6A7C

Human dihydrofolate reductase complexed with NADPH and BT1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Hybrid Inhibitors of Malarial Dihydrofolate Reductase with Dual Binding Modes That Can Forestall Resistance.

Tarnchompoo, B.Chitnumsub, P.Jaruwat, A.Shaw, P.J.Vanichtanankul, J.Poen, S.Rattanajak, R.Wongsombat, C.Tonsomboon, A.Decharuangsilp, S.Anukunwithaya, T.Arwon, U.Kamchonwongpaisan, S.Yuthavong, Y.

(2018) ACS Med Chem Lett 9: 1235-1240

  • DOI: 10.1021/acsmedchemlett.8b00389
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The S108N mutation of dihydrofolate reductase (DHFR) renders <i>Plasmodium falciparum </i> malaria parasites resistant to pyrimethamine through steric clash with the rigid side chain of the inhibitor. Inhibitors with flexible side chains can avoid t ...

    The S108N mutation of dihydrofolate reductase (DHFR) renders Plasmodium falciparum malaria parasites resistant to pyrimethamine through steric clash with the rigid side chain of the inhibitor. Inhibitors with flexible side chains can avoid this clash and retain effectiveness against the mutant. However, other mutations such as N108S reversion confer resistance to flexible inhibitors. We designed and synthesized hybrid inhibitors with two structural types in a single molecule, which are effective against both wild-type and multiple mutants of P. falciparum through their selective target binding, as demonstrated by X-ray crystallography. Furthermore, the hybrid inhibitors can forestall the emergence of new resistant mutants, as shown by selection of mutants resistant to hybrid compound BT1 from a diverse PfDHFR random mutant library expressed in a surrogate bacterial system. These results show that it is possible to develop effective antifolate antimalarials to which the range of parasite resistance mutations is greatly reduced.


    Organizational Affiliation

    National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A
186Homo sapiensMutation(s): 0 
Gene Names: DHFR
EC: 1.5.1.3
Find proteins for P00374 (Homo sapiens)
Go to Gene View: DHFR
Go to UniProtKB:  P00374
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
9QO
Query on 9QO

Download SDF File 
Download CCD File 
A
5-(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-6-ethylpyrimidine-2,4-diamine
C21 H28 N8 O2
IMDBCJZTZFNOKU-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.172 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 82.942α = 90.00
b = 82.942β = 90.00
c = 77.489γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
AUTOMARdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited States52992

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release