SMTL ID : 4ijq.1

Human hypoxanthine-guanine phosphoribosyltransferase in complex with [(2-((Guanine-9H-yl)methyl)propane-1,3-diyl)bis(oxy)]bis(methylene))diphosphonic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x SV2: [{2-[(guanine-9-yl)methyl]propane-1,3-diyl}bis(oxymethylene)]bis(phosphonic acid)(Non-covalent)

SV2.1: 15 residues within 4Å: Chain A: K.108, I.141, I.142, D.143, T.144, G.145, K.146, T.147, K.171, K.191, F.192, V.193, D.199 Ligands: SO4.2, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.141 Hydrogen bonds: A:D.143, A:D.143, A:T.144, A:G.145, A:K.146, A:T.147, A:T.147, A:K.171, A:V.193, A:V.193, A:D.199 Water bridges: A:T.144, A:T.147, A:M.148, A:D.199, A:R.205 SV2.5: 14 residues within 4Å: Chain B: I.141, I.142, D.143, T.144, G.145, K.146, T.147, K.171, K.191, F.192, V.193, D.199 Ligands: SO4.7, MG.8 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.141 Hydrogen bonds: B:D.143, B:T.144, B:G.145, B:K.146, B:T.147, B:T.147, B:T.147, B:K.171, B:V.193, B:V.193, B:D.199 Water bridges: B:T.144, B:T.144, B:M.148, B:R.175, B:D.199 pi-Stacking: B:F.192 pi-Cation interactions: B:F.192 SV2.9: 14 residues within 4Å: Chain C: I.141, I.142, D.143, T.144, G.145, K.146, T.147, K.171, K.191, F.192, V.193, D.199 Ligands: MG.11, SO4.12 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:D.143, C:T.144, C:G.145, C:K.146, C:T.147, C:K.171, C:V.193, C:V.193, C:D.199 Water bridges: C:D.143, C:M.148 pi-Stacking: C:F.192 SV2.14: 13 residues within 4Å: Chain D: I.142, D.143, T.144, G.145, K.146, T.147, K.171, K.191, F.192, V.193, D.199 Ligands: MG.13, SO4.16 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:D.143, D:D.143, D:T.144, D:G.145, D:K.146, D:T.147, D:K.171, D:V.193, D:V.193, D:D.199 Water bridges: D:M.148, D:R.205 pi-Stacking: D:F.192

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: L.73, K.74, G.75, D.140, D.199, R.205 Ligands: SV2.1, MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:L.73, A:K.74, A:G.75 Water bridges: A:G.76, A:R.106, A:K.108, A:D.199, A:R.205 Salt bridges: A:R.205 SO4.7: 8 residues within 4Å: Chain B: L.73, K.74, G.75, D.140, D.199, R.205 Ligands: SV2.5, MG.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.74, B:G.75, B:D.140 Water bridges: B:G.76, B:R.106, B:D.199, B:R.205, B:R.205 Salt bridges: B:R.205 SO4.12: 8 residues within 4Å: Chain C: L.73, K.74, G.75, D.140, D.199, R.205 Ligands: SV2.9, MG.11 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.74, C:G.75 Water bridges: C:G.76, C:D.199, C:R.205 Salt bridges: C:R.205 SO4.16: 9 residues within 4Å: Chain D: L.73, K.74, G.75, D.140, D.199, R.205 Ligands: MG.13, SV2.14, MG.15 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.74, D:G.75 Water bridges: D:G.76, D:D.199, D:R.205 Salt bridges: D:R.205

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.139, D.140 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.140, H2O.1, H2O.1, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain A: D.199, R.205 Ligands: SV2.1, SO4.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.199, H2O.1, H2O.1, H2O.1 MG.6: 2 residues within 4Å: Chain B: E.139, D.140 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.139, B:D.140, H2O.3, H2O.3, H2O.3, H2O.6 MG.8: 4 residues within 4Å: Chain B: D.199, R.205 Ligands: SV2.5, SO4.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.199, H2O.4, H2O.4, H2O.5 MG.10: 2 residues within 4Å: Chain C: E.139, D.140 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.139, C:D.140, H2O.6, H2O.6, H2O.6, H2O.9 MG.11: 5 residues within 4Å: Chain C: D.199, E.202, R.205 Ligands: SV2.9, SO4.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.199 MG.13: 3 residues within 4Å: Chain D: D.199 Ligands: SV2.14, SO4.16 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.199, D:D.199, H2O.10, H2O.11, H2O.11 MG.15: 3 residues within 4Å: Chain D: E.139, D.140 Ligands: SO4.16 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.139, D:D.140, H2O.9, H2O.9, H2O.9, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keough, D.T. et al., Acyclic nucleoside phosphonates containing a second phosphonate group are potent inhibitors of 6-oxopurine phosphoribosyltransferases and have antimalarial activity. J.Med.Chem. (2013)

Release Date

2013-03-27

Peptides

Hypoxanthine-guanine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hypoxanthine-guanine phosphoribosyltransferase