SMTL ID : 7qgm.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: D.36, H.38, D.85, H.220, N.245 Ligands: ZN.2, BOI.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.38, A:D.85 ZN.2: 7 residues within 4Å: Chain A: D.85, N.117, H.118, H.220, H.243 Ligands: ZN.1, BOI.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.85, A:D.85, A:H.220, A:H.243 ZN.5: 7 residues within 4Å: Chain B: D.36, H.38, D.85, H.220, N.245 Ligands: ZN.6, BOI.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.38, B:D.85 ZN.6: 7 residues within 4Å: Chain B: D.85, N.117, H.118, H.220, H.243 Ligands: ZN.5, BOI.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.85, B:D.85, B:H.220, B:H.243

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: K.208, N.213, D.237, G.298 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.237, A:G.298 CA.7: 4 residues within 4Å: Chain B: K.208, N.213, D.237, G.298 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.237, B:G.298

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: 24 residues within 4Å: Chain A: H.38, D.85, Q.88, N.117, H.118, D.121, L.184, S.185, N.186, H.220, H.243, N.245, R.354, N.390, G.392, G.393, R.395, F.417, G.447, E.448, F.500, D.506 Ligands: ZN.1, ZN.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.121 Hydrogen bonds: A:D.85, A:H.118, A:N.245, A:R.354, A:R.354, A:N.390, A:G.392, A:R.395, A:R.395, A:R.395, A:G.447, A:D.506, A:D.506 pi-Stacking: A:F.500 BOI.8: 24 residues within 4Å: Chain B: H.38, D.85, Q.88, N.117, H.118, D.121, L.184, S.185, N.186, H.220, H.243, N.245, R.354, N.390, G.392, G.393, R.395, F.417, G.447, E.448, F.500, D.506 Ligands: ZN.5, ZN.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:D.121 Hydrogen bonds: B:D.85, B:H.118, B:N.245, B:R.354, B:R.354, B:N.390, B:G.392, B:R.395, B:R.395, B:R.395, B:G.447, B:D.506, B:D.506 pi-Stacking: B:F.500

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