1VZK

A Thiophene Based Diamidine Forms a "Super" AT Binding Minor Groove Agent


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.295 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Thiophene-Based Diamidine Forms a "Super" at Binding Minor Groove Agent

Mallena, S.Lee, M.P.H.Bailly, C.Neidle, S.Kumar, A.Boykin, D.W.Wilson, W.D.

(2004) J Am Chem Soc 142: 13659

  • DOI: 10.1021/ja048175m
  • Primary Citation of Related Structures:  
    1VZK

  • PubMed Abstract: 
  • The DNA minor groove is the interaction site for many enzymes and transcription control proteins and as a result, development of compounds that target the minor groove is an active research area. In an effort to develop biologically active minor groove agents, we are preparing and exploring the DNA interactions of a systematic set of diamidine derivatives with a powerful array of methods including DNase I footprinting, biosensor-SPR methods, and X-ray crystallography ...

    The DNA minor groove is the interaction site for many enzymes and transcription control proteins and as a result, development of compounds that target the minor groove is an active research area. In an effort to develop biologically active minor groove agents, we are preparing and exploring the DNA interactions of a systematic set of diamidine derivatives with a powerful array of methods including DNase I footprinting, biosensor-SPR methods, and X-ray crystallography. Surprisingly, conversion of the parent phenyl-furan-phenyl diamidine to a phenyl-thiophene-benzimidazole derivative yields a compound with over 10-fold-increased affinity for the minor groove at AT sequences. Single conversion of the furan to a thiophene or a phenyl to benzimidazole does not cause a similar increase in affinity. X-ray results indicate a small bond angle difference between the C-S-C angle of thiophene and the C-O-C angle of furan that, when amplified out to the terminal amidines of the benzimidazole compounds, yields a very significant difference in the positions of the amidines and their DNA interaction strength.


    Organizational Affiliation

    Department of Chemistry, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302-4098, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP *CP*G)-3'A, B12N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    D1B (Subject of Investigation/LOI)
    Query on D1B

    Download Ideal Coordinates CCD File 
    C [auth A]2-(5-{4-[AMINO(IMINO)METHYL]PHENYL}-2-THIENYL)-1H-BENZIMIDAZOLE-6- CARBOXIMIDAMIDE DIHYDROCHLORIDE
    C19 H16 N6 S
    MSQVFIHMHRAMOC-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    D [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.77 Å
    • R-Value Free: 0.295 
    • R-Value Observed: 0.227 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 25.677α = 90
    b = 39.921β = 90
    c = 65.185γ = 90
    Software Package:
    Software NamePurpose
    SHELXL-97refinement
    DENZOdata reduction
    SCALEPACKdata scaling
    CNSphasing

    Structure Validation

    View Full Validation Report



    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2004-10-25
      Type: Initial release
    • Version 1.1: 2011-05-08
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2019-05-22
      Changes: Data collection, Other, Refinement description