SMTL ID : 7qgl.1

Human CD73 (ecto 5'-nucleotidase) in complex with MRS4602 (a 3-methyl-CMPCP derivative, compound 21 in paper) in the open state

Coordinates

PDB Format Compare

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.3 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.1, H2O.3 ZN.9: 6 residues within 4Å: Chain B: D.10, D.59, N.91, H.194, H.217 Ligands: ZN.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.59, B:H.194, B:H.217, H2O.28 ZN.10: 4 residues within 4Å: Chain B: D.10, H.12, D.59 Ligands: ZN.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.26, H2O.28

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: K.182, N.187, D.211, G.272 Ligands: 1PE.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.187, A:D.211, A:D.211, A:G.272, H2O.3 CA.11: 5 residues within 4Å: Chain B: K.182, N.187, D.211, G.272 Ligands: 1PE.15 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.187, B:D.211, B:D.211, B:G.272, H2O.28

2 x BW0: [[(2~{R},3~{S},4~{R},5~{R})-5-[(4~{E})-4-[(4-methoxycarbonylphenyl)methoxyimino]-3-methyl-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid(Non-covalent)

BW0.4: 15 residues within 4Å: Chain A: D.21, S.23, K.24, V.26, R.328, N.364, G.366, G.367, R.369, P.390, F.391, G.421, E.422, F.474, D.480 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.391 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 BW0.12: 15 residues within 4Å: Chain B: D.21, S.23, K.24, V.26, R.328, N.364, G.366, G.367, R.369, P.390, F.391, G.421, E.422, F.474, D.480 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.391 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

8 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.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 1PE.6: 7 residues within 4Å: Chain A: S.370, P.371, I.372, N.376, E.383, N.384, A.387 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.371, A:N.376, A:N.384 Water bridges: A:E.383 1PE.7: 11 residues within 4Å: Chain A: D.179, K.182, N.187, R.208, G.209, D.211, R.247, R.271, G.272, N.273 Ligands: CA.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.179, A:K.182, A:G.209 Water bridges: A:R.247 1PE.8: 8 residues within 4Å: Chain A: E.154, F.157, H.357, L.397, Q.399, K.468, R.491, D.493 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.399, A:K.468, A:D.493, A:D.493 1PE.13: 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 1PE.14: 7 residues within 4Å: Chain B: S.370, P.371, I.372, N.376, E.383, N.384, A.387 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.371, B:N.376, B:N.384 Water bridges: B:E.383 1PE.15: 11 residues within 4Å: Chain B: D.179, K.182, N.187, R.208, G.209, D.211, R.247, R.271, G.272, N.273 Ligands: CA.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.179, B:K.182, B:G.209 Water bridges: B:R.247 1PE.16: 8 residues within 4Å: Chain B: E.154, F.157, H.357, L.397, Q.399, K.468, R.491, D.493 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.399, B:K.468, B:D.493, B:D.493

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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