SMTL ID : 7qga.1

Human CD73 (ecto 5'-nucleotidase) in complex with MRS4598 (a 3-methyl-CMPCP derivative, compound 16 in paper) in the open state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.10, D.59, N.91, H.194, H.217 Ligands: ZN.2 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.2: 4 residues within 4Å: Chain A: D.10, H.12, D.59 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:H.12, A:D.59, H2O.2, H2O.4 ZN.7: 6 residues within 4Å: Chain B: D.10, D.59, N.91, H.194, H.217 Ligands: ZN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.59, B:H.194, B:H.217, H2O.31 ZN.8: 4 residues within 4Å: Chain B: D.10, H.12, D.59 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:H.12, B:D.59, H2O.28, H2O.31

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.19 CA.9: 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.29, H2O.45

2 x BOI: [[(2~{R},3~{S},4~{R},5~{R})-5-[(4~{E})-4-[(4-chlorophenyl)methoxyimino]-3-methyl-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid(Non-covalent)

BOI.4: 12 residues within 4Å: Chain A: D.21, S.23, R.328, N.364, G.366, G.367, R.369, F.391, G.421, E.422, F.474, D.480 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.328, A:R.328, A:N.364, A:R.369, A:R.369, A:G.421, A:D.480, A:D.480 Water bridges: A:D.480 pi-Stacking: A:F.391, A:F.391, A:F.474 BOI.10: 12 residues within 4Å: Chain B: D.21, S.23, R.328, N.364, G.366, G.367, R.369, F.391, G.421, E.422, F.474, D.480 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.328, B:R.328, B:N.364, B:R.369, B:R.369, B:G.421, B:D.480, B:D.480 Water bridges: B:D.480 pi-Stacking: B:F.391, B:F.391, B:F.474

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 7 residues within 4Å: Chain A: F.39, V.42, Q.43, R.46, A.81, L.82, R.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.46, A:R.83 PG4.6: 8 residues within 4Å: Chain A: S.370, P.371, I.372, N.376, T.379, E.383, N.384, A.387 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.371, A:N.376, A:N.384 PG4.11: 7 residues within 4Å: Chain B: F.39, V.42, Q.43, R.46, A.81, L.82, R.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.46, B:R.83 PG4.12: 8 residues within 4Å: Chain B: S.370, P.371, I.372, N.376, T.379, E.383, N.384, A.387 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.371, B:N.376, B:N.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scortichini, M. et al., Structure-Activity Relationship of 3-Methylcytidine-5'-alpha , beta-methylenediphosphates as CD73 Inhibitors. J.Med.Chem. (2022)

Release Date

2022-02-16

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'-nucleotidase

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