7XI7

Human dihydrofolate reductase complexed with P39


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Insight into Effective Inhibitors' Binding to Toxoplasma gondii Dihydrofolate Reductase Thymidylate Synthase.

Vanichtanankul, J.Yoomuang, A.Taweechai, S.Saeyang, T.Pengon, J.Yuvaniyama, J.Tarnchompoo, B.Yuthavong, Y.Kamchonwongpaisan, S.

(2022) ACS Chem Biol 17: 1691-1702

  • DOI: https://doi.org/10.1021/acschembio.1c00627
  • Primary Citation of Related Structures:  
    7FGW, 7FGX, 7FGY, 7XI7

  • PubMed Abstract: 

    Pyrimethamine (Pyr), a known dihydrofolate reductase (DHFR) inhibitor, has long been used to treat toxoplasmosis caused by Toxoplasma gondii (Tg) infection. However, Pyr is effective only at high doses with associated toxicity to patients, calling for safer alternative treatments. In this study, we investigated a series of Pyr analogues, previously developed as DHFR inhibitors of Plasmodium falciparum bifunctional DHFR-thymidylate synthase (PfDHFR-TS), for their activity against T. gondii DHFR-TS (TgDHFR-TS). Of these, a set of compounds with a substitution at the C 6 position of the pyrimidine ring exhibited high binding affinities (in a low nanomolar range) against TgDHFR-TS and in vitro T. gondii inhibitory activity. Three-dimensional structures of TgDHFR-TS reported here include the ternary complexes with Pyr, P39, or P40. A comparison of these structures showed the minor steric strain between the p -chlorophenyl group of Pyr and Thr83 of TgDHFR-TS. Such a conflict was relieved in the complexes with the two analogues, P39 and P40, explaining their highest binding affinities described herein. Moreover, these structures suggested that the hydrophobic environment in the active-site pocket could be used for drug design to increase the potency and selectivity of antifolate inhibitors. These findings would accelerate the development of new antifolate drugs to treat toxoplasmosis.


  • Organizational Affiliation

    National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase187Homo sapiensMutation(s): 0 
Gene Names: DHFR
EC: 1.5.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P00374 (Homo sapiens)
Explore P00374 
Go to UniProtKB:  P00374
PHAROS:  P00374
GTEx:  ENSG00000228716 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00374
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.1α = 90
b = 83.1β = 90
c = 78.71γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
DIALSdata scaling
MOLREPphasing

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: 2022-06-29
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description