5XIH | pdb_00005xih

Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with inhibitor 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5XIH

Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1016/j.str.2017.07.015
  • Primary Citation Related Structures: 
    5XIF, 5XIG, 5XIH, 5XII, 5XIJ, 5XIK, 5XIL, 5XIO, 5XIP, 5XIQ

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 235.47 kDa 
  • Atom Count: 16,426 
  • Modeled Residue Count: 1,901 
  • Deposited Residue Count: 2,000 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prolyl-tRNA synthetase (ProRS)
A, B, C, D
500Toxoplasma gondii ME49Mutation(s): 0 
Gene Names: TGME49_219850
EC: 6.1.1.15
UniProt
Find proteins for S8G8I1 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore S8G8I1 
Go to UniProtKB:  S8G8I1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS8G8I1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP

Query on ANP



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B],
N [auth C],
U [auth D]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
86U

Query on 86U



Download:Ideal Coordinates CCD File
H [auth A],
M [auth B],
Q [auth C],
X [auth D]
6,7-bis(fluoranyl)-3-[3-[(2R)-3-oxidanylidenepiperidin-2-yl]propyl]quinazolin-4-one
C16 H17 F2 N3 O2
AULNDINGOXSVFS-CYBMUJFWSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A]
R [auth C]
S [auth C]
T [auth C]
Y [auth D]
I [auth A],
R [auth C],
S [auth C],
T [auth C],
Y [auth D],
Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
K [auth B]
L [auth B]
O [auth C]
F [auth A],
G [auth A],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
V [auth D],
W [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.71α = 89.71
b = 90.763β = 80.58
c = 93.034γ = 75.77
Software Package:
Software NamePurpose
MxCuBEdata reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data 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: 2018-03-07
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description