SMTL ID : 6ye1.1

Human Ecto-5'-nucleotidase (CD73) in complex with the AMPCP derivative A894 (compound 2n in publication) in the closed form (crystal form IV)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.11, H.13, D.60, N.220 Ligands: ZN.2, OO2.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.11, A:H.13, A:D.60 ZN.2: 8 residues within 4Å: Chain A: D.11, D.60, N.92, H.93, H.195, H.218 Ligands: ZN.1, OO2.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.60, A:H.195, A:H.218 ZN.4: 6 residues within 4Å: Chain B: D.11, H.13, D.60, N.220 Ligands: ZN.5, OO2.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.11, B:H.13, B:D.60 ZN.5: 7 residues within 4Å: Chain B: D.11, D.60, N.92, H.195, H.218 Ligands: ZN.4, OO2.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.60, B:H.195, B:H.218

2 x OO2: [(2~{R},3~{S},4~{R},5~{R})-5-[2-chloranyl-6-(cyclopentylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxymethylphosphonic acid(Non-covalent)

OO2.3: 21 residues within 4Å: Chain A: D.11, H.13, D.60, N.92, H.93, D.96, L.159, S.160, H.195, 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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.392, A:F.392 Hydrogen bonds: A:N.92, A:L.159, A:R.329, A:R.329, A:N.365, A:G.367, A:R.370, A:R.370, A:G.422, A:D.481, A:D.481 pi-Stacking: A:F.392, A:F.475, A:F.475 OO2.6: 20 residues within 4Å: Chain B: D.11, H.13, D.60, N.92, H.93, 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.4, ZN.5 12 PLIP interactions: 12 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:G.422, B:D.481, B:D.481 pi-Stacking: B:F.392, B:F.475

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
B

B
A

5'-nucleotidase

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