1D22

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

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

  • Primary Citation of Related Structures:  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 ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*(5CM)P*GP*TP*(AS)P*(5CM)P*G)-3')A,B6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGU
Query on NGU

Download SDF File 
Download CCD File 
B
U-58872, HYDROXY DERIVATIVE OF NOGALAMYCIN
C39 H49 N O17
LZNCBRPUGPTNSO-JYOBTZKQSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
A, B
DNA LINKINGC10 H16 N3 O7 PDC
AS
Query on AS
A, B
DNA LINKINGC10 H14 N5 O5 P SDA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 26.270α = 90.00
b = 26.270β = 90.00
c = 100.230γ = 120.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-07-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance