8WGM | pdb_00008wgm

Quadruple mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S, N51I+C59R+S108N+I164L) complexed with LA1, NADPH and dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Flexible 2,4-diaminopyrimidine bearing a butyrolactone as Plasmodium falciparum dihydrofolate reductase inhibitors.

Decharuangsilp, S.Arwon, U.Hoarau, M.Vanichtanankul, J.Saeyang, T.Jantra, T.Rattanajak, R.Thiabma, R.Sooksai, N.Kongkasuriyachai, D.Kamchonwongpaisan, S.Yuthavong, Y.

(2024) Bioorg Chem 153: 107789-107789

  • DOI: https://doi.org/10.1016/j.bioorg.2024.107789
  • Primary Citation of Related Structures:  
    8WGM, 8WGN

  • PubMed Abstract: 

    Recently, P218, a new flexible antifolate targeting Plasmodium falciparum dihydrofolate reductase (PfDHFR), has entered its clinical trial with good safety profile and effective Pf infection prevention. However, it carries a free carboxyl terminal, which is hydrophilic and prone to metabolic glucuronidation. Here, a new series of P218 analogues carrying butyrolactone has been synthesized with the purpose of enhancing lipophilicity and minimizing metabolic instability. The inhibition constants against the mutant PfDHFR enzymes are in sub-nanomolar level and the antimalarial activity against antifolate-resistant parasites are in the low micromolar range. The crystal structure of the most potent analogue LA1 bound enzyme complex indicates interaction with multiple residues, including Arg122 and Phe116 in the active site. In vitro log D 7.4 and kinetic solubility confirmed a higher lipophilicity of this butyrolactone series as compared to P218. These outcomes suggest the possibility to further develop butyrolactone derivatives as non-carboxyl antiplasmodial antifolates.


  • 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. Electronic address: sasithorn.dec@biotec.or.th.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthase
A, B
608Plasmodium falciparum VS/1Mutation(s): 4 
Gene Names: 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
WCQ (Subject of Investigation/LOI)
Query on WCQ

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
(3~{E})-3-[[2-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]oxypropoxy]phenyl]methylidene]oxolan-2-one
C20 H24 N4 O4
IYGGQEQHKUVGBG-WYMLVPIESA-N
UMP
Query on UMP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.355α = 90
b = 156.283β = 90
c = 165γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PROTEUM PLUSdata collection
PROTEUM PLUSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science and Technology Development Agency (NSTDA)ThailandP1850116

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-09-25
    Changes: Database references