5IFU

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Glyburide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/acsinfecdis.6b00078
  • Primary Citation of Related Structures:  4NCX, 4Q15, 4WI1

  • 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 ...

    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

    Center for Emerging and Reemerging Infectious Disease (CERID), University of Washington , 750 Republican Street, Seattle, Washington 98109, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proline--tRNA ligase
A, B
506Plasmodium falciparumGene Names: proRS
EC: 6.1.1.15
Find proteins for Q8I5R7 (Plasmodium falciparum)
Go to UniProtKB:  Q8I5R7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
GBM
Query on GBM

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Download CCD File 
A, B
5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
Glibenclamide, Glyburide
C23 H28 Cl N3 O5 S
ZNNLBTZKUZBEKO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.185 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 138.310α = 90.00
b = 138.310β = 90.00
c = 156.660γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references