6BO7

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.856 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Design of Plasmodium vivax Hypoxanthine-Guanine Phosphoribosyltransferase Inhibitors as Potential Antimalarial Therapeutics.

Keough, D.T., Rejman, D., Pohl, R., Zbornikova, E., Hockova, D., Croll, T., Edstein, M.D., Birrell, G.W., Chavchich, M., Naesens, L.M.J., Pierens, G.K., Brereton, I.M., Guddat, L.W.

(2018) ACS Chem. Biol. 13: 82-90

  • DOI: 10.1021/acschembio.7b00916
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) are the foremost causative agents of malaria. Due to the development of resistance to current antimalarial medications, new drugs for this parasitic disease need to be discovered. The activity of h ...

    Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) are the foremost causative agents of malaria. Due to the development of resistance to current antimalarial medications, new drugs for this parasitic disease need to be discovered. The activity of hypoxanthine-guanine-[xanthine]-phosphoribosyltransferase, HG[X]PRT, is reported to be essential for the growth of both of these parasites, making it an excellent target for antimalarial drug discovery. Here, we have used rational structure-based methods to design an inhibitor, [3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine, of PvHGPRT and PfHGXPRT that has Ki values of 8 and 7 nM, respectively, for these two enzymes. The crystal structure of PvHGPRT in complex with this compound has been determined to 2.85 Å resolution. The corresponding complex with human HGPRT was also obtained to allow a direct comparison of the binding modes of this compound with the two enzymes. The tetra-(ethyl l-phenylalanine) tetraamide prodrug of this compound was synthesized, and it has an IC50 of 11.7 ± 3.2 μM against Pf lines grown in culture and a CC50 in human A549 cell lines of 102 ± 11 μM, thus giving it a ∼10-fold selectivity index.

    Organizational Affiliation: 

    School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane 4072, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypoxanthine phosphoribosyltransferase
A, B, C, D, E, F, G, H, I, J, K, L
238Plasmodium vivax (strain Salvador I)Mutation(s): 0 
EC: 2.4.2.8
Find proteins for A5K7E9 (Plasmodium vivax (strain Salvador I))
Go to UniProtKB:  A5K7E9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
YPG
Query on YPG
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
[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-yl]-3-oxidanylidene-propyl]phosphonic acid
[3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine
C14 H22 N6 O10 P2
RBYFDIJTTUISNF-MRTMQBJTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.856 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.230 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.784α = 90.00
b = 219.854β = 90.00
c = 254.139γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1030353

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-31
    Type: Database references
  • Version 1.2: 2020-01-08
    Type: Author supporting evidence