4OCD

In and Out the minor groove: Interaction of an AT rich-DNA with the CD27 drug


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.236 

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Literature

In and out of the minor groove: interaction of an AT-rich DNA with the drug CD27

Acosta-Reyes, F.J.Dardonville, C.de Koning, H.P.Natto, M.Subirana, J.A.Campos, J.L.

(2014) Acta Crystallogr.,Sect.D D70: 1614-1621

  • DOI: 10.1107/S139900471400697X

  • PubMed Abstract: 
  • The DNA of several pathogens is very rich in AT base pairs. Typical examples include the malaria parasite Plasmodium falciparum and the causative agents of trichomoniasis and trypanosomiases. This fact has prompted studies of drugs which interact wit ...

    The DNA of several pathogens is very rich in AT base pairs. Typical examples include the malaria parasite Plasmodium falciparum and the causative agents of trichomoniasis and trypanosomiases. This fact has prompted studies of drugs which interact with the minor groove of DNA, some of which are used in medical practice. Previous studies have been performed almost exclusively with the AATT sequence. New features should be uncovered through the study of different DNA sequences. In this paper, the crystal structure of the complex of the DNA duplex d(AAAATTTT)2 with the dicationic drug 4,4'-bis(imidazolinylamino)diphenylamine (CD27) is presented. The drug binds to the minor groove of DNA as expected, but it shows two new features that have not previously been described: (i) the drugs protrude from the DNA and interact with neighbouring molecules, so that they may act as cross-linking agents, and (ii) the drugs completely cover the whole minor groove of DNA and displace bound water. Thus, they may prevent the access to DNA of proteins such as AT-hook proteins. These features are also expected for other minor-groove binding drugs when associated with all-AT DNA. These findings allow a better understanding of this family of compounds and will help in the development of new, more effective drugs. New data on the biological interaction of CD27 with the causative agent of trichomoniasis, Trichomonas vaginalis, are also reported.


    Organizational Affiliation

    Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
d(AAAATTTT)A,B,C8N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MWB
Query on MWB

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A, B, C
N1-(4,5-dihydro-1H-imidazol-2-yl)-N4-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzene-1,4-diamine
CD27
C18 H21 N7
AJWTXSLKVJNYAB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.236 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.013α = 90.00
b = 78.013β = 90.00
c = 91.552γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release