SMTL ID : 4rad.2 (1 other biounit)

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 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x 3L5: (2-{[2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl][2-(2-phosphonoethoxy)ethyl]amino}ethyl)phosphonic acid(Non-covalent)

3L5.1: 23 residues within 4Å: Chain A: V.66, L.67, K.68, G.69, G.70, L.101, E.133, D.134, I.135, I.136, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, V.188, L.192, D.193, R.199 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:K.68, A:D.137, A:T.138, A:T.138, A:G.139, A:K.140, A:T.141, A:T.141, A:T.141, A:K.165, A:V.187, A:V.187, A:D.193, A:R.199, A:R.199 Water bridges: A:E.133, A:D.134, A:M.142, A:D.193 Salt bridges: A:D.134 3L5.2: 22 residues within 4Å: Chain B: L.101, K.102, S.103, I.113, D.134, I.135, I.136, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, V.188, L.192, D.193, R.199 Ligands: MG.3, MG.4 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:S.103, B:D.137, B:D.137, B:T.138, B:T.138, B:G.139, B:K.140, B:T.141, B:T.141, B:K.165, B:V.187, B:D.193, B:D.193, B:R.199 Water bridges: B:T.138, B:T.141, B:M.142, B:D.193, B:D.193, B:E.196 Salt bridges: B:D.134 pi-Stacking: B:F.186 3L5.5: 16 residues within 4Å: Chain C: I.135, I.136, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, V.188, L.192, D.193, R.199 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:I.135, C:D.137, C:T.138, C:T.138, C:G.139, C:K.140, C:T.141, C:T.141, C:T.141, C:K.165, C:V.187, C:D.193, C:D.193 Water bridges: C:R.199, C:R.199 Salt bridges: C:D.134 3L5.7: 23 residues within 4Å: Chain D: L.67, K.68, G.69, R.100, L.101, K.102, D.134, I.135, I.136, D.137, T.138, G.139, K.140, T.141, K.165, K.185, F.186, V.187, V.188, L.192, D.193, R.199 Ligands: MG.8 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:L.67, D:L.67, D:K.68, D:G.69, D:R.100, D:D.137, D:T.138, D:T.138, D:G.139, D:K.140, D:T.141, D:T.141, D:T.141, D:K.165, D:V.187, D:V.187, D:D.193, D:R.199, D:R.199 Water bridges: D:I.135, D:T.141, D:M.142, D:D.193, D:D.193

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain B: E.133, D.134, I.135, I.136, T.141 Ligands: 3L5.2 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.133, B:I.135, H2O.6 MG.4: 2 residues within 4Å: Chain B: D.193 Ligands: 3L5.2 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.193, H2O.4, H2O.6 MG.6: 5 residues within 4Å: Chain C: G.69, E.133, D.134, I.135 Ligands: 3L5.5 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.133, C:D.134, C:D.134, H2O.8, H2O.8 MG.8: 4 residues within 4Å: Chain D: E.133, D.134, I.135 Ligands: 3L5.7 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.133, D:D.134, H2O.8, H2O.10, H2O.10

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
E

B
F

C
G

D
H

Hypoxanthine-guanine phosphoribosyltransferase

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