1DSM

(-)-duocarmycin SA covalently linked to duplex DNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: LOWEST RESTRAINT VIOLATIONS 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structural basis for in situ activation of DNA alkylation by duocarmycin SA

Smith, J.A.Bifulco, G.Case, D.A.Boger, D.L.Gomez-Paloma, L.Chazin, W.J.

(2000) J.Mol.Biol. 300: 1195-1204

  • DOI: 10.1006/jmbi.2000.3887

  • PubMed Abstract: 
  • Duocarmycin SA is a member of a growing class of interesting lead compounds for chemotherapy, distinguished by the manner in which they bind to and react with DNA substrates. The first three-dimensional structure of a DNA adduct of an unnatural enant ...

    Duocarmycin SA is a member of a growing class of interesting lead compounds for chemotherapy, distinguished by the manner in which they bind to and react with DNA substrates. The first three-dimensional structure of a DNA adduct of an unnatural enantiomer from this family has been determined by (1)H NMR methods. Comparison to the previously determined structure of the natural enantiomer bound in the same DNA-binding site provides unique insights into the similarities and critical distinctions producing the respective alkylation products and site selectivities. The results also support the hypothesis that the duocarmycin SA alkylation reaction is catalyzed by the binding to DNA, and provide a deeper understanding of the structural basis for this unique mode of activation.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*AP*CP*TP*AP*AP*TP*TP*GP*AP*C)-3'A11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*TP*CP*AP*AP*TP*TP*AP*GP*TP*C)-3'B11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DSA
Query on DSA

Download SDF File 
Download CCD File 
A
4-HYDROXY-8-METHYL-6-(4,5,6-TRIMETHOXY-1H-INDOLE-2-CARBONYL)-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID METHYL ESTER
(+)DUOCARMYCIN SA
C25 H25 N3 O7
JMVYAMWFXLCMJM-NSHDSACASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: LOWEST RESTRAINT VIOLATIONS 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-02
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance