459D

DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG

Structural Biology Knowledgebase: 459D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.209

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 459D

Classification: DNA

Total Structure Weight: 7945.40

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*(CBR)P*AP*TP*AP*TP*TP*TP*GP*CP*G)-3') A 12 synthetic COMPLEXED WITH 2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2', 5''- TRI-BENZIMIDAZOLE
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*AP*TP*GP*CP*G)-3') B 12 synthetic COMPLEXED WITH 2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2', 5''- TRI-BENZIMIDAZOLE

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TBZ
Query on TBZ

B 2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)- 2,5',2',5''-TRI-BENZIMIDAZOLE
TRIBIZ; TRIS(BENZIMIDAZOLE) DERIVATIVE (Synonym)
C32 H29 N8 O
MEDNUDGNJOXVKL-NRFANRHFSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CBR
Query on CBR
A DNA LINKING C9 H13 Br N3 O7 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.209
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 25.50 α = 90.00
b = 40.42 β = 90.00
c = 65.55 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1999-03-10
  • Released Date: 1999-06-28
  • Deposition author(s): Aymami, J., Nunn, C.M., Neidle, S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4