SMTL ID : 6bo7.1 (2 other biounits)

Crystal structure of Plasmodium vivax 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 2.86 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.149, D.150 Ligands: YPG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.149, A:E.149, A:D.150 MG.2: 2 residues within 4Å: Chain A: D.209 Ligands: YPG.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.209 MG.4: 3 residues within 4Å: Chain B: E.149, D.150 Ligands: YPG.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.149, B:E.149, B:D.150 MG.5: 3 residues within 4Å: Chain B: D.209, R.215 Ligands: YPG.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.209, B:D.209 MG.7: 3 residues within 4Å: Chain C: E.149, D.150 Ligands: YPG.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.150 MG.8: 3 residues within 4Å: Chain C: D.209, R.215 Ligands: YPG.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.209, C:D.209 MG.10: 3 residues within 4Å: Chain D: E.149, D.150 Ligands: YPG.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.149, D:E.149, D:D.150 MG.11: 3 residues within 4Å: Chain D: D.209, R.215 Ligands: YPG.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.209, D:D.209

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.3: 22 residues within 4Å: Chain A: L.81, K.82, G.83, R.117, E.149, I.151, I.152, D.153, T.154, G.155, K.156, T.157, L.158, K.181, A.201, F.202, V.203, L.208, D.209, R.215 Ligands: MG.1, MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:L.81, A:K.82, A:G.83, A:D.153, A:D.153, A:T.154, A:T.154, A:T.154, A:G.155, A:K.156, A:T.157, A:T.157, A:T.157, A:K.181, A:V.203, A:V.203, A:V.203, A:D.209, A:R.215, A:R.215 YPG.6: 20 residues within 4Å: Chain B: K.82, G.83, R.117, E.149, I.151, I.152, D.153, T.154, G.155, K.156, T.157, K.181, A.201, F.202, V.203, L.208, D.209, R.215 Ligands: MG.4, MG.5 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:L.81, B:K.82, B:G.83, B:D.153, B:D.153, B:T.154, B:T.154, B:T.154, B:G.155, B:K.156, B:T.157, B:T.157, B:T.157, B:K.181, B:V.203, B:V.203, B:V.203, B:R.215, B:R.215 YPG.9: 20 residues within 4Å: Chain C: K.82, G.83, R.117, E.149, I.151, I.152, D.153, T.154, G.155, K.156, T.157, K.181, A.201, F.202, V.203, L.208, D.209, R.215 Ligands: MG.7, MG.8 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:K.82, C:G.83, C:R.117, C:R.117, C:E.149, C:D.153, C:T.154, C:T.154, C:T.154, C:T.154, C:G.155, C:T.157, C:T.157, C:T.157, C:L.158, C:V.203, C:V.203, C:V.203, C:R.215, C:R.215 YPG.12: 19 residues within 4Å: Chain D: K.82, G.83, R.117, E.149, I.151, D.153, T.154, G.155, K.156, T.157, K.181, A.201, F.202, V.203, L.208, D.209, R.215 Ligands: MG.10, MG.11 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:K.82, D:G.83, D:R.117, D:R.117, D:E.149, D:D.153, D:T.154, D:T.154, D:T.154, D:G.155, D:K.156, D:T.157, D:T.157, D:T.157, D:V.203, D:V.203, D:V.203, D:R.215, D:R.215

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. (2018)

Release Date

2017-12-13

Peptides

Hypoxanthine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hypoxanthine phosphoribosyltransferase

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