1DA0

DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURE OF D(CGATCG) COMPLEXED WITH DAUNOMYCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNA-drug interactions. The crystal structure of d(CGATCG) complexed with daunomycin.

Moore, M.H.Hunter, W.N.d'Estaintot, B.L.Kennard, O.

(1989) J Mol Biol 206: 693-705

  • DOI: 10.1016/0022-2836(89)90577-9
  • Primary Citation of Related Structures:  
    1DA0

  • PubMed Abstract: 
  • The structure of a d(CGATCG)-daunomycin complex has been determined by single crystal X-ray diffraction techniques. Refinement, with the location of 40 solvent molecules, using data up to 1.5 A, converged with a final crystallographic residual, R = 0.25 (RW = 0 ...

    The structure of a d(CGATCG)-daunomycin complex has been determined by single crystal X-ray diffraction techniques. Refinement, with the location of 40 solvent molecules, using data up to 1.5 A, converged with a final crystallographic residual, R = 0.25 (RW = 0.22). The tetragonal crystals are in space group P4(1)2(1)2, with cell dimensions of a = 27.98 A and c = 52.87 A. The self-complementary d(CGATCG) forms a distorted right-handed helix with a daunomycin molecule intercalated at each d(CpG) step. The daunomycin aglycon chromophore is oriented at right-angles to the long axis of the DNA base-pairs. This head-on intercalation is stabilized by direct hydrogen bonds and indirectly via solvent-mediated, hydrogen-bonding interactions between the chromophore and its intercalation site base-pairs. The cyclohexene ring and amino sugar substituent lie in the minor groove. The amino sugar N-3' forms a hydrogen bond with O-2 of the next neighbouring thymine. This electrostatic interaction helps position the sugar in a way that results in extensive van der Waals contacts between the drug and the DNA. There is no interaction between daunosamine and the DNA sugar-phosphate backbone. We present full experimental details and all relevant conformational parameters, and use the comparison with a d(CGTACG)-daunomycin complex to rationalize some neighbouring sequence effects involved in daunomycin binding.


    Organizational Affiliation

    University Chemical Laboratory, Cambridge, U.K.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')A6N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    DM1 (Subject of Investigation/LOI)
    Query on DM1

    Download Ideal Coordinates CCD File 
    B [auth A]DAUNOMYCIN
    C27 H29 N O10
    STQGQHZAVUOBTE-VGBVRHCVSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.50 Å
    • R-Value Observed: 0.250 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 27.98α = 90
    b = 27.98β = 90
    c = 52.87γ = 90
    Software Package:
    Software NamePurpose
    NUCLSQrefinement

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1993-07-15
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance