1FTD

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

• PDB DOI: https://doi.org/10.2210/pdb1FTD/pdb
• NAKB: 1FTD

• Classification: DNA
• Mutation(s): No 


• Deposited: 2000-09-12 Released: 2001-02-26 
• Deposition Author(s): Mann, J., Baron, A., Opoku-Boahen, Y., Johansson, E., Parkinson, G., Kelland, L.R., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.292 
• R-Value Work: 0.244 
• R-Value Observed: 0.242 

Literature

A new class of symmetric bisbenzimidazole-based DNA minor groove-binding agents showing antitumor activity.

Mann, J., Baron, A., Opoku-Boahen, Y., Johansson, E., Parkinson, G., Kelland, L.R., Neidle, S.

(2001) J Med Chem 44: 138-144

• PubMed: 11170623 
• DOI: https://doi.org/10.1021/jm000297b
• Primary Citation of Related Structures:  
  1FTD


• PubMed Abstract: 
  

  The synthesis and evaluation of the novel head-to-head bisbenzimidazole compound 2,2-bis[4'-(3' '-dimethylamino-1' '-propyloxy)phenyl]-5,5-bi-1H-benzimidazole is described. An X-ray crystallographic study of a complex with the DNA dodecanucleotide sequence d(CGCGAATTCGCG) shows the compound bound in the A/T minor groove region of a B-DNA duplex and that the head-to-head bisbenzimidazole motif hydrogen-bonds to the edges of all four consecutive A:T base pairs. The compound showed potent growth inhibition with a mean IC(50) across an ovarian carcinoma cell line panel of 0.31 microM, with no significant cross-resistance in two acquired cisplatin-resistant cell lines and a low level of cross-resistance in the P-glycoprotein overexpressing acquired doxorubicin-resistant cell line. Studies with the hollow fiber assay and in vivo tumor xenografts showed some evidence of antitumor activity.

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Organizational Affiliation: 

Chemistry Department, Reading University, Whiteknights, Reading RG6 6AD, UK.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.94 kDa 
• Atom Count: 616 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')	A, B	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E97	D [auth A]	[3-(4-{2'-[4-(3-DIMETHYLAMINO-PROPOXY)-PHENYL]-3H,3'H-[5,5']BIBENZOIMIDAZOLYL-2-YL}-PHENOXY)-PROPYL]-DIMETHYL-AMINE C36 H40 N6 O2 MZGMYDKOHYOXKR-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.292 
• R-Value Work: 0.244 
• R-Value Observed: 0.242 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.15	α = 90
b = 39.94	β = 90
c = 65.65	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
SHELXL-97	refinement
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-26 
Deposition Author(s): Mann, J., Baron, A., Opoku-Boahen, Y., Johansson, E., Parkinson, G., Kelland, L.R., Neidle, S.

Revision History  

• Version 1.0: 2001-02-26
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations