Structures of Mycobacterium tuberculosis 6-oxopurine phosphoribosyltransferase which is a potential target for drug development against this disease

Experimental Data Snapshot

  • Resolution: 2.03 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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First Crystal Structures of Mycobacterium tuberculosis 6-Oxopurine Phosphoribosyltransferase: Complexes with GMP and Pyrophosphate and with Acyclic Nucleoside Phosphonates Whose Prodrugs Have Antituberculosis Activity.

Eng, W.S.Hockova, D.Spacek, P.Janeba, Z.West, N.P.Woods, K.Naesens, L.M.Keough, D.T.Guddat, L.W.

(2015) J Med Chem 58: 4822-4838

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00611
  • Primary Citation of Related Structures:  
    4RHT, 4RHU, 4RHX, 4RHY

  • PubMed Abstract: 

    Human tuberculosis is a chronic infectious disease affecting millions of lives. Because of emerging resistance to current medications, new therapeutic drugs are needed. One potential new target is hypoxanthine-guanine phosphoribosyltransferase (MtHGPRT), a key enzyme of the purine salvage pathway. Here, newly synthesized acyclic nucleoside phosphonates (ANPs) have been shown to be competitive inhibitors of MtHGPRT with Ki values as low as 0.69 μM. Prodrugs of these compounds arrest the growth of a virulent strain of M. tuberculosis with MIC50 values as low as 4.5 μM and possess low cytotoxicity in mammalian cells (CC50 values as high as >300 μM). In addition, the first crystal structures of MtHGPRT (2.03-2.76 Å resolution) have been determined, three of these in complex with novel ANPs and one with GMP and pyrophosphate. These data provide a solid foundation for the further development of ANPs as selective inhibitors of MtHGPRT and as antituberculosis agents.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypoxanthine-guanine phosphoribosyltransferase
A, B, C, D
201Mycobacterium tuberculosis H37RaMutation(s): 0 
Find proteins for P9WHQ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHQ9 
Go to UniProtKB:  P9WHQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHQ9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3QF

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
[2-([2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl]{2-[(2-oxoethyl)(2-phosphonoethyl)amino]ethyl}amino)ethyl]phosphonic acid
C15 H27 N7 O8 P2
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
J [auth B]
L [auth C]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
O [auth D],
P [auth D]
Binding Affinity Annotations 
IDSourceBinding Affinity
3QF Binding MOAD:  4RHX Ki: 1600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.03 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.439α = 90
b = 85.723β = 98.77
c = 88.139γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations