SMTL ID : 6ye2.1

Human Ecto-5'-nucleotidase (CD73) in complex with the AMPCP derivative A1202 (compound 4a in publication) in the closed form (crystal form IV)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 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, OO5.3 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: 8 residues within 4Å: Chain A: D.11, D.60, N.92, H.93, H.195, H.218 Ligands: ZN.1, OO5.3 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, OO5.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.11, B:H.13, B:D.60, H2O.13 ZN.6: 8 residues within 4Å: Chain B: D.11, D.60, N.92, H.93, H.195, H.218 Ligands: ZN.5, OO5.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.60, B:H.195, B:H.218

2 x OO5: [(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-(cyclopentylamino)pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxymethylphosphonic acid(Non-covalent)

OO5.3: 21 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, R.329, N.365, G.367, G.368, R.370, F.392, G.422, F.475, D.481 Ligands: ZN.1, ZN.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.392 Hydrogen bonds: A:L.159, A:R.329, A:R.329, A:N.365, A:R.370, A:R.370, A:G.422, A:D.481, A:D.481 Water bridges: A:R.370 pi-Stacking: A:F.392, A:F.475, A:F.475 OO5.7: 21 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, R.329, N.365, G.367, G.368, R.370, F.392, G.422, F.475, D.481 Ligands: ZN.5, ZN.6 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.392 Hydrogen bonds: B:N.92, B:L.159, B:R.329, B:R.329, B:N.365, B:R.370, B:R.370, B:G.422, B:D.481, B:D.481 Water bridges: B:N.220, B:N.220 pi-Stacking: B:F.392, B:F.475, B:F.475

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: K.183, N.188, D.212, G.273 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.188, A:D.212, A:D.212, A:G.273, H2O.1 CA.8: 5 residues within 4Å: Chain B: K.183, N.188, G.210, D.212, G.273 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.188, B:D.212, B:D.212, B:G.273, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharif, E.U. et al., Discovery of Potent and Selective Methylenephosphonic Acid CD73 Inhibitors. J.Med.Chem. (2021)

Release Date

2021-01-20

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'-nucleotidase

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