6LH9

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with compound 46 and NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Flexible diaminodihydrotriazine inhibitors of Plasmodium falciparum dihydrofolate reductase: Binding strengths, modes of binding and their antimalarial activities.

Kamchonwongpaisan, S.Charoensetakul, N.Srisuwannaket, C.Taweechai, S.Rattanajak, R.Vanichtanankul, J.Vitsupakorn, D.Arwon, U.Thongpanchang, C.Tarnchompoo, B.Vilaivan, T.Yuthavong, Y.

(2020) Eur J Med Chem 195: 112263-112263

  • DOI: 10.1016/j.ejmech.2020.112263
  • Primary Citation of Related Structures:  
    6LEZ, 6LEV, 6LEU, 6LHJ, 6LHI, 6LH9

  • PubMed Abstract: 
  • A series of flexible diaminodihydrotriazines or cycloguanil (Cyc) analogues are developed and shown to inhibit P. falciparum dihydrofolate reductase (PfDHFR) of the wild type or those carrying either single (S108N), double (C59R + S108N and A16V + S108T), triple (N51I + C59R + S108N and C59R + S108N + I164L) or quadruple (N51I + C59R + S108N + I164L) mutations, responsible for antifolate resistance ...

    A series of flexible diaminodihydrotriazines or cycloguanil (Cyc) analogues are developed and shown to inhibit P. falciparum dihydrofolate reductase (PfDHFR) of the wild type or those carrying either single (S108N), double (C59R + S108N and A16V + S108T), triple (N51I + C59R + S108N and C59R + S108N + I164L) or quadruple (N51I + C59R + S108N + I164L) mutations, responsible for antifolate resistance. The flexibility of the side chain at position N 1 has been included in the design so as to avoid unfavourable steric interaction with the side chain of residue 108 of the resistant mutants. The inhibition constants of many inhibitors for the mutant enzymes are in the low nanomolar region. Regaining of drug binding efficacies was achieved with both A16V and S108N series of mutants. X-ray studies of some enzyme-inhibitor complexes designed for optimal interaction with the mutant enzymes reveal the modes of binding in line with the K i values. A number of these compounds show excellent antimalarial activities against resistant P. falciparum bearing the mutant enzymes, and exhibit low cytotoxicity to mammalian cells, making them good candidates for further development as antimalarial drugs.


    Organizational Affiliation

    National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand. Electronic address: yongyuth@biotec.or.th.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthaseA, B608Plasmodium falciparumMutation(s): 0 
Gene Names: DHFR-TSV1/S
UniProt
Find proteins for D9N170 (Plasmodium falciparum)
Explore D9N170 
Go to UniProtKB:  D9N170
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
EA0 (Subject of Investigation/LOI)
Query on EA0

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]2-[[4,6-bis(azanyl)-2,2-dimethyl-1,3,5-triazin-1-yl]oxy]-N-(4-chlorophenyl)ethanamide
C13 H17 Cl N6 O2
NFSDKWLTDMRPDV-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A], F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.703α = 90
b = 155.878β = 90
c = 164.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report




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: 2020-12-09
    Type: Initial release