2B3E

Crystal structure of DB819-D(CGCGAATTCGCG)2 complex.

• PDB DOI: https://doi.org/10.2210/pdb2B3E/pdb
• NAKB: 2B3E

• Classification: DNA
• Mutation(s): No 


• Deposited: 2005-09-20 Released: 2005-11-22 
• Deposition Author(s): Campbell, N.H., Evans, D.A., Lee, M.P., Parkinson, G.N., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Targeting the DNA minor groove with fused ring dicationic compounds: Comparison of in silico screening and a high-resolution crystal structure.

Campbell, N.H., Evans, D.A., Lee, M.P., Parkinson, G.N., Neidle, S.

(2006) Bioorg Med Chem Lett 16: 15-19

• PubMed: 16263285 
• DOI: https://doi.org/10.1016/j.bmcl.2005.10.036
• Primary Citation of Related Structures:  
  2B3E


• PubMed Abstract: 
  

  The crystal structure of the DNA minor groove biphenyl benzimidazole diamidine ligand DB819 has been determined, bound to the DNA sequence d(CGCGAATTCGCG)(2), at a resolution of 1.36 Angstrom. Conditions for reliable in silico docking that reproduce the observed position of the ligand in the minor groove have been determined.

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Organizational Affiliation: 

Cancer Research UK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, UK.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.76 kDa 
• Atom Count: 624 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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
DBN	D [auth A]	6-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)-2-{5-[4-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)PHENYL]THIEN-2-YL}-1H-BENZIMIDAZOLE C23 H20 N6 S KPAUDMFCLSTUBG-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.196	α = 90
b = 39.96	β = 90
c = 65.525	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-22 
Deposition Author(s): Campbell, N.H., Evans, D.A., Lee, M.P., Parkinson, G.N., Neidle, S.

Revision History  

• Version 1.0: 2005-11-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description