102D

SEQUENCE-DEPENDENT DRUG BINDING TO THE MINOR GROOVE OF DNA: THE CRYSTAL STRUCTURE OF THE DNA DODECAMER D(CGCAAATTTGCG)2 COMPLEXED WITH PROPAMIDINE

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 1994-12-15 Released: 1995-02-07 
  • Deposition Author(s): Nunn, C.M., Neidle, S.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 

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Literature

Sequence-dependent drug binding to the minor groove of DNA: crystal structure of the DNA dodecamer d(CGCAAATTTGCG)2 complexed with propamidine.

Nunn, C.M.Neidle, S.

(1995) J Med Chem 38: 2317-2325

  • DOI: 10.1021/jm00013a008
  • Primary Citation of Related Structures:  
    102D

  • PubMed Abstract: 
  • The DNA-binding ligand propamidine, an analogue of the drug pentamidine which is used in the treatment of acquired immune deficiency syndrome (AIDS)-associated Pneumocystis carinii, has been cocrystallized with the DNA sequence d(CGCAAATTTGCG)2, and the crystal structure of the complex has been determined using data from 8 to 2 ...

    The DNA-binding ligand propamidine, an analogue of the drug pentamidine which is used in the treatment of acquired immune deficiency syndrome (AIDS)-associated Pneumocystis carinii, has been cocrystallized with the DNA sequence d(CGCAAATTTGCG)2, and the crystal structure of the complex has been determined using data from 8 to 2.2 A resolution. The R factor converged to 15.5% with the inclusion of 73 water molecules. The structure shows binding of the propamidine molecule within the AT tract of the DNA minor groove with a shift from the center of the duplex toward the 3' end of ca. 2 A. The long AT tract of six base pairs in length allows the propamidine many potential binding sites in the DNA groove, and its binding is seen to occur where there is least perturbation to the DNA from that seen in the native structure. The interactions with bases are distinct from those previously observed for the sequence d(CGCGAATTCGCG)2.


    Organizational Affiliation

    CRC Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, U.K.



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

    Download Ideal Coordinates CCD File 
    C [auth B]1,3-BIS(AMIDINOPHENOXY)PROPANE
    C17 H20 N4 O2
    WTFXJFJYEJZMFO-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Work: 0.155 
    • R-Value Observed: 0.155 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 24.78α = 90
    b = 41.16β = 90
    c = 65.51γ = 90
    Software Package:
    Software NamePurpose
    X-PLORrefinement
    XENGENdata scaling

    Structure Validation

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    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    • Deposited Date: 1994-12-15 
    • Released Date: 1995-02-07 
    • Deposition Author(s): Nunn, C.M., Neidle, S.

    Revision History  (Full details and data files)

    • Version 1.0: 1995-02-07
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance