8S0V | pdb_00008s0v

Crystal structure of Cryptosporidium parvum - Trypanosoma cruzi mutant lysyl tRNA synthetase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.208 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.193 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Antitrypanosomal quinazolines targeting lysyl-tRNA synthetase show partial efficacy in a mouse model of acute Chagas disease.

Tulloch, L.B.Tawell, H.Taylor, A.E.Lima, M.L.Dawson, A.Carvalho, S.Wall, R.J.Corpas-Lopez, V.Dey, G.Duggan, J.Magalhaes, L.G.Torrie, L.S.Frame, L.Robinson, D.Patterson, S.Tinti, M.Weaver, G.W.Robinson, W.J.Cal, M.Kaiser, M.Maser, P.Sjo, P.Perry, B.Kelly, J.M.Francisco, A.F.Bhambra, A.S.Wyllie, S.

(2025) Sci Transl Med 17: eadu4564-eadu4564

  • DOI: https://doi.org/10.1126/scitranslmed.adu4564
  • Primary Citation of Related Structures:  
    8S0V

  • PubMed Abstract: 

    The protozoan parasite Trypanosoma cruzi causes Chagas disease, which is among the deadliest parasitic infections in Latin America. Current therapies are toxic and lack efficacy against the chronic stage of infection; thus, new drugs are urgently needed. Here, we describe a previously unidentified series of quinazoline compounds with potential against Trypanosoma cruzi and the related trypanosomatid parasites Trypanosoma brucei and Leishmania donovani . We demonstrated partial efficacy of a lead quinazoline compound in a mouse model of acute Chagas disease. Mechanism of action studies using several orthogonal approaches showed that this quinazoline compound series targeted the ATP-binding pocket of T. cruzi lysyl-tRNA synthetase 1 (KRS1). A high-resolution crystal structure of KRS1 bound to the drug indicated binding interactions that led to KRS1 inhibition. Our study identified KRS1 as a druggable target for treating T. cruzi infection in a mouse model. This quinazoline series shows potential for treating Chagas disease but will require further development to become a future treatment for this neglected disease.


  • Organizational Affiliation

    Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase
A, B
536Cryptosporidium parvum IowaMutation(s): 4 
Gene Names: cgd4_2370
EC: 6.1.1.6
UniProt
Find proteins for Q5CR27 (Cryptosporidium parvum (strain Iowa II))
Explore Q5CR27 
Go to UniProtKB:  Q5CR27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5CR27
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H4X (Subject of Investigation/LOI)
Query on A1H4X

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
~{N}7-cyclopentyl-5,6,8-tris(fluoranyl)-2-methyl-quinazoline-4,7-diamine
C14 H15 F3 N4
HQXRSISDOUCDLI-UHFFFAOYSA-N
LYS
Query on LYS

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
TRS
Query on TRS

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
M [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.208 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.193 (DCC) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.136α = 90
b = 116.697β = 90
c = 142.882γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom218448/Z/19/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 2.0: 2025-07-09
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2025-07-16
    Changes: Database references