8TPY

Structure of human hypoxanthine guanine phosphoribzosyltransferase in complex with [2S,4R] 4-Guanin-9-yl-2-hydroxymethyl-1-N-(3-phosphonopropionyl)pyrrolidine

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2023-08-06 Released: 2024-05-08 
  • Deposition Author(s): Guddat, L.W.
  • Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Development of Prolinol Containing Inhibitors of Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase: Rational Structure-Based Drug Design.

Keough, D.T.Petrova, M.King, G.Kratochvil, M.Pohl, R.Dolezelova, E.Zikova, A.Guddat, L.W.Rejman, D.

(2024) J Med Chem 67: 7158-7175

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00021
  • Primary Citation of Related Structures:  
    8TPV, 8TPY, 8TR1, 8TS4

  • PubMed Abstract: 

    Inhibition of hypoxanthine-guanine-xanthine phosphoribosyltransferase activity decreases the pool of 6-oxo and 6-amino purine nucleoside monophosphates required for DNA and RNA synthesis, resulting in a reduction in cell growth. Therefore, inhibitors of this enzyme have potential to control infections, caused by Plasmodium falciparum and Plasmodium vivax , Trypanosoma brucei , Mycobacterium tuberculosis , and Helicobacter pylori . Five compounds synthesized here that contain a purine base covalently linked by a prolinol group to one or two phosphonate groups have K i values ranging from 3 nM to >10 μM, depending on the structure of the inhibitor and the biological origin of the enzyme. X-ray crystal structures show that, on binding, these prolinol-containing inhibitors stimulated the movement of active site loops in the enzyme. Against TBr in cell culture, a prodrug exhibited an EC 50 of 10 μM. Thus, these compounds are excellent candidates for further development as drug leads against infectious diseases as well as being potential anticancer agents.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypoxanthine-guanine phosphoribosyltransferase
A, B, C, D
218Homo 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: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.461α = 90
b = 93.42β = 90
c = 129.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-05-08 
  • Deposition Author(s): Guddat, L.W.

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

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references