SMTL ID : 6twf.1

Human CD73 (ecto 5'-nucleotidase) in complex with PSB12604 (an AOPCP derivative, compound 21 in publication) in the closed state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: D.60, N.92, H.93, H.195, H.218 Ligands: ZN.2, O05.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.60, A:H.195, A:H.218 ZN.2: 9 residues within 4Å: Chain A: D.11, H.13, D.60, H.93, H.195, H.218, R.370 Ligands: ZN.1, O05.4 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.5: 7 residues within 4Å: Chain B: D.60, N.92, H.93, H.195, H.218 Ligands: ZN.6, O05.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.60, B:H.195, B:H.218 ZN.6: 9 residues within 4Å: Chain B: D.11, H.13, D.60, H.93, H.195, H.218, R.370 Ligands: ZN.5, O05.8 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

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: N.188, G.210, D.212, G.273, N.274 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:N.188, A:D.212, A:D.212 CA.7: 5 residues within 4Å: Chain B: N.188, G.210, D.212, G.273, N.274 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:N.188, B:D.212, B:D.212

2 x O05: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-piperazin-4-ium-1-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid(Non-covalent)

O05.4: 23 residues within 4Å: Chain A: D.11, D.60, N.92, H.93, L.159, N.161, H.195, H.218, N.220, R.329, N.365, G.367, G.368, R.370, F.392, G.393, G.394, G.422, P.473, N.474, F.475 Ligands: ZN.1, ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.92, A:H.93, A:H.218, A:R.329, A:N.365, A:R.370, A:R.370, A:F.392 Water bridges: A:N.220, A:N.220 pi-Stacking: A:F.475, A:F.475 O05.8: 23 residues within 4Å: Chain B: D.11, D.60, N.92, H.93, L.159, N.161, H.195, H.218, N.220, R.329, N.365, G.367, G.368, R.370, F.392, G.393, G.394, G.422, P.473, N.474, F.475 Ligands: ZN.5, ZN.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.92, B:H.93, B:H.218, B:R.329, B:N.365, B:R.370, B:R.370, B:F.392 Water bridges: B:N.220, B:N.220 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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