5J59 | pdb_00005j59

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (Chem 1893)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.207 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted N93Click on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Structure-guided design of novel Trypanosoma brucei Methionyl-tRNA synthetase inhibitors.

Huang, W.Zhang, Z.Barros-Alvarez, X.Koh, C.Y.Ranade, R.M.Gillespie, J.R.Creason, S.A.Shibata, S.Verlinde, C.L.Hol, W.G.Buckner, F.S.Fan, E.

(2016) Eur J Med Chem 124: 1081-1092

  • DOI: https://doi.org/10.1016/j.ejmech.2016.10.024
  • Primary Citation of Related Structures:  
    5J58, 5J59, 5J5A

  • PubMed Abstract: 

    A screening hit 1 against Trypanosoma brucei methionyl-tRNA synthetase was optimized using a structure-guided approach. The optimization led to the identification of two novel series of potent inhibitors, the cyclic linker and linear linker series. Compounds of both series were potent in a T. brucei growth inhibition assay while showing low toxicity to mammalian cells. The best compound of each series, 16 and 31, exhibited EC 50 s of 39 and 22 nM, respectively. Compounds 16 and 31 also exhibited promising PK properties after oral dosing in mice. Moreover, compound 31 had moderately good brain permeability, with a brain/plasma ratio of 0.27 at 60 min after IP injection. This study provides new lead compounds for arriving at new treatments of human African trypanosomiasis (HAT).


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionyl-tRNA synthetase, putative
A, B
542Trypanosoma brucei brucei TREU927Mutation(s): 6 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38C91
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.31α = 90
b = 106.4β = 90
c = 207.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted N93Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Refinement description