SMTL ID : 9hj4.1

Crystal structure of CD73 (ecto-5'-nucleotidase) complexed to 8-butylthioadenosine 5'monophosphate (compound 3 in publication) in the open enzyme state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: D.10, D.59, N.91, H.92, H.194, H.217 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:H.194, A:H.217, H2O.2 ZN.2: 8 residues within 4Å: Chain A: D.10, H.12, D.59, H.92, H.194, H.217, S.494 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:H.12, A:D.59, H2O.2, H2O.2 ZN.7: 7 residues within 4Å: Chain B: D.10, D.59, N.91, H.92, H.194, H.217 Ligands: ZN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.59, B:H.194, B:H.217, H2O.26 ZN.8: 8 residues within 4Å: Chain B: D.10, H.12, D.59, H.92, H.194, H.217, S.494 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:H.12, B:D.59, H2O.26, H2O.27

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: N.187, K.188, D.211, G.272, N.273 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.187, A:D.211, A:G.272, H2O.6, H2O.13 CA.9: 5 residues within 4Å: Chain B: N.187, K.188, D.211, G.272, N.273 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.187, B:D.211, B:G.272, H2O.30, H2O.38

2 x 01: [(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-8-butylsulfanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

01.4: 10 residues within 4Å: Chain A: R.328, N.364, G.366, G.367, R.369, F.391, G.421, P.472, F.474, D.480 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.364, A:G.366, A:G.366, A:R.369, A:G.421 Water bridges: A:N.473, A:N.473, A:F.474, A:D.480, A:D.480 Salt bridges: A:R.328, A:R.369 pi-Stacking: A:F.391, A:F.391, A:F.474, A:F.474 01.10: 10 residues within 4Å: Chain B: R.328, N.364, G.366, G.367, R.369, F.391, G.421, P.472, F.474, D.480 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.364, B:G.366, B:G.366, B:R.369, B:G.421 Water bridges: B:N.473, B:N.473, B:F.474, B:D.480, B:D.480 Salt bridges: B:R.328, B:R.369 pi-Stacking: B:F.391, B:F.391, B:F.474, B:F.474

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 7 residues within 4Å: Chain A: F.39, V.42, Q.43, R.46, A.81, L.82, R.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.46, A:R.83, A:R.83 1PE.11: 7 residues within 4Å: Chain B: F.39, V.42, Q.43, R.46, A.81, L.82, R.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.46, B:R.83, B:R.83

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 9 residues within 4Å: Chain A: S.370, P.371, I.372, N.376, T.381, E.383, N.384, A.387, V.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.384 Water bridges: A:N.376, A:T.381 PGE.12: 9 residues within 4Å: Chain B: S.370, P.371, I.372, N.376, T.381, E.383, N.384, A.387, V.388 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.384 Water bridges: B:N.376, B:T.381

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bi, C. et al., Synthesis, Characterization, Interactions, and Immunomodulatory Function of Ectonucleotidase CD39/CD73 Inhibitor 8-Butylthioadenosine 5'-Monophosphate. Acs Pharmacol Transl Sci (2025)

Release Date

2025-05-28

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'-nucleotidase

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