5GN5

Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with cumarin derivative-17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase ofTrypanosoma brucei brucei.

Balogun, E.O.Inaoka, D.K.Shiba, T.Tsuge, C.May, B.Sato, T.Kido, Y.Nara, T.Aoki, T.Honma, T.Tanaka, A.Inoue, M.Matsuoka, S.Michels, P.A.M.Watanabe, Y.I.Moore, A.L.Harada, S.Kita, K.

(2019) FASEB J 33: 13002-13013

  • DOI: 10.1096/fj.201901342R
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • African trypanosomiasis, sleeping sickness in humans or nagana in animals, is a potentially fatal neglected tropical disease and a threat to 65 million human lives and 100 million small and large livestock animals in sub-Saharan Africa. Available tre ...

    African trypanosomiasis, sleeping sickness in humans or nagana in animals, is a potentially fatal neglected tropical disease and a threat to 65 million human lives and 100 million small and large livestock animals in sub-Saharan Africa. Available treatments for this devastating disease are few and have limited efficacy, prompting the search for new drug candidates. Simultaneous inhibition of the trypanosomal glycerol kinase (TGK) and trypanosomal alternative oxidase (TAO) is considered a validated strategy toward the development of new drugs. Our goal is to develop a TGK-specific inhibitor for coadministration with ascofuranone (AF), the most potent TAO inhibitor. Here, we report on the identification of novel compounds with inhibitory potency against TGK. Importantly, one of these compounds (compound 17) and its derivatives (17a and 17b) killed trypanosomes even in the absence of AF. Inhibition kinetics revealed that derivative 17b is a mixed-type and competitive inhibitor for TGK and TAO, respectively. Structural data revealed the molecular basis of this dual inhibitory action, which, in our opinion, will aid in the successful development of a promising drug to treat trypanosomiasis. Although the EC 50 of compound 17b against trypanosome cells was 1.77 µM, it had no effect on cultured human cells, even at 50 µM.-Balogun, E. O., Inaoka, D. K., Shiba, T., Tsuge, C., May, B., Sato, T., Kido, Y., Nara, T., Aoki, T., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Michels, P. A. M., Watanabe, Y.-I., Moore, A. L., Harada, S., Kita, K. Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase of Trypanosoma brucei brucei.


    Organizational Affiliation

    Department of Molecular Infection Dynamics, Shionogi Global Infectious Disease Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol kinaseA, B, C, D514Trypanosoma brucei gambienseMutation(s): 0 
Gene Names: gk
EC: 2.7.1.30
Find proteins for D3KVM3 (Trypanosoma brucei gambiense)
Explore D3KVM3 
Go to UniProtKB:  D3KVM3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XZ
Query on 6XZ

Download CCD File 
A, B, C, D
4-[[4-(4-methoxyphenyl)piperazin-1-yl]methyl]-7,8-bis(oxidanyl)chromen-2-one
C21 H22 N2 O5
NSCKGTDRMZINFP-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, C, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.03α = 90
b = 63.205β = 90.01
c = 154.848γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japanese Society for the Promotion of ScienceJapan26253025

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references
  • Version 1.2: 2019-12-11
    Changes: Database references