6QU4 | pdb_00006qu4

Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb405

• PDB DOI: https://doi.org/10.2210/pdb6QU4/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma brucei brucei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-26 Released: 2020-03-18 
• Deposition Author(s): McNae, I.W., Dornan, J., Walkinshaw, M.D.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

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

• PubMed: 33594070 
• DOI: https://doi.org/10.1038/s41467-021-21273-6
• Primary Citation 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.

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Organizational Affiliation: 
• Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK.
Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK.
Cambridge MedChem Consulting, Cambridge, UK.
Centre for Cardiovascular Science, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK.
York Biomedical Research Institute, Hull York Medical School, University of York, York, UK.
Institute of Infection Immunity and Inflammation, College of Medical Veterinary Life-Sciences, University of Glasgow, Glasgow, UK.
York Biomedical Research Institute, Department of Biology, University of York, York, UK.
Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK. [e-mail].
Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 225.65 kDa 
• Atom Count: 14,089 
• Modeled Residue Count: 1,795 
• Deposited Residue Count: 2,028 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent 6-phosphofructokinase	A, B, C, D	507	Trypanosoma brucei brucei	Mutation(s): 0  Gene Names: pfk EC: 2.7.1.11
UniProt
Find proteins for O15648 (Trypanosoma brucei brucei) Explore O15648  Go to UniProtKB:  O15648

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JJ2	E [auth A], H [auth B], K [auth C], N [auth D]	1-[(3,4-dichlorophenyl)methyl]-5-[2-(dimethylamino)ethyl]pyrrolo[3,2-c]pyridin-4-one C18 H19 Cl2 N3 O PJFCDRDJURVQPH-UHFFFAOYSA-N
CIT	F [auth A], I [auth B], L [auth C], O [auth D]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	G [auth A], J [auth B], M [auth C], P [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.584	α = 90
b = 165.088	β = 90
c = 83.384	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): McNae, I.W., Dornan, J., Walkinshaw, M.D.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• 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