Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 339.09 kDa 
• Atom Count: 21877 
• Modelled Residue Count: 2612 
• Deposited Residue Count: 2856 
• Unique protein chains: 1

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

• PDB DOI: 10.2210/pdb6BO7/pdb
• Entry: 6BO7 supersedes: 5HHU

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-18 Released: 2017-12-13 
• Deposition Author(s): Guddat, L.W., Keough, D.T., Rejman, D.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.256 
• R-Value Work: 0.230 
• R-Value Observed: 0.231 

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

• PubMed: 29161011 
• DOI: 10.1021/acschembio.7b00916
• Primary Citation of Related Structures:  
  5HIA, 6BNJ, 6BO7


• 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 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 K _i 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 IC ₅₀ of 11.7 ± 3.2 μM against Pf lines grown in culture and a CC ₅₀ in human A549 cell lines of 102 ± 11 μM, thus giving it a ∼10-fold selectivity index.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxanthine phosphoribosyltransferase	A, B, C, D, E, F, G, H, I, J, K, L	238	Plasmodium vivax	Mutation(s): 0  Gene Names: PVC01_080017300, PVP01_0812500, PVT01_080017400 EC: 2.4.2.8
UniProt
Find proteins for A5K7E9 (Plasmodium vivax (strain Salvador I)) Explore A5K7E9  Go to UniProtKB:  A5K7E9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YPG	BA [auth E], EA [auth F], HA [auth G], KA [auth H], NA [auth I], O [auth A], QA [auth J], R [auth B], U [auth C], UA [auth K], X [auth D], YA [auth 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-y l]-3-oxidanylidene-propyl]phosphonic acid C14 H22 N6 O10 P2 RBYFDIJTTUISNF-MRTMQBJTSA-N
MG	AA [auth E], CA [auth F], DA [auth F], FA [auth G], GA [auth G], IA [auth H], JA [auth H], LA [auth I], M [auth A], MA [auth I], N [auth A], OA [auth J], P [auth B], PA [auth J], Q [auth B], RA [auth K], S [auth C], SA [auth K], T [auth C], TA [auth K], V [auth D], VA [auth L], W [auth D], WA [auth L], XA [auth L], Y [auth E], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.256 
• R-Value Work: 0.230 
• R-Value Observed: 0.231 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.784	α = 90
b = 219.854	β = 90
c = 254.139	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-11-18 
• Released Date: 2017-12-13 
Deposition Author(s): Guddat, L.W., Keough, D.T., Rejman, D.
• This entry supersedes: 5HHU

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1030353

Revision History  

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