SMTL ID : 6bnj.1

Human hypoxanthine guanine phosphoribosyltransferase in complex with [3R,4R]-4-guanin-9-yl-3-((R)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-tetramer

Ligands

4 x WPG: (3-{(3R,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-[(2R)-2-hydroxy-2-phosphonoethoxy]pyrrolidin-1-yl}-3-oxopropy l)phosphonic acid(Non-covalent)

WPG.1: 20 residues within 4Å: Chain A: L.68, K.69, G.70, L.102, I.136, I.137, D.138, T.139, G.140, K.141, T.142, K.166, K.186, F.187, V.188, L.193, D.194, R.200 Ligands: MG.2, MG.3 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:K.69, A:G.70, A:D.138, A:T.139, A:T.139, A:T.139, A:G.140, A:K.141, A:T.142, A:T.142, A:T.142, A:K.166, A:V.188, A:V.188, A:V.188, A:R.200, A:R.200 Water bridges: A:G.71, A:R.101, A:D.135, A:D.135, A:T.139, A:T.139, A:M.143, A:D.194, A:D.194, A:D.194 WPG.4: 19 residues within 4Å: Chain B: L.68, K.69, G.70, I.136, I.137, D.138, T.139, G.140, K.141, T.142, K.166, K.186, F.187, V.188, L.193, D.194, R.200 Ligands: MG.5, MG.6 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:K.69, B:G.70, B:D.135, B:D.138, B:T.139, B:T.139, B:T.139, B:G.140, B:K.141, B:T.142, B:T.142, B:T.142, B:K.166, B:V.188, B:V.188, B:V.188, B:R.200, B:R.200 Water bridges: B:D.138, B:K.141, B:K.141, B:M.143, B:D.194, B:D.194, B:D.194 pi-Stacking: B:F.187 WPG.7: 20 residues within 4Å: Chain C: L.68, K.69, G.70, D.135, I.136, I.137, D.138, T.139, G.140, K.141, T.142, K.166, K.186, F.187, V.188, L.193, D.194, R.200 Ligands: MG.8, MG.9 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:L.68, C:K.69, C:G.70, C:D.138, C:T.139, C:T.139, C:T.139, C:G.140, C:K.141, C:T.142, C:T.142, C:T.142, C:K.166, C:V.188, C:V.188, C:V.188, C:R.200, C:R.200 Water bridges: C:G.71, C:T.139, C:T.139, C:M.143, C:D.194, C:D.194, C:D.194 WPG.10: 19 residues within 4Å: Chain D: L.68, K.69, G.70, I.136, I.137, D.138, T.139, G.140, K.141, T.142, K.166, K.186, F.187, V.188, L.193, D.194, R.200 Ligands: MG.11, MG.12 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:K.69, D:G.70, D:D.135, D:D.138, D:T.139, D:T.139, D:T.139, D:G.140, D:K.141, D:T.142, D:T.142, D:T.142, D:K.166, D:V.188, D:V.188, D:V.188, D:R.200, D:R.200 Water bridges: D:L.68, D:G.71, D:R.101, D:D.138, D:M.143, D:D.194 pi-Cation interactions: D:F.187

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.134, D.135 Ligands: WPG.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.135, H2O.1, H2O.2, H2O.3, H2O.4 MG.3: 3 residues within 4Å: Chain A: D.194, R.200 Ligands: WPG.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.194, H2O.4, H2O.4, H2O.5 MG.5: 3 residues within 4Å: Chain B: E.134, D.135 Ligands: WPG.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.134, B:E.134, B:D.135, H2O.8, H2O.8 MG.6: 2 residues within 4Å: Chain B: D.194 Ligands: WPG.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.194, H2O.7, H2O.9, H2O.9 MG.8: 3 residues within 4Å: Chain C: E.134, D.135 Ligands: WPG.7 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.134, C:D.135, H2O.11, H2O.11, H2O.11, H2O.12 MG.9: 3 residues within 4Å: Chain C: D.194, R.200 Ligands: WPG.7 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.194, H2O.11, H2O.12, H2O.14 MG.11: 3 residues within 4Å: Chain D: E.134, D.135 Ligands: WPG.10 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.134, D:D.135, H2O.17, H2O.18, H2O.18, H2O.19 MG.12: 2 residues within 4Å: Chain D: D.194 Ligands: WPG.10 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.194, H2O.17, H2O.19, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keough, D.T. et al., Design of Plasmodium vivax Hypoxanthine-Guanine Phosphoribosyltransferase Inhibitors as Potential Antimalarial Therapeutics. ACS Chem. Biol. (2018)

Release Date

2017-12-06

Peptides

Hypoxanthine-guanine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hypoxanthine-guanine phosphoribosyltransferase