N6-disubstituted acyclic ADP analog (compound 26 in publication) in the closed state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 9 residues within 4Å: Chain A: D.10, H.12, D.59, H.92, H.194, H.217, R.369 Ligands: ZN.2, 01.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.10, A:H.12, A:D.59 ZN.2: 7 residues within 4Å: Chain A: D.59, N.91, H.92, H.194, H.217 Ligands: ZN.1, 01.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.59, A:H.194, A:H.217 ZN.5: 10 residues within 4Å: Chain B: D.10, H.12, D.59, H.92, H.194, H.217, N.219, R.369 Ligands: ZN.6, 01.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.10, B:H.12, B:D.59 ZN.6: 8 residues within 4Å: Chain B: D.10, D.59, N.91, H.92, H.194, H.217 Ligands: ZN.5, 01.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.59, B:H.194, B:H.217

2 x 01: [5-[2-chloranyl-6-[methyl-(phenylmethyl)amino]purin-9-yl]pentoxy-oxidanyl-phosphoryl]methylphosphonic acid

01.3: 26 residues within 4Å: Chain A: D.10, H.12, D.59, Q.62, N.91, H.92, D.95, L.158, S.159, N.160, H.217, R.328, N.364, G.366, G.367, R.369, F.391, G.392, G.393, G.421, P.472, N.473, F.474, N.477 Ligands: ZN.1, ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:N.160, A:F.391 Hydrogen bonds: A:N.91, A:H.92, A:R.328, A:R.328, A:R.369, A:R.369 pi-Stacking: A:F.391, A:F.391, A:F.474 01.7: 22 residues within 4Å: Chain B: D.10, H.12, D.59, N.91, H.92, L.158, H.217, R.328, N.364, G.366, G.367, R.369, F.391, G.393, G.421, P.472, N.473, F.474, N.477, D.480 Ligands: ZN.5, ZN.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.391 Hydrogen bonds: B:N.91, B:H.92, B:R.328, B:R.328, B:R.369, B:R.369 pi-Stacking: B:F.391, B:F.391

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: F.39, V.42, Q.43, R.46, R.83 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Federico, S. et al., Acyclic purine and pyrimidine nucleotide analogs as ecto-5'-nucleotidase (CD73) inhibitors. Eur.J.Med.Chem. (2025)

Release Date

2025-05-28

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'-nucleotidase

Related Entries With Identical Sequence