SMTL ID : 5w8v.1

HUMAN HGPRT in complex with [(2-[(guanin-9-yl)methyl]propane-1,3-diyl)bis(oxy)]bis(methylene)diphosphonic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x 9YP: {[(2R)-2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methyl]-3-(2-phosphonoethoxy)propoxy]methyl}phosphonic acid(Non-covalent)

9YP.1: 12 residues within 4Å: Chain A: I.133, D.135, T.136, G.137, K.138, T.139, K.163, K.183, F.184, V.185, L.190, D.191 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:D.135, A:D.135, A:T.136, A:G.137, A:K.138, A:T.139, A:T.139, A:T.139, A:K.163, A:V.185, A:V.185, A:V.185, A:D.191 Water bridges: A:L.65, A:L.65, A:G.67, A:D.132, A:D.135, A:M.140, A:R.167, A:D.191, A:R.197 9YP.3: 12 residues within 4Å: Chain B: I.133, D.135, T.136, G.137, K.138, T.139, K.163, K.183, F.184, V.185, L.190, D.191 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:I.133 Hydrogen bonds: B:D.135, B:T.136, B:G.137, B:K.138, B:T.139, B:T.139, B:K.163, B:V.185, B:V.185, B:D.191, B:D.191, B:D.191 Water bridges: B:L.65, B:L.65, B:L.65, B:L.65, B:G.67, B:L.99, B:D.132, B:T.136, B:T.136, B:M.140, B:R.197, B:R.197 9YP.5: 13 residues within 4Å: Chain C: I.133, I.134, D.135, T.136, G.137, K.138, T.139, K.163, K.183, F.184, V.185, D.191 Ligands: MG.6 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:D.135, C:T.136, C:T.136, C:G.137, C:K.138, C:T.139, C:T.139, C:K.163, C:V.185, C:V.185, C:V.185, C:D.191 Water bridges: C:L.65, C:K.66, C:G.67, C:G.67, C:D.132, C:T.136, C:T.139, C:M.140, C:R.167, C:R.167, C:D.191, C:D.191, C:D.191, C:R.197 9YP.7: 12 residues within 4Å: Chain D: I.133, I.134, D.135, T.136, G.137, K.138, T.139, K.163, K.183, F.184, V.185, D.191 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.133 Hydrogen bonds: D:D.135, D:T.136, D:G.137, D:K.138, D:T.139, D:K.163, D:V.185, D:V.185, D:V.185, D:D.191 Water bridges: D:D.132, D:T.136, D:T.139, D:M.140, D:R.197, D:R.197

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.131, D.132 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.131, A:D.132, H2O.2, H2O.2, H2O.3, H2O.3 MG.4: 2 residues within 4Å: Chain B: E.131, D.132 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.131, B:D.132, H2O.6, H2O.7, H2O.7, H2O.9 MG.6: 3 residues within 4Å: Chain C: E.131, D.132 Ligands: 9YP.5 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.131, H2O.10, H2O.10, H2O.11, H2O.12 MG.8: 2 residues within 4Å: Chain D: E.131, D.132 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.131, D:D.132, H2O.17, H2O.17, H2O.17, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spacek, P. et al., Synthesis and Evaluation of Asymmetric Acyclic Nucleoside Bisphosphonates as Inhibitors of Plasmodium falciparum and Human Hypoxanthine-Guanine-(Xanthine) Phosphoribosyltransferase. J. Med. Chem. (2017)

Release Date

2017-08-30

Peptides

Hypoxanthine-guanine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hypoxanthine-guanine phosphoribosyltransferase