1D22

BINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO DNA: STRUCTURAL COMPARISON


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Binding of the antitumor drug nogalamycin and its derivatives to DNA: structural comparison.

Gao, Y.G.Liaw, Y.C.Robinson, H.Wang, A.H.

(1990) Biochemistry 29: 10307-10316

  • DOI: 10.1021/bi00497a004
  • Primary Citation of Related Structures:  
    1D22, 1D21

  • PubMed Abstract: 
  • The three-dimensional molecular structures of the complexes between a novel antitumor drug nogalamycin and its derivative U-58872 with a modified DNA hexamer d[m5CGT(pS)Am5CG] have been determined at 1.7- and 1.8-A resolution, respectively, by X-ray diffraction analyses ...

    The three-dimensional molecular structures of the complexes between a novel antitumor drug nogalamycin and its derivative U-58872 with a modified DNA hexamer d[m5CGT(pS)Am5CG] have been determined at 1.7- and 1.8-A resolution, respectively, by X-ray diffraction analyses. Both structures (in space group P6(1)) have been refined with constrained refinement procedure to final R factors of 0.208 (3386 reflections) and 0.196 (2143 reflections). In both complexes, two nogalamycins bind to the DNA hexamer double helix in a 2:1 ratio with the elongated aglycon chromophore intercalated between the CpG steps at both ends of the helix. The aglycon chromophore spans across the GC Watson-Crick base pairs with its nogalose lying in the minor groove and the aminoglucose lying in the major groove of the distorted B-DNA double helix. Most of the sugars remain in the C2'-endo pucker family, except three deoxycytidine residues (terminal C1, C7, and internal C5). All nucleotides are in the anti conformation. Specific hydrogen bonds are found in the complex between the drug and guanine-cytosine bases in both grooves of the helix. One hydroxyl group of the aminoglucose donates a hydrogen bond to the N7 of guanine, while the other receives a hydrogen bond from the N4 amino group of cytosine. The orientation of these two hydrogen bonds suggests that nogalamycin prefers a GC base pair with its aglycon chromophore intercalating at the 5'-side of a guanine (between NpG), or at the 3'-side of a cytosine (between CpN) with the sugars pointing toward the GC base pair. The binding of nogalamycin to DNA requires that the base pairs in DNA open up transiently to allow the bulky sugars to go through, suggesting that nogalamycin prefers GC sequences embedded in a stretch of AT sequences.


    Related Citations: 
    • NMR Studies on the Binding of Antitumor Drug Nogalamycin to DNA Hexamer d(CGTACG)
      Robinson, H., Liaw, Y.-C., Van Der Marel, G.A., Van Boom, J.H., Wang, A.H.-J.
      (1990) Nucleic Acids Res 18: 4851
    • Antitumor Drug Nogalamycin Binds DNA in Both Grooves Simultaneously: Molecular Structure of Nogalamycin-DNA Complex
      Liaw, Y.-C., Gao, Y.-G., Robinson, H., Van Der Marel, G.A., Van Boom, J.H., Wang, A.H.-J.
      (1989) Biochemistry 28: 9913

    Organizational Affiliation

    Department of Physiology and Biophysics, University of Illinois, Urbana 61801.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*(5CM)P*GP*TP*(AS)P*(5CM)P*G)-3')A, B6N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    NGU (Subject of Investigation/LOI)
    Query on NGU

    Download Ideal Coordinates CCD File 
    C [auth B], D [auth B]U-58872, HYDROXY DERIVATIVE OF NOGALAMYCIN
    C39 H49 N O17
    LZNCBRPUGPTNSO-JYOBTZKQSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.80 Å
    • R-Value Observed: 0.196 
    • Space Group: P 61
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 26.27α = 90
    b = 26.27β = 90
    c = 100.23γ = 120
    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: 1991-07-15
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance