SMTL ID : 6twa.1

Human CD73 (ecto 5'-nucleotidase) in complex with PSB12646 (an AOPCP derivative, compound 20 in publication) in the closed state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: D.11, H.13, D.60, H.195, H.218, R.370 Ligands: ZN.2, O02.3 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: 8 residues within 4Å: Chain A: D.11, D.60, N.92, H.93, H.195, H.218 Ligands: ZN.1, O02.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.60, A:H.195, A:H.218 ZN.5: 8 residues within 4Å: Chain B: D.11, H.13, D.60, H.195, H.218, R.370 Ligands: ZN.6, O02.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.11, B:H.13, B:D.60, H2O.6 ZN.6: 8 residues within 4Å: Chain B: D.11, D.60, N.92, H.93, H.195, H.218 Ligands: ZN.5, O02.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.60, B:H.195, B:H.218

2 x O02: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-diazanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid(Non-covalent)

O02.3: 22 residues within 4Å: Chain A: D.11, H.13, D.60, N.92, H.93, L.159, S.160, 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 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.92, A:L.159, A:H.218, 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 Water bridges: A:D.499, A:D.499 pi-Stacking: A:F.392, A:F.475, A:F.475 O02.7: 22 residues within 4Å: Chain B: D.11, H.13, D.60, N.92, H.93, L.159, S.160, 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.5, ZN.6 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.92, B:L.159, B:H.218, 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 Water bridges: B:D.499 pi-Stacking: B:F.392, B:F.475, B:F.475

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: K.183, N.188, K.189, I.190, D.212, G.273, N.274 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.188, A:D.212, A:G.273, H2O.2, H2O.5 CA.8: 7 residues within 4Å: Chain B: K.183, N.188, K.189, I.190, D.212, G.273, N.274 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.188, B:D.212, B:G.273, H2O.7, H2O.9

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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