7EVU

Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with HFG and JE6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Double drugging of prolyl-tRNA synthetase provides a new paradigm for anti-infective drug development.

Manickam, Y.Malhotra, N.Mishra, S.Babbar, P.Dusane, A.Laleu, B.Bellini, V.Hakimi, M.A.Bougdour, A.Sharma, A.

(2022) PLoS Pathog 18: e1010363-e1010363

  • DOI: https://doi.org/10.1371/journal.ppat.1010363
  • Primary Citation of Related Structures:  
    7EVU, 7EVV

  • PubMed Abstract: 

    Toxoplasmosis is caused by Toxoplasma gondii and in immunocompromised patients it may lead to seizures, encephalitis or death. The conserved enzyme prolyl-tRNA synthetase (PRS) is a validated druggable target in Toxoplasma gondii but the traditional 'single target-single drug' approach has its caveats. Here, we describe two potent inhibitors namely halofuginone (HFG) and a novel ATP mimetic (L95) that bind to Toxoplasma gondii PRS simultaneously at different neighbouring sites to cover all three of the enzyme substrate subsites. HFG and L95 act as one triple-site inhibitor in tandem and form an unusual ternary complex wherein HFG occupies the 3'-end of tRNA and the L-proline (L-pro) binding sites while L95 occupies the ATP pocket. These inhibitors exhibit nanomolar IC50 and EC50 values independently, and when given together reveal an additive mode of action in parasite inhibition assays. This work validates a novel approach and lays a structural framework for further drug development based on simultaneous targeting of multiple pockets to inhibit druggable proteins.


  • Organizational Affiliation

    Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prolyl-tRNA synthetase (ProRS)
A, B
500Toxoplasma gondiiMutation(s): 0 
Gene Names: TGRH88_057780
UniProt
Find proteins for A0A7J6JUK2 (Toxoplasma gondii)
Explore A0A7J6JUK2 
Go to UniProtKB:  A0A7J6JUK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7J6JUK2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HFG (Subject of Investigation/LOI)
Query on HFG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one
C16 H17 Br Cl N3 O3
LVASCWIMLIKXLA-CABCVRRESA-N
JE6 (Subject of Investigation/LOI)
Query on JE6

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide
C22 H22 N4 O2
FLWLQSFDWRRFDA-JOCHJYFZSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
G [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.754α = 92.16
b = 70.83β = 101.44
c = 76.036γ = 115.61
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description