SMTL ID : 6z9b.1

Human Ecto-5'-nucleotidase (CD73) in complex with AOPCP derivative A830 (compound 16 in publication) in the closed form (crystal form III)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.11, H.13, D.60 Ligands: ZN.2, QCQ.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.2: 7 residues within 4Å: Chain A: D.11, D.60, N.92, H.195, H.218 Ligands: ZN.1, QCQ.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.60, A:H.195, A:H.218 ZN.5: 5 residues within 4Å: Chain B: D.11, H.13, D.60 Ligands: ZN.6, QCQ.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.12 ZN.6: 7 residues within 4Å: Chain B: D.11, D.60, N.92, H.195, H.218 Ligands: ZN.5, QCQ.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.60, B:H.195, B:H.218

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: N.188, D.212, G.273 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.188, A:D.212, A:G.273, H2O.4, H2O.9 CA.7: 3 residues within 4Å: Chain B: N.188, D.212, G.273 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.188, B:D.212, B:G.273, H2O.15, H2O.20

2 x QCQ: [[(2~{R},3~{R},4~{S},5~{R})-5-[2-chloranyl-6-[(phenylmethyl)amino]purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid(Non-covalent)

QCQ.4: 24 residues within 4Å: Chain A: D.11, H.13, D.60, N.92, H.93, D.96, L.159, S.160, N.161, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:D.96, A:N.161 Hydrogen bonds: A:N.220, A:R.329, A:R.329, A:N.365, A:G.367, A:R.370, A:R.370, A:D.481 Water bridges: A:F.392 pi-Stacking: A:F.392, A:F.475, A:F.475 QCQ.8: 24 residues within 4Å: Chain B: D.11, H.13, D.60, N.92, H.93, D.96, L.159, S.160, N.161, 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 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:D.96, B:N.161 Hydrogen bonds: B:N.92, B:N.220, B:R.329, B:R.329, B:N.365, B:G.367, B:R.370, B:R.370, B:D.481 Water bridges: B:F.392 pi-Stacking: B:F.392, B:F.475, B:F.475

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lawson, K.V. et al., Discovery of AB680: A Potent and Selective Inhibitor of CD73. J.Med.Chem. (2020)

Release Date

2020-07-22

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'-nucleotidase

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