102D

SEQUENCE-DEPENDENT DRUG BINDING TO THE MINOR GROOVE OF DNA: THE CRYSTAL STRUCTURE OF THE DNA DODECAMER D(CGCAAATTTGCG)2 COMPLEXED WITH PROPAMIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sequence-dependent drug binding to the minor groove of DNA: crystal structure of the DNA dodecamer d(CGCAAATTTGCG)2 complexed with propamidine.

Nunn, C.M.Neidle, S.

(1995) J.Med.Chem. 38: 2317-2325


  • PubMed Abstract: 
  • The DNA-binding ligand propamidine, an analogue of the drug pentamidine which is used in the treatment of acquired immune deficiency syndrome (AIDS)-associated Pneumocystis carinii, has been cocrystallized with the DNA sequence d(CGCAAATTTGCG)2, and ...

    The DNA-binding ligand propamidine, an analogue of the drug pentamidine which is used in the treatment of acquired immune deficiency syndrome (AIDS)-associated Pneumocystis carinii, has been cocrystallized with the DNA sequence d(CGCAAATTTGCG)2, and the crystal structure of the complex has been determined using data from 8 to 2.2 A resolution. The R factor converged to 15.5% with the inclusion of 73 water molecules. The structure shows binding of the propamidine molecule within the AT tract of the DNA minor groove with a shift from the center of the duplex toward the 3' end of ca. 2 A. The long AT tract of six base pairs in length allows the propamidine many potential binding sites in the DNA groove, and its binding is seen to occur where there is least perturbation to the DNA from that seen in the native structure. The interactions with bases are distinct from those previously observed for the sequence d(CGCGAATTCGCG)2.


    Organizational Affiliation

    CRC Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')A,B12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TNT
Query on TNT

Download SDF File 
Download CCD File 
B
1,3-BIS(AMIDINOPHENOXY)PROPANE
C17 H20 N4 O2
WTFXJFJYEJZMFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 24.780α = 90.00
b = 41.160β = 90.00
c = 65.510γ = 90.00
Software Package:
Software NamePurpose
XENGENdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1994-12-15 
  • Released Date: 1995-02-07 
  • Deposition Author(s): Nunn, C.M., Neidle, S.

Revision History 

  • Version 1.0: 1995-02-07
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance