SMTL ID : 6tvx.1

Human CD73 (ecto 5'-nucleotidase) in complex with PSB12676 (an AOPCP derivative, compound 9 in paper) in the closed state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: D.11, H.13, D.60, H.195, R.370 Ligands: ZN.2, NYW.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.11, A:H.13, A:D.60, H2O.1 ZN.2: 6 residues within 4Å: Chain A: D.60, N.92, H.195, H.218 Ligands: ZN.1, NYW.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.60, A:H.195, A:H.218 ZN.4: 7 residues within 4Å: Chain B: D.11, H.13, D.60, H.195, R.370 Ligands: ZN.5, NYW.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.11, B:H.13, B:D.60, H2O.1 ZN.5: 6 residues within 4Å: Chain B: D.60, N.92, H.195, H.218 Ligands: ZN.4, NYW.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.60, B:H.195, B:H.218

2 x NYW: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid(Non-covalent)

NYW.3: 21 residues within 4Å: Chain A: H.13, D.60, N.92, H.93, L.159, H.195, H.218, N.220, R.329, N.365, G.367, G.368, R.370, F.392, G.422, E.423, P.473, F.475, D.481 Ligands: ZN.1, ZN.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.92, A:N.220, A:N.220, A:R.329, A:R.329, A:N.365, A:N.365, A:G.367, A:R.370, A:R.370, A:G.422, A:D.481, A:D.481 pi-Stacking: A:F.475, A:F.475 NYW.6: 21 residues within 4Å: Chain B: H.13, D.60, N.92, H.93, L.159, H.195, H.218, N.220, R.329, N.365, G.367, G.368, R.370, F.392, G.422, E.423, P.473, F.475, D.481 Ligands: ZN.4, ZN.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:N.92, B:N.220, B:N.220, B:R.329, B:R.329, B:N.365, B:N.365, B:G.367, B:R.370, B:R.370, B:G.422, B:D.481, B:D.481 pi-Stacking: B:F.475, B:F.475

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

2020-02-19

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'-nucleotidase

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