Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum 3D7

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Biochemical and Structural Characterization of Selective Allosteric Inhibitors of the Plasmodium falciparum Drug Target, Prolyl-tRNA-synthetase.

Hewitt, S.N.Dranow, D.M.Horst, B.G.Abendroth, J.A.Forte, B.Hallyburton, I.Jansen, C.Baragana, B.Choi, R.Rivas, K.L.Hulverson, M.A.Dumais, M.Edwards, T.E.Lorimer, D.D.Fairlamb, A.H.Gray, D.W.Read, K.D.Lehane, A.M.Kirk, K.Myler, P.J.Wernimont, A.Walpole, C.Stacy, R.Barrett, L.K.Gilbert, I.H.Van Voorhis, W.C.

(2017) ACS Infect Dis 3: 34-44

  • DOI: https://doi.org/10.1021/acsinfecdis.6b00078
  • Primary Citation of Related Structures:  
    4NCX, 4Q15, 4WI1, 5IFU

  • PubMed Abstract: 

    Plasmodium falciparum (Pf) prolyl-tRNA synthetase (ProRS) is one of the few chemical-genetically validated drug targets for malaria, yet highly selective inhibitors have not been described. In this paper, approximately 40,000 compounds were screened to identify compounds that selectively inhibit PfProRS enzyme activity versus Homo sapiens (Hs) ProRS. X-ray crystallography structures were solved for apo, as well as substrate- and inhibitor-bound forms of PfProRS. We identified two new inhibitors of PfProRS that bind outside the active site. These two allosteric inhibitors showed >100 times specificity for PfProRS compared to HsProRS, demonstrating this class of compounds could overcome the toxicity related to HsProRS inhibition by halofuginone and its analogues. Initial medicinal chemistry was performed on one of the two compounds, guided by the cocrystallography of the compound with PfProRS, and the results can instruct future medicinal chemistry work to optimize these promising new leads for drug development against malaria.

  • Organizational Affiliation

    Departments of Global Health and Biomedical Informatics and Medical Education, University of Washington , Seattle, Washington 98195, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proline--tRNA ligase
A, B
506Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: proRSPFL0670cPRSPF3D7_1213800
Find proteins for Q8I5R7 (Plasmodium falciparum (isolate 3D7))
Explore Q8I5R7 
Go to UniProtKB:  Q8I5R7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I5R7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.96α = 90
b = 91.38β = 129.48
c = 110.84γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-20
    Changes: Data collection, Refinement description