SMTL ID : 6xuq.1

Human Ecto-5'-nucleotidase (CD73) in complex with A1618 (compound 1b in publication) in the closed state in crystal form III

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 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, O1T.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.29, A:H.31, A:D.78, H2O.1 ZN.2: 7 residues within 4Å: Chain A: D.29, D.78, N.110, H.213, H.236 Ligands: ZN.1, O1T.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.78, A:H.213, A:H.236 ZN.5: 5 residues within 4Å: Chain B: D.29, H.31, D.78 Ligands: ZN.6, O1T.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.29, B:H.31, B:D.78, H2O.9 ZN.6: 7 residues within 4Å: Chain B: D.29, D.78, N.110, H.213, H.236 Ligands: ZN.5, O1T.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.78, B:H.213, B:H.236

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.1, H2O.8 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.9, H2O.16

2 x O1T: [[(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-[[(1~{S})-1-(4-fluorophenyl)ethyl]amino]pyrazolo[3,4-b]pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid(Non-covalent)

O1T.4: 23 residues within 4Å: Chain A: H.31, D.78, Q.81, N.110, H.111, D.114, L.177, S.178, N.179, 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 16 PLIP interactions: 16 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:N.238, A:R.347, A:R.347, A:N.383, A:R.388, A:R.388, A:G.440, A:D.499 pi-Stacking: A:F.493, A:F.493 O1T.8: 23 residues within 4Å: Chain B: H.31, D.78, Q.81, N.110, H.111, D.114, L.177, S.178, N.179, 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 16 PLIP interactions: 16 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:N.238, B:R.347, B:R.347, B:N.383, 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

Beatty, J.W. et al., Discovery of Potent and Selective Non-Nucleotide Small Molecule Inhibitors of CD73. J.Med.Chem. (2020)

Release Date

2020-04-22

Peptides

5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'-nucleotidase

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