7CTY

Wild type plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS), fragment 263, NADP+, dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.234 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of new non-pyrimidine scaffolds as Plasmodium falciparum DHFR inhibitors by fragment-based screening.

Hoarau, M.Vanichtanankul, J.Srimongkolpithak, N.Vitsupakorn, D.Yuthavong, Y.Kamchonwongpaisan, S.

(2021) J Enzyme Inhib Med Chem 36: 198-206

  • DOI: https://doi.org/10.1080/14756366.2020.1854244
  • Primary Citation of Related Structures:  
    7CTW, 7CTY, 7CTZ

  • PubMed Abstract: 

    In various malaria-endemic regions, the appearance of resistance has precluded the use of pyrimidine-based antifolate drugs. Here, a three-step fragment screening was used to identify new non-pyrimidine Plasmodium falciparum dihydrofolate reductase ( Pf DHFR) inhibitors. Starting from a 1163-fragment commercial library, a two-step differential scanning fluorimetry screen identified 75 primary fragment hits. Subsequent enzyme inhibition assay identified 11 fragments displaying IC 50 in the 28-695 μM range and selectivity for Pf DHFR. In addition to the known pyrimidine, three new anti- Pf DHFR chemotypes were identified. Fragments from each chemotype were successfully co-crystallized with Pf DHFR, revealing a binding in the active site, in the vicinity of catalytic residues, which was confirmed by molecular docking on all fragment hits. Finally, comparison with similar non-hit fragments provides preliminary input on available growth vectors for future drug development.


  • Organizational Affiliation

    National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthase
A, B
608Plasmodium falciparumMutation(s): 0 
Gene Names: DHFR-TSdhfr-ts
UniProt
Find proteins for Q8I1R6 (Plasmodium falciparum (isolate 3D7))
Explore Q8I1R6 
Go to UniProtKB:  Q8I1R6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I1R6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.143α = 90
b = 154.088β = 90
c = 163.598γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata scaling
Cootmodel building
PROTEUM PLUSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Center for Genetic Engineering and Biotechnology (Thailand)Thailand--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Data collection
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description