3KJS

Crystal Structure of T. cruzi DHFR-TS with 3 high affinity DHFR inhibitors: DQ1 inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis and characterization of potent inhibitors of Trypanosoma cruzi dihydrofolate reductase.

Schormann, N.Velu, S.E.Murugesan, S.Senkovich, O.Walker, K.Chenna, B.C.Shinkre, B.Desai, A.Chattopadhyay, D.

(2010) Bioorg.Med.Chem. 18: 4056-4066

  • DOI: 10.1016/j.bmc.2010.04.020

  • PubMed Abstract: 
  • Dihydrofolate reductase (DHFR) of the parasite Trypanosoma cruzi (T. cruzi) is a potential target for developing drugs to treat Chagas' disease. We have undertaken a detailed structure-activity study of this enzyme. We report here synthesis and chara ...

    Dihydrofolate reductase (DHFR) of the parasite Trypanosoma cruzi (T. cruzi) is a potential target for developing drugs to treat Chagas' disease. We have undertaken a detailed structure-activity study of this enzyme. We report here synthesis and characterization of six potent inhibitors of the parasitic enzyme. Inhibitory activity of each compound was determined against T. cruzi and human DHFR. One of these compounds, ethyl 4-(5-[(2,4-diamino-6-quinazolinyl)methyl]amino-2-methoxyphenoxy)butanoate (6b) was co-crystallized with the bifunctional dihydrofolate reductase-thymidylate synthase enzyme of T. cruzi and the crystal structure of the ternary enzyme:cofactor:inhibitor complex was determined. Molecular docking was used to analyze the potential interactions of all inhibitors with T. cruzi DHFR and human DHFR. Inhibitory activities of these compounds are discussed in the light of enzyme-ligand interactions. Binding affinities of each inhibitor for the respective enzymes were calculated based on the experimental or docked binding mode. An estimated 60-70% of the total binding energy is contributed by the 2,4-diaminoquinazoline scaffold.


    Organizational Affiliation

    Department of Medicine, University of Alabama, Birmingham, Birmingham, AL 35294, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase-thymidylate synthase
A, B, C, D
521Trypanosoma cruziMutation(s): 0 
Find proteins for Q8T5T8 (Trypanosoma cruzi)
Go to UniProtKB:  Q8T5T8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAP
Query on NAP

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Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DQ1
Query on DQ1

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Download CCD File 
A, B, C, D
ethyl 4-(5-{[(2,4-diaminoquinazolin-6-yl)methyl]amino}-2-methoxyphenoxy)butanoate
C22 H27 N5 O4
YUHXPHNBJFUHSN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DQ1Ki: 1.3 - 5.7 nM (99) BINDINGDB
DQ1IC50: 23.8 nM (99) BINDINGDB
DQ1Ki: 1.3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 175.620α = 90.00
b = 175.620β = 90.00
c = 249.905γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
d*TREKdata reduction
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance