Crystal structure of hte Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain complex with a post-transfer editing analogue of norvaline (Nv2AA)

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Cryptosporidium and Toxoplasma Parasites are Inhibited by a Benzoxaborole Targeting Leucyl-tRNA Synthetase.

Palencia, A.Liu, R.Lukarska, M.Gut, J.Bougdour, A.Touquet, B.Wang, E.Li, X.Alley, M.R.K.Freund, Y.R.Rosenthal, P.J.Hakimi, M.Cusack, S.

(2016) Antimicrob Agents Chemother 60: 5817

  • DOI: https://doi.org/10.1128/AAC.00873-16
  • Primary Citation of Related Structures:  
    5FOG, 5FOL, 5FOM, 5FON

  • PubMed Abstract: 

    The apicomplexan parasites Cryptosporidium and Toxoplasma are serious threats to human health. Cryptosporidiosis is a severe diarrheal disease in malnourished children and immunocompromised individuals, with the only FDA-approved drug treatment currently being nitazoxanide. The existing therapies for toxoplasmosis, an important pathology in immunocompromised individuals and pregnant women, also have serious limitations. With the aim of developing alternative therapeutic options to address these health problems, we tested a number of benzoxaboroles, boron-containing compounds shown to be active against various infectious agents, for inhibition of the growth of Cryptosporidium parasites in mammalian cells. A 3-aminomethyl benzoxaborole, AN6426, with activity in the micromolar range and with activity comparable to that of nitazoxanide, was identified and further characterized using biophysical measurements of affinity and crystal structures of complexes with the editing domain of Cryptosporidium leucyl-tRNA synthetase (LeuRS). The same compound was shown to be active against Toxoplasma parasites, with the activity being enhanced in the presence of norvaline, an amino acid that can be mischarged by LeuRS. Our observations are consistent with AN6426 inhibiting protein synthesis in both Cryptosporidium and Toxoplasma by forming a covalent adduct with tRNA(Leu) in the LeuRS editing active site and suggest that further exploitation of the benzoxaborole scaffold is a valid strategy to develop novel, much needed antiparasitic agents.

  • Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France, and University Grenoble Alpes-CNRS-EMBL International Unit (UMI 3265) for Virus Host-Cell Interactions, UMI 3265, Grenoble, France Institute for Advanced Biosciences, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France andres.palencia@univ-grenoble-alpes.fr cusack@embl.fr.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
292Cryptosporidium muris RN66Mutation(s): 0 
Find proteins for B6AA20 (Cryptosporidium muris (strain RN66))
Explore B6AA20 
Go to UniProtKB:  B6AA20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6AA20
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on VRT

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
M [auth D]
C15 H23 N7 O4
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
K [auth C]
C2 H6 O2
Query on K

Download Ideal Coordinates CCD File 
L [auth C],
N [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.73α = 90
b = 107.73β = 90
c = 309.51γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2016-10-05
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description