7BT5

Crystal structure of plasmodium LysRS complexing with an antitumor compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Inhibition of Plasmodium falciparum Lysyl-tRNA synthetase via an anaplastic lymphoma kinase inhibitor.

Zhou, J.Huang, Z.Zheng, L.Hei, Z.Wang, Z.Yu, B.Jiang, L.Wang, J.Fang, P.

(2020) Nucleic Acids Res 48: 11566-11576

  • DOI: https://doi.org/10.1093/nar/gkaa862
  • Primary Citation of Related Structures:  
    7BT5

  • PubMed Abstract: 

    Aminoacyl-tRNA synthetases are attractive targets for the development of antibacterial, antifungal, antiparasitic agents and for the treatment of other human diseases. Lysyl-tRNA synthetase (LysRS) from this family has been validated as a promising target for the development of antimalarial drugs. Here, we developed a high-throughput compatible assay and screened 1215 bioactive compounds to identify Plasmodium falciparum cytoplasmic LysRS (PfLysRS) inhibitor. ASP3026, an anaplastic lymphoma kinase inhibitor that was used in clinical trials for the treatment of B-cell lymphoma and solid tumors, was identified as a novel PfLysRS inhibitor. ASP3026 suppresses the enzymatic activity of PfLysRS at nanomolar potency, which is >380-fold more effective than inhibition of the human counterpart. In addition, the compound suppressed blood-stage P. falciparum growth. To understand the molecular mechanism of inhibition by ASP3026, we further solved the cocrystal structure of PfLysRS-ASP3026 at a resolution of 2.49 Å, providing clues for further optimization of the compound. Finally, primary structure-activity relationship analyses indicated that the inhibition of PfLysRS by ASP3026 is highly structure specific. This work not only provides a new chemical scaffold with good druggability for antimalarial development but also highlights the potential for repurposing kinase-inhibiting drugs to tRNA synthetase inhibitors to treat human diseases.


  • Organizational Affiliation

    State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase
A, B
516Plasmodium falciparumMutation(s): 0 
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: 2.49 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.749α = 90
b = 166.401β = 90
c = 70.918γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21778067
National Natural Science Foundation of China (NSFC)China21778064
National Natural Science Foundation of China (NSFC)China21977107
National Natural Science Foundation of China (NSFC)China21977108

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2020-12-02
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description