SMTL ID : 8tpv.1

Structure of human hypoxanthine guanine phosphoribzosyltransferase in complex with [2S,4R]-4-Guanin-9-yl-2-(2-phosphonoethoxymethyl)-1-N-(3-phosphonopropionyl)pyrrolidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-tetramer

Ligands

4 x JEI: (3-{(2S,4R)-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-[(2-phosphonoethoxy)methyl]pyrrolidin-1-yl}-3-oxopropyl)phosphonic acid

JEI.1: 20 residues within 4Å: Chain A: 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, V.189, L.193, D.194, R.200 Ligands: MG.2, MG.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.136 Hydrogen bonds: A:K.69, A:G.70, A:D.138, A:T.139, A:G.140, A:K.141, A:T.142, A:T.142, A:K.166, A:V.188, A:V.188, A:V.188, A:D.194, A:R.200, A:R.200 Water bridges: A:G.71, A:M.143, A:D.194, A:D.194 pi-Stacking: A:F.187 JEI.4: 20 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, V.189, L.193, D.194, R.200 Ligands: MG.5, MG.6 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.136 Hydrogen bonds: B:L.68, B:K.69, B:G.70, B:D.138, B:D.138, B:T.139, B:G.140, B:K.141, B:T.142, B:T.142, B:K.166, B:V.188, B:V.188, B:V.188, B:D.194, B:R.200, B:R.200 Water bridges: B:G.71, B:T.139, B:T.142, B:M.143 pi-Stacking: B:F.187 JEI.7: 20 residues within 4Å: Chain C: 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, V.189, L.193, D.194, R.200 Ligands: MG.8, MG.9 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:I.136 Hydrogen bonds: C:K.69, C:G.70, C:D.138, C:T.139, C:G.140, C:K.141, 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 pi-Stacking: C:F.187 JEI.10: 19 residues within 4Å: Chain D: L.68, K.69, G.70, I.136, D.138, T.139, G.140, K.141, T.142, K.166, K.186, F.187, V.188, V.189, L.193, D.194, R.200 Ligands: MG.11, MG.12 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:K.69, D:G.70, D:D.138, D:T.139, D:G.140, D:K.141, D:T.142, D:K.166, D:V.188, D:V.188, D:V.188, D:D.194, D:R.200, D:R.200 Water bridges: D:G.71, D:M.143, D:D.194, D:D.194, D:D.194, D:D.194 pi-Stacking: D:F.187

8 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keough, D.T. et al., Development of Prolinol Containing Inhibitors of Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase: Rational Structure-Based Drug Design. J.Med.Chem. (2024)

Release Date

2024-05-08

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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