SMTL ID : 8tpy.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x JG6: {3-[(2S,4R)-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-(hydroxymethyl)pyrrolidin-1-yl]-3-oxopropyl}phosphonic acid

JG6.1: 14 residues within 4Å: Chain A: 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, Y.195 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.138, A:T.139, A:G.140, A:K.141, A:T.142, A:V.188, A:V.188, A:D.194 Water bridges: A:T.139, A:T.142 pi-Stacking: A:F.187 JG6.3: 16 residues within 4Å: Chain B: 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, Y.195 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:D.138, B:D.138, B:T.139, 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:D.194 Water bridges: B:M.143 pi-Stacking: B:F.187 pi-Cation interactions: B:F.187 JG6.5: 13 residues within 4Å: Chain C: 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 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: 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:D.194 Water bridges: C:T.139, C:M.143 pi-Stacking: C:F.187 pi-Cation interactions: C:F.187 JG6.7: 14 residues within 4Å: Chain D: 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 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:D.138, D:T.139, D:G.140, D:K.141, D:T.142, D:T.142, D:K.166, D:V.188, D:V.188, D:D.194 Water bridges: D:I.136, D:T.139, D:T.139 pi-Stacking: D:F.187 pi-Cation interactions: D:F.187

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.70, G.71, E.134, D.135 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.134, A:D.135 MG.4: 4 residues within 4Å: Chain B: K.69, E.134, D.135 Ligands: JG6.3 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.2 MG.6: 4 residues within 4Å: Chain C: K.69, G.70, E.134, D.135 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.134, C:D.135, H2O.3, H2O.3, H2O.3 MG.8: 5 residues within 4Å: Chain D: K.69, G.70, G.71, E.134, D.135 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.134, D:D.135, H2O.4, H2O.4

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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