4WI1

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

Nakazawa Hewitt, S.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.S.Stacy, R.Barrett, L.K.Gilbert, I.H.Van Voorhis, W.C.

(2016) ACS Infect Dis 

  • DOI: 10.1021/acsinfecdis.6b00078
  • Structures With Same Primary Citation

  • 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

    Seattle Structural Genomics Center for Infectious Disease (SSGCID) , Seattle, Washington 98109, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proline--tRNA ligase
A, B
506Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: proRSPFL0670c
EC: 6.1.1.15
Find proteins for Q8I5R7 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I5R7
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3O6
Query on 3O6

Download CCD File 
A, B
1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea
C18 H13 F5 N4 O
BJWCFFZTMUBHLH-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download CCD File 
A, B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3O6IC50:  74000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.18α = 90
b = 91.34β = 129.53
c = 110.91γ = 90
Software Package:
Software NamePurpose
ARPmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Advisory, Derived calculations, Refinement description