SMTL ID : 4rao.1

Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, Plasmodium falciparum and vivax 6-oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

4 x 3L7: (2-{[2-(6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](2-{[(E)-2-phosphonoethenyl]oxy}ethyl)amino}ethyl)phosphonic acid(Non-covalent)

3L7.1: 17 residues within 4Å: Chain A: L.67, K.68, G.69, I.135, I.136, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, D.193, R.199 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.68, A:G.69, A:D.137, A:D.137, A:T.138, A:G.139, A:K.140, A:T.141, A:T.141, A:K.165, A:V.187, A:V.187, A:R.199, A:R.199 Water bridges: A:G.70, A:M.142, A:M.142, A:D.193 pi-Stacking: A:F.186 3L7.4: 14 residues within 4Å: Chain B: R.100, I.135, I.136, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, D.193 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.100, B:D.137, B:D.137, B:T.138, B:G.139, B:K.140, B:T.141, B:K.165, B:V.187, B:V.187 Water bridges: B:M.142, B:R.199 pi-Stacking: B:F.186 3L7.7: 17 residues within 4Å: Chain C: L.67, K.68, G.69, I.135, I.136, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, D.193, R.199 Ligands: MG.9 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:K.68, C:G.69, C:D.137, C:D.137, C:D.137, C:T.138, C:G.139, C:K.140, C:T.141, C:T.141, C:K.165, C:V.187, C:V.187, C:R.199, C:R.199 Water bridges: C:G.70, C:M.142 pi-Stacking: C:F.186 3L7.10: 18 residues within 4Å: Chain D: L.67, K.68, G.69, R.100, I.135, I.136, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, D.193, R.199 Ligands: MG.12 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:K.68, D:G.69, D:D.137, D:T.138, D:G.139, D:K.140, D:T.141, D:K.165, D:V.187, D:V.187, D:R.199, D:R.199 Water bridges: D:G.70, D:I.135, D:T.138, D:T.138, D:G.139, D:M.142 pi-Stacking: D:F.186

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.133, D.134 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.134, H2O.1, H2O.1, H2O.2, H2O.2 MG.3: 2 residues within 4Å: Chain A: D.193 Ligands: 3L7.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.193, H2O.2, H2O.2 MG.5: 2 residues within 4Å: Chain B: E.133, D.134 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.133, B:E.133, B:D.134 MG.6: 2 residues within 4Å: Chain B: D.193 Ligands: 3L7.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.193, H2O.3, H2O.4, H2O.4, H2O.4 MG.8: 2 residues within 4Å: Chain C: E.133, D.134 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.133, C:D.134, H2O.5, H2O.6, H2O.6 MG.9: 2 residues within 4Å: Chain C: D.193 Ligands: 3L7.7 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.193, H2O.5, H2O.5, H2O.6, H2O.6 MG.11: 2 residues within 4Å: Chain D: E.133, D.134 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.133, D:D.134, H2O.7, H2O.8, H2O.8 MG.12: 2 residues within 4Å: Chain D: D.193 Ligands: 3L7.10 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.193, H2O.7, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keough, D.T. et al., Aza-acyclic Nucleoside Phosphonates Containing a Second Phosphonate Group As Inhibitors of the Human, Plasmodium falciparum and vivax 6-Oxopurine Phosphoribosyltransferases and Their Prodrugs As Antimalarial Agents. J.Med.Chem. (2015)

Release Date

2015-01-07

Peptides

Hypoxanthine-guanine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hypoxanthine-guanine phosphoribosyltransferase

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