110D

ANTHRACYCLINE-DNA INTERACTIONS AT UNFAVOURABLE BASE BASE-PAIR TRIPLET-BINDING SITES: STRUCTURES OF D(CGGCCG)/DAUNOMYCIN AND D(TGGCCA)/ADRIAMYCIN COMPL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.208 

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This is version 1.2 of the entry. See complete history


Literature

Anthracycline-DNA interactions at unfavourable base-pair triplet-binding sites: structures of d(CGGCCG)/daunomycin and d(TGGCCA)/adriamycin complexes.

Leonard, G.A.Hambley, T.W.McAuley-Hecht, K.Brown, T.Hunter, W.N.

(1993) Acta Crystallogr D Biol Crystallogr 49: 458-467

  • DOI: 10.1107/S090744499300527X
  • Primary Citation of Related Structures:  
    110D, 1DA9

  • PubMed Abstract: 
  • The structures of two hexanucleotide-anthracycline complexes d(CGGCCG)/daunomycin and d(TGGCCA)/adriamycin have been determined using single-crystal X-ray diffraction techniques. In both cases the anthracycline molecule is bound to non-preferred d(YGG) base-pair triplet sites ...

    The structures of two hexanucleotide-anthracycline complexes d(CGGCCG)/daunomycin and d(TGGCCA)/adriamycin have been determined using single-crystal X-ray diffraction techniques. In both cases the anthracycline molecule is bound to non-preferred d(YGG) base-pair triplet sites. For both complexes the crystals are tetragonal and belong to the space group P4(1)2(1)2. Unit-cell dimensions are a = 28.07 (2), c = 53.35 (1) and a = 28.01 (1), c = 52.99 (1) A, respectively, and the asymmetric unit of both structures consists of one strand of DNA, one drug molecule and approximately 50 water molecules. For the d(CGGCCG) complex the refinement converged with an R factor of 0.21 for 1108 reflections with F >/= 2sigma(F) in the resolution range 7.0-1.9 A. For the complex involving d(TGGCCA) the final R value was 0.22 for 1475 reflections in the range 7.0-1.7 A with the same criterion for observed data. Both complexes are essentially isomorphous with related structures but differ in terms of the number of favourable van der Waals interactions of the amino sugars of the drug molecules with the DNA duplexes and the formation in the minor groove of heterodromic pentagonal arrangements of hydrogen bonds involving water molecules which link the amino sugars to the DNA. These differences in structure are used to rationalize the lack of affinity of daunomycin-type anthracyclines for d(YGG) and d(YGC) sites.


    Organizational Affiliation

    Department of Chemistry, University of Manchester, England.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*GP*CP*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: 1.90 Å
    • R-Value Observed: 0.208 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 28.07α = 90
    b = 28.07β = 90
    c = 53.35γ = 90
    Software Package:
    Software NamePurpose
    NUCLSQrefinement

    Structure Validation

    View Full Validation Report



    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1993-04-15
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance