453D | pdb_0000453d

5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'-BENZIMIDAZOLE COMPLEX

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 1999-02-18 Released: 2000-05-15 
  • Deposition Author(s): Neidle, S.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.251 (Depositor) 
  • R-Value Work: 
    0.234 (Depositor), 0.224 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 453D

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Symmetric bis-benzimidazoles, a new class of sequence-selective DNA-binding molecules

Neidle, S., Mann, J., Rayner, E.J., Baron, A., Opoku-Boahen, Y., Simpson, I.J., Smith, N.J., Fox, K.R., Hartley, J.A., Kelland, L.R.

(1999) Chem Commun (Camb) : 929-930

Macromolecule Content 

  • Total Structure Weight: 7.75 kDa 
  • Atom Count: 692 
  • Modeled Residue Count: 24 
  • Deposited Residue Count: 24 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
A, B
12N/A
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E96

Query on E96


Download:Ideal Coordinates CCD File
C [auth A]4-{[4-HYDROXY-PHENYL]-1H-BENZIMIDAZOLE-5-YL}-BENZIMIDAZOLE-2-YL-[4-HYDROXY-BENZENE]
C26 H18 N4 O2
LUIYJLIHLJLIPT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.251 (Depositor) 
  • R-Value Work:  0.234 (Depositor), 0.224 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.46α = 90
b = 39.96β = 90
c = 65.66γ = 90
Software Package:
Software NamePurpose
SHELXSphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

  • Released Date: 2000-05-15 
    • Deposition Author(s): Neidle, S.

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-15
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations