9KUN | pdb_00009kun

Crystal structure of ligand-free trypanosome alternative oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.258 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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Literature

Uncovering the Unusual Inhibition Mechanism of a Trypanosome Alternative Oxidase Inhibitor Displaying Broad-Spectrum Activity against African Animal Trypanosomes.

Ebiloma, G.U.Balogun, E.O.Arai, N.Otani, M.Baldassarri, C.Alhejely, A.Cueto-Diaz, E.De Koning, H.P.Dardonville, C.Shiba, T.

(2025) J Med Chem 68: 17155-17174

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00631
  • Primary Citation of Related Structures:  
    9KUN, 9M2A

  • PubMed Abstract: 

    The glucose-dependent respiration of bloodstream forms of the parasite Trypanosoma brucei depends on an unusual and essential mitochondrial electron-transport system, consisting of glycerol-3-phosphate dehydrogenase and the trypanosome alternative oxidase (TAO). We report here the discovery of an allosteric inhibitor of TAO that displays highly potent activity (EC 50 values in the range 1-20 nM) against the important veterinary pathogens T. b. brucei , Trypanosoma evansi , Trypanosoma equiperdum , and Trypanosoma congolense , i.e., >5-fold greater potency than the standard drugs. The methylene-linked 2-methyl-4-hydroxybenzoate 2-pyridinyldiphenylphosphonium derivative ( 1 ) was the best inhibitor of recombinant TAO (IC 50 = 1.3 nM) via a noncompetitive/allosteric mechanism ( K i = 3.46 nM). Remarkably, X-ray crystallography showed that 1 was bound to a site of TAO ∼25 Å from the catalytic pocket. Although 1 demonstrated good safety toward mammalian cells in vitro (selectivity index >2300), it did not fully clear parasitemia in experimental animals, attributable to a high hepatic clearance.


  • Organizational Affiliation
    • School of Science, Engineering & Environment, University of Salford, Manchester M5 4NT, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alternative oxidase, mitochondrial
A, B, C, D
271Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: AOX
EC: 1
UniProt
Find proteins for Q26710 (Trypanosoma brucei brucei)
Explore Q26710 
Go to UniProtKB:  Q26710
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ26710
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BOG (Subject of Investigation/LOI)
Query on BOG

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth B]
J [auth B]
M [auth C]
E [auth A],
F [auth A],
I [auth B],
J [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
OH (Subject of Investigation/LOI)
Query on OH

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C],
R [auth D]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.258 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.416α = 90
b = 223.007β = 115.28
c = 62.858γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release