5TQU | pdb_00005tqu

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5TQU/pdb

• Classification: Ligase/Ligase Inhibitor
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-24 Released: 2017-04-12 
• Deposition Author(s): Barros-Alvarez, X., Hol, W.G.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.241 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

From Cells to Mice to Target: Characterization of NEU-1053 (SB-443342) and Its Analogues for Treatment of Human African Trypanosomiasis.

Devine, W.G., Diaz-Gonzalez, R., Ceballos-Perez, G., Rojas, D., Satoh, T., Tear, W., Ranade, R.M., Barros-Alvarez, X., Hol, W.G., Buckner, F.S., Navarro, M., Pollastri, M.P.

(2017) ACS Infect Dis 3: 225-236

• PubMed: 28110521 
• DOI: https://doi.org/10.1021/acsinfecdis.6b00202
• Primary Citation Related Structures: 
  5TQU


• PubMed Abstract: 
  

  Human African trypanosomiasis is a neglected tropical disease that is lethal if left untreated. Existing therapeutics have limited efficacy and severe associated toxicities. 2-(2-(((3-((1H-Benzo[d]imidazol-2-yl)amino)propyl)amino)methyl)-4,6-dichloro-1H-indol-1-yl)ethan-1-ol (NEU-1053) has recently been identified from a high-throughput screen of >42,000 compounds as a highly potent and fast-acting trypanocidal agent capable of curing a bloodstream infection of Trypanosoma brucei in mice. We have designed a library of analogues to probe the structure-activity relationship and improve the predicted central nervous system (CNS) exposure of NEU-1053. We report the activity of these inhibitors of T. brucei, the efficacy of NEU-1053 in a murine CNS model of infection, and identification of the target of NEU-1053 via X-ray crystallography.

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Organizational Affiliation: 
• Department of Chemistry & Chemical Biology, Northeastern University 360 Huntington Avenue, Boston, Massachusetts, United States.
Instituto de Parasitologia y Biomedicina "Lopez-Neyra", Consejo Superior de Investigaciones Cientificas (CSIC) , Granada 18100, Spain.
Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de los Andes , Mérida, Venezuela.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 123.43 kDa 
• Atom Count: 8,348 
• Modeled Residue Count: 1,026 
• Deposited Residue Count: 1,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionyl-tRNA synthetase, putative	A, B	542	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: Tb10.70.6470 EC: 6.1.1.10
UniProt
Find proteins for Q38C91 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q38C91  Go to UniProtKB:  Q38C91

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I53	D [auth B]	2-[2-[[3-(1~{H}-benzimidazol-2-ylamino)propylamino]methyl]-4,6-bis(chloranyl)indol-1-yl]ethanol C21 H23 Cl2 N5 O JCEOIIIPEPYSSD-UHFFFAOYSA-N
MET	C [auth A]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
SO4	F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.241 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.96	α = 90
b = 106.32	β = 90
c = 207.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
HKL-2000	data reduction
PHASER	phasing
HKL-2000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-12 
Deposition Author(s): Barros-Alvarez, X., Hol, W.G.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	RO1 AI084004 and RO1 AI097177

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Refinement description
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description