SMTL ID : 4rab.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 Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-tetramer

Ligands

4 x 3L3: [(E)-2-(2-{[2-(2-amino-8-bromo-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)ethenyl]phosphonic acid(Non-covalent)

3L3.1: 15 residues within 4Å: Chain A: I.135, I.136, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, L.192, D.193 Ligands: MG.2, PO4.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:D.137, A:T.138, A:T.138, 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:V.187 Water bridges: A:D.137, A:M.142 pi-Stacking: A:F.186 3L3.4: 15 residues within 4Å: Chain B: I.135, I.136, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, L.192, D.193 Ligands: MG.5, PO4.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:D.137, B:T.138, B:T.138, B:T.138, B:G.139, B:K.140, B:T.141, B:T.141, B:V.187, B:V.187, B:V.187, B:D.193 Water bridges: B:M.142 pi-Stacking: B:F.186 pi-Cation interactions: B:F.186 3L3.7: 15 residues within 4Å: Chain C: I.135, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, L.192, D.193 Ligands: MG.8, MG.9, PO4.10 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:D.137, C:T.138, C:T.138, 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:V.187, C:D.193 Water bridges: C:M.142 pi-Stacking: C:F.186 pi-Cation interactions: C:F.186 3L3.11: 15 residues within 4Å: Chain D: I.135, I.136, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, L.192, D.193 Ligands: MG.13, PO4.14 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:D.137, D:T.138, D:T.138, D:T.138, D:G.139, D:K.140, D:T.141, D:K.165, D:V.187, D:V.187, D:V.187 Water bridges: D:M.142 pi-Stacking: D:F.186 pi-Cation interactions: D:F.186

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.133, D.134, I.135 Ligands: 3L3.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.133, A:E.133, A:D.134, A:I.135, H2O.2 MG.5: 4 residues within 4Å: Chain B: E.133, D.134, I.135 Ligands: 3L3.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.133, B:E.133, B:D.134 MG.8: 4 residues within 4Å: Chain C: E.133, D.134, I.135 Ligands: 3L3.7 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.133, C:D.134, H2O.4, H2O.4, H2O.4 MG.9: 4 residues within 4Å: Chain C: D.193, R.199 Ligands: 3L3.7, PO4.10 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.193, H2O.4 MG.12: 3 residues within 4Å: Chain D: E.133, D.134 Ligands: PO4.14 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.133, D:D.134, H2O.6, H2O.6, H2O.6 MG.13: 3 residues within 4Å: Chain D: D.193 Ligands: 3L3.11, PO4.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.193

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 7 residues within 4Å: Chain A: L.67, K.68, G.69, D.134, D.193, R.199 Ligands: 3L3.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.68, A:G.69, A:D.193 Salt bridges: A:R.199 PO4.6: 6 residues within 4Å: Chain B: L.67, K.68, G.69, D.193, R.199 Ligands: 3L3.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.68, B:G.69 Salt bridges: B:R.199 PO4.10: 7 residues within 4Å: Chain C: L.67, K.68, G.69, D.193, R.199 Ligands: 3L3.7, MG.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.68, C:G.69 Water bridges: C:D.193, C:D.193 Salt bridges: C:R.199 PO4.14: 8 residues within 4Å: Chain D: L.67, K.68, G.69, D.193, R.199 Ligands: 3L3.11, MG.12, MG.13 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.67, D:K.68, D:G.69 Water bridges: D:G.70 Salt bridges: D:R.199

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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