SMTL ID : 6z9d.1

Human Ecto-5'-nucleotidase (CD73) in complex with AOPCP derivative AB680 (compound 55 in publication) in the closed form (crystal form III)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.29, H.31, D.78 Ligands: ZN.2, QDH.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.29, A:H.31, A:D.78, H2O.1, H2O.1 ZN.2: 6 residues within 4Å: Chain A: D.78, N.110, H.213, H.236 Ligands: ZN.1, QDH.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.78, A:H.213, A:H.236, H2O.1 ZN.5: 5 residues within 4Å: Chain B: D.29, H.31, D.78 Ligands: ZN.6, QDH.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.29, B:H.31, B:D.78, H2O.12, H2O.13 ZN.6: 6 residues within 4Å: Chain B: D.78, N.110, H.213, H.236 Ligands: ZN.5, QDH.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.78, B:H.213, B:H.236, H2O.12

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: N.206, D.230, G.291 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.206, A:D.230, A:G.291, H2O.2, H2O.10 CA.7: 3 residues within 4Å: Chain B: N.206, D.230, G.291 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.206, B:D.230, B:G.291, H2O.13, H2O.22

2 x QDH: [[(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-[[(1~{S})-1-(2-fluorophenyl)ethyl]amino]pyrazolo[3,4-b]pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid(Non-covalent)

QDH.4: 23 residues within 4Å: Chain A: H.31, D.78, Q.81, N.110, H.111, D.114, L.177, N.179, H.213, H.236, N.238, R.347, N.383, G.385, G.386, R.388, F.410, G.440, P.491, F.493, D.499 Ligands: ZN.1, ZN.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:D.114, A:F.410, A:F.410, A:F.410, A:F.493 Hydrogen bonds: A:N.110, A:L.177, A:N.238, A:R.347, A:R.347, A:N.383, A:G.385, A:R.388, A:R.388, A:G.440, A:D.499 pi-Stacking: A:F.493, A:F.493 QDH.8: 23 residues within 4Å: Chain B: H.31, D.78, Q.81, N.110, H.111, D.114, L.177, N.179, H.213, H.236, N.238, R.347, N.383, G.385, G.386, R.388, F.410, G.440, P.491, F.493, D.499 Ligands: ZN.5, ZN.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:D.114, B:F.410, B:F.410, B:F.410, B:F.493 Hydrogen bonds: B:N.110, B:L.177, B:N.238, B:R.347, B:R.347, B:N.383, B:G.385, B:R.388, B:R.388, B:G.440, B:D.499 pi-Stacking: B:F.493, B:F.493

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lawson, K.V. et al., Discovery of AB680: A Potent and Selective Inhibitor of CD73. J.Med.Chem. (2020)

Release Date

2020-09-16

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'-nucleotidase

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