SMTL ID : 6xug.1

Human Ecto-5'-nucleotidase (CD73) in complex with A2410 (compound 53 in publication) in the closed form in crystal form IV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.10, H.12, D.59 Ligands: ZN.2, PO4.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:H.12, A:D.59, H2O.4 ZN.2: 7 residues within 4Å: Chain A: D.10, D.59, N.91, H.194, H.217 Ligands: ZN.1, PO4.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:H.194, A:H.217, H2O.4 ZN.6: 5 residues within 4Å: Chain B: D.10, H.12, D.59 Ligands: ZN.7, PO4.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:H.12, B:D.59, H2O.17, H2O.19 ZN.7: 7 residues within 4Å: Chain B: D.10, D.59, N.91, H.194, H.217 Ligands: ZN.6, PO4.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.59, B:H.194, B:H.217, H2O.19

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: N.187, D.211, G.272 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.187, A:D.211, A:G.272, H2O.2, H2O.6 CA.8: 3 residues within 4Å: Chain B: N.187, D.211, G.272 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.187, B:D.211, B:G.272, H2O.18, H2O.25

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 11 residues within 4Å: Chain A: D.10, H.12, D.59, N.91, H.92, H.217, R.328, R.369 Ligands: ZN.1, ZN.2, O1Q.5 8 PLIP interactions: 8 interactions with chain A Water bridges: A:H.217, A:N.219, A:R.328 Salt bridges: A:H.12, A:H.92, A:H.217, A:R.328, A:R.369 PO4.9: 10 residues within 4Å: Chain B: H.12, D.59, N.91, H.92, H.217, R.328, R.369 Ligands: ZN.6, ZN.7, O1Q.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.91 Water bridges: B:N.219, B:R.328, B:R.328 Salt bridges: B:H.12, B:H.92, B:H.217, B:R.328, B:R.369

2 x O1Q: 4-chloranyl-1-(1~{H}-indazol-6-yl)-6-[2-(3-methylphenyl)pyrazol-3-yl]benzotriazole(Non-covalent)

O1Q.5: 21 residues within 4Å: Chain A: N.91, H.92, D.95, P.156, F.157, L.158, S.159, N.160, H.217, N.364, G.366, G.367, F.391, G.421, N.473, F.474, N.477, G.478, G.479, D.480 Ligands: PO4.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.391, A:F.391, A:F.391, A:F.474, A:F.474, A:F.474 Hydrogen bonds: A:N.364, A:G.421, A:D.480 Water bridges: A:R.328, A:R.328 pi-Stacking: A:F.391, A:F.391, A:F.474, A:F.474 O1Q.10: 20 residues within 4Å: Chain B: N.91, H.92, D.95, P.156, F.157, L.158, S.159, N.160, H.217, N.364, G.366, G.367, F.391, G.421, N.473, F.474, N.477, G.479, D.480 Ligands: PO4.9 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.158, B:F.391, B:F.391, B:F.391, B:F.474, B:F.474 Hydrogen bonds: B:N.364, B:G.421, B:D.480 Water bridges: B:N.160 pi-Stacking: B:F.391, B:F.391, B:F.474, B:F.474, B:F.474

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beatty, J.W. et al., Discovery of Potent and Selective Non-Nucleotide Small Molecule Inhibitors of CD73. J.Med.Chem. (2020)

Release Date

2020-04-22

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'-nucleotidase

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