7CTW | pdb_00007ctw

Wild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with fragment 820, NADPH, dUMP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 
    0.295 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.204 (DCC) 

Starting Model: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 145.45 kDa 
  • Atom Count: 8,977 
  • Modeled Residue Count: 1,057 
  • Deposited Residue Count: 1,216 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthase
A, B
608Plasmodium falciparumMutation(s): 0 
Gene Names: DHFR-TS, dhfr-ts
EC: 2.1.1.45 (UniProt), 1.5.1.3 (UniProt)
UniProt
Find proteins for P13922 (Plasmodium falciparum (isolate K1 / Thailand))
Explore P13922 
Go to UniProtKB:  P13922
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13922
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free:  0.295 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.204 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.185α = 90
b = 154.73β = 90
c = 163.816γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
Cootmodel building

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Center for Genetic Engineering and Biotechnology (Thailand)ThailandP1850116

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    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