SMTL ID : 9i1h.1

Crystal structure of human CD73 (ecto-5'-nucleotidase) in complex with the AMPCP analog PSB-12730 in the closed state (crystal form IV)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 9 residues within 4Å: Chain A: D.36, H.38, D.85, H.118, H.220, H.243, R.395 Ligands: ZN.2, 01.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.36, A:H.38, A:D.85 ZN.2: 8 residues within 4Å: Chain A: D.36, D.85, N.117, H.118, H.220, H.243 Ligands: ZN.1, 01.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.85, A:H.220, A:H.243 ZN.4: 9 residues within 4Å: Chain B: D.36, H.38, D.85, H.118, H.220, H.243, R.395 Ligands: ZN.5, 01.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.36, B:H.38, B:D.85 ZN.5: 8 residues within 4Å: Chain B: D.36, D.85, N.117, H.118, H.220, H.243 Ligands: ZN.4, 01.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.85, B:H.220, B:H.243

2 x 01: [[(2~{R},3~{S},4~{R},5~{R})-5-[2-chloranyl-6-[(phenylmethyl)-propyl-amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid

01.3: 26 residues within 4Å: Chain A: D.36, H.38, D.85, N.117, H.118, D.121, L.184, S.185, N.186, H.243, S.244, N.245, R.354, N.390, G.392, G.393, R.395, F.417, G.419, G.447, P.498, N.499, F.500, D.506 Ligands: ZN.1, ZN.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.117, A:N.117, 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:G.447, A:D.506 pi-Stacking: A:F.500, A:F.500 01.6: 27 residues within 4Å: Chain B: H.38, D.85, N.117, H.118, D.121, L.184, S.185, N.186, H.220, H.243, S.244, N.245, R.354, N.390, G.392, G.393, R.395, F.417, G.419, G.447, E.448, P.498, N.499, F.500, D.506 Ligands: ZN.4, ZN.5 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.117, B:N.117, 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:G.447, B:D.506, B:D.506 pi-Stacking: B:F.417, B:F.500, B:F.500

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Idris, R.M. et al., Design, development and evaluation of a tritium-labeled radiotracer for ecto-5'-nucleotidase (CD73) - A versatile research tool and diagnostic agent for personalized medicine. Biomed Pharmacother (2025)

Release Date

2025-06-11

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'-nucleotidase

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