6M0T

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin derivative (CL-2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design, Synthesis, and Structural Analysis of Cladosporin-Based Inhibitors of Malaria Parasites.

Babbar, P.Das, P.Manickam, Y.Mankad, Y.Yadav, S.Parvez, S.Sharma, A.Reddy, D.S.

(2021) ACS Infect Dis 7: 1777-1794

  • DOI: https://doi.org/10.1021/acsinfecdis.1c00092
  • Primary Citation of Related Structures:  
    6M0T

  • PubMed Abstract: 

    Here we have described a systematic structure activity relationship (SAR) of a set of compounds inspired from cladosporin, a tool compound that targets parasite ( Plasmodium falciparum ) lysyl tRNA synthetase (KRS). Four sets of analogues, synthesized based on point changes in the chemical scaffold of cladosporin and other logical modifications and hybridizations, were assessed using high throughput enzymatic and parasitic assays along with in vitro pharmacokinetics. Co-crystallization of the most potent compound in our series ( CL-2 ) with Pf KRS revealed its structural basis of enzymatic binding and potency. Further, we report that CL-2 has performed better than cladosporin in terms of metabolic stability. It thus represents a new lead for further optimization toward the development of antimalarial drugs. Collectively, along with a lead compound, the series offers insights on how even the slightest chemical modification might play an important role in enhancing or decreasing the potency of a chemical scaffold.


  • Organizational Affiliation

    Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase
A, B, C, D
507Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1350100
EC: 6.1.1.6
UniProt
Find proteins for Q8IDJ8 (Plasmodium falciparum (isolate 3D7))
Explore Q8IDJ8 
Go to UniProtKB:  Q8IDJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IDJ8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 299.56α = 90
b = 59.14β = 90
c = 141.88γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaPR13636

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description