6QU3

Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb360


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Fast acting allosteric phosphofructokinase inhibitors block trypanosome glycolysis and cure acute African trypanosomiasis in mice.

McNae, I.W.Kinkead, J.Malik, D.Yen, L.H.Walker, M.K.Swain, C.Webster, S.P.Gray, N.Fernandes, P.M.Myburgh, E.Blackburn, E.A.Ritchie, R.Austin, C.Wear, M.A.Highton, A.J.Keats, A.J.Vong, A.Dornan, J.Mottram, J.C.Michels, P.A.M.Pettit, S.Walkinshaw, M.D.

(2021) Nat Commun 12: 1052-1052

  • DOI: https://doi.org/10.1038/s41467-021-21273-6
  • Primary Citation of Related Structures:  
    6QU3, 6QU4, 6QU5

  • PubMed Abstract: 

    The parasitic protist Trypanosoma brucei is the causative agent of Human African Trypanosomiasis, also known as sleeping sickness. The parasite enters the blood via the bite of the tsetse fly where it is wholly reliant on glycolysis for the production of ATP. Glycolytic enzymes have been regarded as challenging drug targets because of their highly conserved active sites and phosphorylated substrates. We describe the development of novel small molecule allosteric inhibitors of trypanosome phosphofructokinase (PFK) that block the glycolytic pathway resulting in very fast parasite kill times with no inhibition of human PFKs. The compounds cross the blood brain barrier and single day oral dosing cures parasitaemia in a stage 1 animal model of human African trypanosomiasis. This study demonstrates that it is possible to target glycolysis and additionally shows how differences in allosteric mechanisms may allow the development of species-specific inhibitors to tackle a range of proliferative or infectious diseases.


  • Organizational Affiliation

    Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent 6-phosphofructokinase
A, B, C, D
507Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: pfk
EC: 2.7.1.11
UniProt
Find proteins for O15648 (Trypanosoma brucei brucei)
Explore O15648 
Go to UniProtKB:  O15648
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15648
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JJ5
Query on JJ5

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
O [auth D]
1-[(3,4-dichlorophenyl)methyl]-7~{H}-pyrrolo[3,2-c]pyridin-4-one
C14 H10 Cl2 N2 O
GULZPFKZRPRXPF-UHFFFAOYSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
P [auth D]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
SEP
Query on SEP

Download Ideal Coordinates CCD File 
H [auth A]PHOSPHOSERINE
C3 H8 N O6 P
BZQFBWGGLXLEPQ-REOHCLBHSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
N [auth C],
Q [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.154α = 90
b = 150.561β = 90
c = 83.993γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description