7SAN

Crystal structure of human hypoxanthine guanine phosphoribzosyltransferase in complex with (4S,7S)-7-hydroxy-4-((guanin-9-yl)methyl)-2,5-dioxaheptan-1,7-diphosphonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 

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Literature

Stereo-Defined Acyclic Nucleoside Phosphonates are Selective and Potent Inhibitors of Parasite 6-Oxopurine Phosphoribosyltransferases.

Klejch, T.Keough, D.T.King, G.Dolezelova, E.Cesnek, M.Budesinsky, M.Zikova, A.Janeba, Z.Guddat, L.W.Hockova, D.

(2022) J Med Chem 65: 4030-4057

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01881
  • Primary Citation of Related Structures:  
    7SAN, 7SB7, 7SCR

  • PubMed Abstract: 

    Pathogens such as Plasmodium and Trypanosoma spp. are unable to synthesize purine nucleobases. They rely on the salvage of these purines and their nucleosides from the host cell to synthesize the purine nucleotides required for DNA/RNA production. The key enzymes in this pathway are purine phosphoribosyltransferases (PRTs). Here, we synthesized 16 novel acyclic nucleoside phosphonates, 12 with a chiral center at C-2', and eight bearing a second chiral center at C-6'. Of these, bisphosphonate ( S , S )- 48 is the most potent inhibitor of the Plasmodium falciparum and P. vivax 6-oxopurine PRTs and the most potent inhibitor of two Trypanosoma brucei ( Tbr ) 6-oxopurine PRTs yet discovered, with K i values as low as 2 nM. Crystal structures of ( S , S )- 48 in complex with human and Tbr 6-oxopurine PRTs show that the inhibitor binds to the enzymes in different conformations, providing an explanation for its potency and selectivity ( i.e. , 35-fold in favor of the parasite enzymes).


  • Organizational Affiliation

    The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 CZ-16000, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypoxanthine-guanine phosphoribosyltransferase
A, B, C, D
217Homo sapiensMutation(s): 3 
Gene Names: HPRT1HPRT
EC: 2.4.2.8
UniProt & NIH Common Fund Data Resources
Find proteins for P00492 (Homo sapiens)
Explore P00492 
Go to UniProtKB:  P00492
PHAROS:  P00492
GTEx:  ENSG00000165704 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00492
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.818α = 90
b = 93.743β = 90
c = 130.46γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
BLU-MAXdata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1147368

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description