SMTL ID : 6tvg.1

Human CD73 (ecto 5'-nucleotidase) in complex with AMPCP in the open state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: D.33, D.82, N.114, H.115, H.217, H.240 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.82, A:H.217, A:H.240, H2O.9 ZN.2: 8 residues within 4Å: Chain A: D.33, H.35, D.82, H.115, H.217, H.240, S.517 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.33, A:H.35, A:D.82, H2O.9, H2O.9 ZN.6: 7 residues within 4Å: Chain B: D.33, D.82, N.114, H.115, H.217, H.240 Ligands: ZN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.82, B:H.217, B:H.240, H2O.30 ZN.7: 8 residues within 4Å: Chain B: D.33, H.35, D.82, H.115, H.217, H.240, S.517 Ligands: ZN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.33, B:H.35, B:D.82, H2O.30, H2O.30

2 x AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

AP2.3: 10 residues within 4Å: Chain A: R.351, N.387, G.389, G.390, R.392, F.414, G.444, E.445, F.497, D.503 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.351, A:R.351, A:N.387, A:G.389, A:R.392, A:R.392, A:G.444, A:D.503 Water bridges: A:S.442, A:D.503 pi-Stacking: A:F.414, A:F.414, A:F.497, A:F.497 AP2.8: 10 residues within 4Å: Chain B: R.351, N.387, G.389, G.390, R.392, F.414, G.444, E.445, F.497, D.503 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.351, B:R.351, B:N.387, B:G.389, B:R.392, B:R.392, B:G.444, B:D.503 Water bridges: B:S.442, B:D.503 pi-Stacking: B:F.414, B:F.414, B:F.497, B:F.497

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: G.219, F.220, E.221, S.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.220, A:E.221 Water bridges: A:G.219, A:M.222 NA.9: 4 residues within 4Å: Chain B: G.219, F.220, E.221, S.241 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.220, B:E.221 Water bridges: B:M.222

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: K.205, N.210, K.211, D.234, G.295, N.296 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.210, A:D.234, A:G.295, H2O.6, H2O.9 CA.10: 6 residues within 4Å: Chain B: K.205, N.210, K.211, D.234, G.295, N.296 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.210, B:D.234, B:G.295, H2O.27, H2O.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhattarai, S. et al., 2-Substituted alpha , beta-Methylene-ADP Derivatives: Potent Competitive Ecto-5'-nucleotidase (CD73) Inhibitors with Variable Binding Modes. J.Med.Chem. (2020)

Release Date

2020-02-26

Peptides

5'-nucleotidase, ecto (CD73), isoform CRA_a: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'-nucleotidase, ecto (CD73), isoform CRA_a

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