6APU

Crystal structure of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltranferase in complex with (2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](3-aminopropyl)amino}ethyl)phosphonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Evaluation of the Trypanosoma brucei 6-oxopurine salvage pathway as a potential target for drug discovery.

Dolezelova, E.Teran, D.Gahura, O.Kotrbova, Z.Prochazkova, M.Keough, D.Spacek, P.Hockova, D.Guddat, L.Zikova, A.

(2018) PLoS Negl Trop Dis 12: e0006301-e0006301

  • DOI: https://doi.org/10.1371/journal.pntd.0006301
  • Primary Citation of Related Structures:  
    6APS, 6APT, 6APU, 6APV, 6AQO, 6AR9

  • PubMed Abstract: 

    Due to toxicity and compliance issues and the emergence of resistance to current medications new drugs for the treatment of Human African Trypanosomiasis are needed. A potential approach to developing novel anti-trypanosomal drugs is by inhibition of the 6-oxopurine salvage pathways which synthesise the nucleoside monophosphates required for DNA/RNA production. This is in view of the fact that trypanosomes lack the machinery for de novo synthesis of the purine ring. To provide validation for this approach as a drug target, we have RNAi silenced the three 6-oxopurine phosphoribosyltransferase (PRTase) isoforms in the infectious stage of Trypanosoma brucei demonstrating that the combined activity of these enzymes is critical for the parasites' viability. Furthermore, we have determined crystal structures of two of these isoforms in complex with several acyclic nucleoside phosphonates (ANPs), a class of compound previously shown to inhibit 6-oxopurine PRTases from several species including Plasmodium falciparum. The most potent of these compounds have Ki values as low as 60 nM, and IC50 values in cell based assays as low as 4 μM. This data provides a solid platform for further investigations into the use of this pathway as a target for anti-trypanosomal drug discovery.


  • Organizational Affiliation

    Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, České Budějovice, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypoxanthine-guanine phosphoribosyltransferase
A, B
216Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: HGPRT
EC: 2.4.2.8
UniProt
Find proteins for Q07010 (Trypanosoma brucei brucei)
Explore Q07010 
Go to UniProtKB:  Q07010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07010
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3L6
Query on 3L6

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B]
(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](3-aminopropyl)amino}ethyl)phosphonic acid
C12 H22 N7 O4 P
JXSWXCFQTAYPAJ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
K [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.883α = 90
b = 108.89β = 90
c = 44.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description