1D14

STRUCTURE OF 11-DEOXYDAUNOMYCIN BOUND TO DNA CONTAINING A PHOSPHOROTHIOATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of 11-deoxydaunomycin bound to DNA containing a phosphorothioate.

Williams, L.D.Egli, M.Ughetto, G.van der Marel, G.A.van Boom, J.H.Quigley, G.J.Wang, A.H.Rich, A.Frederick, C.A.

(1990) J.Mol.Biol. 215: 313-320

  • DOI: 10.1016/S0022-2836(05)80349-3

  • PubMed Abstract: 
  • The anthracyclines form an important family of cancer chemotherapeutic agents with a strong dependence of clinical properties on minor differences in chemical structure. We describe the X-ray crystallographic solution of the three-dimensional structu ...

    The anthracyclines form an important family of cancer chemotherapeutic agents with a strong dependence of clinical properties on minor differences in chemical structure. We describe the X-ray crystallographic solution of the three-dimensional structure of the anthracycline 11-deoxydaunomycin plus d(CGTsACG). In this complex, two drug molecules bind to each hexamer duplex. Both the drug and the DNA are covalently modified in this complex in contrast with the three previously reported DNA-anthracycline complexes. In the 11-deoxydaunomycin complex the 11 hydroxyl group is absent and a phosphate oxygen at the TpA step has been replaced by a sulfur atom leading to a phosphorothioate with absolute stereochemistry R. Surprisingly, removal of a hydroxyl group from the 11 position does not alter the relative orientation of the intercalated chromophore. However, it appears that the phosphorothioate modification influenced the crystallization and caused the 11-deoxydaunomycin-d(CGTsACG) complex to crystallize into a different lattice (space group P2) with different lattice contacts and packing forces than the non-phosphorothioated DNA-anthracycline complexes (space group P4(1)2(1)2). In the minor groove of the DNA, the unexpected position of the amino-sugar of 11-deoxydaunomycin supports the hypothesis that in solution the position of the amino sugar is dynamic.


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*(AS)P*CP*G)-3')A6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DM3
Query on DM3

Download SDF File 
Download CCD File 
A
6-DEOXYDAUNOMYCIN
C27 H29 N O9
ZCLQMQOBRBUQOR-GRRPPOEGSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AS
Query on AS
A
DNA LINKINGC10 H14 N5 O5 P SDA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 17.730α = 90.00
b = 19.130β = 98.01
c = 26.360γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-10-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance