7DPI

Plasmodium falciparum cytoplasmic Phenylalanyl-tRNA synthetase in complex with BRD7929


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.294 
  • R-Value Observed: 0.299 

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Ligand Structure Quality Assessment 


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Literature

Inhibition of Plasmodium falciparum phenylalanine tRNA synthetase provides opportunity for antimalarial drug development.

Sharma, M.Mutharasappan, N.Manickam, Y.Harlos, K.Melillo, B.Comer, E.Tabassum, H.Parvez, S.Schreiber, S.L.Sharma, A.

(2022) Structure 30: 962-972.e3

  • DOI: https://doi.org/10.1016/j.str.2022.03.017
  • Primary Citation of Related Structures:  
    7DPI

  • PubMed Abstract: 

    Bicyclic azetidine compounds possess antimalarial activity via targeting of the cytoplasmic Plasmodium falciparum (Pf) protein translation enzyme phenylalanine-tRNA synthetase (cFRS). These drugs kill parasites both in vitro and in vivo, including the blood, liver, and transmission developmental stages. Here we present the co-crystal structure of PfcFRS with a potent inhibitor, the bicyclic azetidine BRD7929. Our studies reveal high-affinity binding of BRD7929 with PfcFRS along with exquisite specificity compared with the human enzyme, leading in turn to potent and selective inhibition of the parasite enzyme. Our co-crystal structure shows that BRD7929 binds in the active site in the α subunit of PfcFRS, where it occupies the amino acid site, an auxiliary site, and partially the ATP site. This structural snapshot of inhibitor-bound PfcFRS thus provides a platform for the structure-guided optimization of novel antimalarial compounds.


  • Organizational Affiliation

    Molecular Medicine, Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India; Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligaseA,
B [auth C]
308Plasmodium falciparumMutation(s): 0 
EC: 6.1.1.20
UniProt
Find proteins for Q8I246 (Plasmodium falciparum (isolate 3D7))
Explore Q8I246 
Go to UniProtKB:  Q8I246
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I246
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanyl-tRNA synthetase beta subunitC [auth B],
D
623Plasmodium falciparumMutation(s): 0 
EC: 6.1.1.20
UniProt
Find proteins for Q8IIW2 (Plasmodium falciparum (isolate 3D7))
Explore Q8IIW2 
Go to UniProtKB:  Q8IIW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IIW2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B79 (Subject of Investigation/LOI)
Query on B79

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
(8R,9S,10S)-10-[(dimethylamino)methyl]-N-(4-methoxyphenyl)-9-[4-(2-phenylethynyl)phenyl]-1,6-diazabicyclo[6.2.0]decane-6-carboxamide
C33 H38 N4 O2
VKRCTZCBMKVHCK-RTOKGZNSSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.294 
  • R-Value Observed: 0.299 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.648α = 90
b = 108.034β = 105.11
c = 140.532γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaPR32713

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references, Refinement description