SMTL ID : 5hia.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

4 x YPG: [3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-y l]-3-oxidanylidene-propyl]phosphonic acid(Non-covalent)

YPG.1: 19 residues within 4Å: Chain A: L.74, K.75, G.76, I.142, I.143, D.144, T.145, G.146, K.147, T.148, K.172, K.192, F.193, V.194, L.199, D.200, R.206 Ligands: MG.2, MG.3 32 PLIP interactions: 32 interactions with chain A Hydrogen bonds: A:L.74, A:K.75, A:G.76, A:D.144, A:D.144, A:T.145, A:T.145, A:T.145, A:T.145, A:G.146, A:K.147, A:K.147, A:T.148, A:T.148, A:T.148, A:K.172, A:V.194, A:V.194, A:V.194, A:R.206, A:R.206 Water bridges: A:G.77, A:R.107, A:M.149, A:M.149, A:D.200, A:D.200, A:D.200, A:D.200, A:E.203, A:E.203 pi-Cation interactions: A:F.193 YPG.4: 19 residues within 4Å: Chain B: L.74, K.75, G.76, I.142, I.143, D.144, T.145, G.146, K.147, T.148, K.172, K.192, F.193, V.194, L.199, D.200, R.206 Ligands: MG.5, MG.6 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:L.74, B:K.75, B:G.76, B:D.144, B:T.145, B:T.145, B:T.145, B:G.146, B:K.147, B:T.148, B:T.148, B:T.148, B:K.172, B:V.194, B:V.194, B:V.194, B:D.200, B:R.206, B:R.206 Water bridges: B:G.77, B:T.145, B:T.145, B:M.149 YPG.7: 19 residues within 4Å: Chain C: L.74, K.75, G.76, I.142, I.143, D.144, T.145, G.146, K.147, T.148, K.172, K.192, F.193, V.194, L.199, D.200, R.206 Ligands: MG.8, MG.9 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:L.74, C:K.75, C:G.76, C:D.144, C:D.144, C:T.145, C:T.145, C:T.145, C:G.146, C:K.147, C:T.148, C:T.148, C:T.148, C:K.172, C:V.194, C:V.194, C:V.194, C:D.200, C:R.206, C:R.206 Water bridges: C:G.77, C:M.149, C:D.200, C:E.203, C:E.203 pi-Stacking: C:F.193 YPG.10: 19 residues within 4Å: Chain D: L.74, K.75, G.76, I.142, I.143, D.144, T.145, G.146, K.147, T.148, K.172, K.192, F.193, V.194, L.199, D.200, R.206 Ligands: MG.11, MG.12 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:L.74, D:K.75, D:G.76, D:D.144, D:T.145, D:T.145, D:T.145, D:G.146, D:K.147, D:T.148, D:T.148, D:T.148, D:K.172, D:V.194, D:V.194, D:V.194, D:R.206, D:R.206 Water bridges: D:G.77, D:R.107, D:T.145, D:T.145, D:M.149, D:D.200, D:D.200, D:D.200

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.200, R.206 Ligands: YPG.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.200, H2O.1, H2O.3, H2O.3 MG.3: 3 residues within 4Å: Chain A: E.140, D.141 Ligands: YPG.1 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.140, A:D.141, H2O.1, H2O.1, H2O.2, H2O.3 MG.5: 3 residues within 4Å: Chain B: D.200, R.206 Ligands: YPG.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.200, H2O.5, H2O.7, H2O.7 MG.6: 3 residues within 4Å: Chain B: E.140, D.141 Ligands: YPG.4 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.140, B:D.141, H2O.5, H2O.5, H2O.5, H2O.6 MG.8: 3 residues within 4Å: Chain C: D.200, R.206 Ligands: YPG.7 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.200, H2O.10, H2O.12, H2O.12 MG.9: 3 residues within 4Å: Chain C: E.140, D.141 Ligands: YPG.7 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.140, C:D.141, H2O.9, H2O.10, H2O.11, H2O.12 MG.11: 3 residues within 4Å: Chain D: D.200, R.206 Ligands: YPG.10 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.200, H2O.14, H2O.16, H2O.16 MG.12: 3 residues within 4Å: Chain D: E.140, D.141 Ligands: YPG.10 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.140, D:D.141, H2O.14, H2O.14, H2O.15, H2O.15

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. (2017)

Release Date

2017-01-18

Peptides

Hypoxanthine-guanine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hypoxanthine-guanine phosphoribosyltransferase