5ZNC

Plasmodium falciparum purine nucleoside phosphorylase in complex with quinine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report



Literature

Identifying purine nucleoside phosphorylase as the target of quinine using cellular thermal shift assay.

Dziekan, J.M.Yu, H.Chen, D.Dai, L.Wirjanata, G.Larsson, A.Prabhu, N.Sobota, R.M.Bozdech, Z.Nordlund, P.

(2019) Sci Transl Med 11

  • DOI: 10.1126/scitranslmed.aau3174
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mechanisms of action (MoAs) have been elusive for most antimalarial drugs in clinical use. Decreasing responsiveness to antimalarial treatments stresses the need for a better resolved understanding of their MoAs and associated resistance mechanisms. ...

    Mechanisms of action (MoAs) have been elusive for most antimalarial drugs in clinical use. Decreasing responsiveness to antimalarial treatments stresses the need for a better resolved understanding of their MoAs and associated resistance mechanisms. In the present work, we implemented the cellular thermal shift assay coupled with mass spectrometry (MS-CETSA) for drug target identification in Plasmodium falciparum , the main causative agent of human malaria. We validated the efficacy of this approach for pyrimethamine, a folic acid antagonist, and E64d, a broad-spectrum cysteine proteinase inhibitor. Subsequently, we applied MS-CETSA to quinine and mefloquine, two important antimalarial drugs with poorly characterized MoAs. Combining studies in the P. falciparum parasite lysate and intact infected red blood cells, we found P. falciparum purine nucleoside phosphorylase (PfPNP) as a common binding target for these two quinoline drugs. Biophysical and structural studies with a recombinant protein further established that both compounds bind within the enzyme's active site. Quinine binds to PfPNP at low nanomolar affinity, suggesting a substantial contribution to its therapeutic effect. Overall, we demonstrated that implementation of MS-CETSA for P. falciparum constitutes a promising strategy to elucidate the MoAs of existing and candidate antimalarial drugs.


    Organizational Affiliation

    Department of Oncology and Pathology, Karolinska Institutet, Stockholm 17177, Sweden.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase
A
245Plasmodium falciparumMutation(s): 0 
Gene Names: PNP
EC: 2.4.2.1
Find proteins for Q8T9Z7 (Plasmodium falciparum)
Go to UniProtKB:  Q8T9Z7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QI9
Query on QI9

Download CCD File 
A
Quinine
C20 H24 N2 O2
LOUPRKONTZGTKE-WZBLMQSHSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.123α = 90
b = 95.123β = 90
c = 47.141γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-04-08 
  • Released Date: 2019-01-16 
  • Deposition Author(s): Chen, D., Nordlund, P.

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release