5XIJ

Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with Inhibitor 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Targeting Prolyl-tRNA Synthetase to Accelerate Drug Discovery against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis

Jain, V.Yogavel, M.Kikuchi, H.Oshima, Y.Hariguchi, N.Matsumoto, M.Goel, P.Touquet, B.Jumani, R.S.Tacchini-Cottier, F.Harlos, K.Huston, C.D.Hakimi, M.A.Sharma, A.

(2017) Structure 25: 1495-1505.e6

  • DOI: 10.1016/j.str.2017.07.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Developing anti-parasitic lead compounds that act on key vulnerabilities are necessary for new anti-infectives. Malaria, leishmaniasis, toxoplasmosis, cryptosporidiosis and coccidiosis together kill >500,000 humans annually. Their causative parasites ...

    Developing anti-parasitic lead compounds that act on key vulnerabilities are necessary for new anti-infectives. Malaria, leishmaniasis, toxoplasmosis, cryptosporidiosis and coccidiosis together kill >500,000 humans annually. Their causative parasites Plasmodium, Leishmania, Toxoplasma, Cryptosporidium and Eimeria display high conservation in many housekeeping genes, suggesting that these parasites can be attacked by targeting invariant essential proteins. Here, we describe selective and potent inhibition of prolyl-tRNA synthetases (PRSs) from the above parasites using a series of quinazolinone-scaffold compounds. Our PRS-drug co-crystal structures reveal remarkable active site plasticity that accommodates diversely substituted compounds, an enzymatic feature that can be leveraged for refining drug-like properties of quinazolinones on a per parasite basis. A compound we termed In-5 exhibited a unique double conformation, enhanced drug-like properties, and cleared malaria in mice. It thus represents a new lead for optimization. Collectively, our data offer insights into the structure-guided optimization of quinazolinone-based compounds for drug development against multiple human eukaryotic pathogens.


    Organizational Affiliation

    Molecular Medicine - Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prolyl-tRNA synthetase (ProRS)
A, B, C, D
500Toxoplasma gondii (strain ATCC 50611 / Me49)Mutation(s): 0 
Find proteins for S8G8I1 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Go to UniProtKB:  S8G8I1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
873
Query on 873

Download SDF File 
Download CCD File 
A, B, C, D
3-[(2R)-2-oxidanyl-3-[(2R,3R)-3-oxidanylpiperidin-2-yl]propyl]quinazolin-4-one
C16 H21 N3 O3
QGNITGLZWOVTKR-KCPJHIHWSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 76.848α = 89.81
b = 93.158β = 104.52
c = 91.012γ = 99.60
Software Package:
Software NamePurpose
MxCuBEdata reduction
HKL-2000data scaling
REFMACrefinement
HKLdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release