1M6F

Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 1M6F

Classification: DNA

Total Structure Weight: 7703.51

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') A, B 12 synthetic

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

B 3-[C-[N'-(3-CARBAMIMIDOYL-BENZYLIDENIUM)- HYDRAZINO]-[[AMINOMETHYLIDENE]AMINIUM]-IMINOMETHYL]- BENZAMIDINIUM
CGP40215A, BIS[[3-(AMINOIMINOMETHYL)PHENYL]METHYLENE] CARBONIMIDIC DIHYDRAZIDE (Synonym)
C17 H22 N9
NSHBIZYDZBQOQB-WDBPGAOMSA-Q
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.202
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 24.10 α = 90.00
b = 39.82 β = 90.00
c = 65.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-07-16
  • Released Date: 2002-11-15
  • Deposition author(s): Nguyen, B., Lee, M.P.H., Hamelberg, D., Joubert, A., Bailly, C., Brun, R., Neidle, S., Wilson, W.D.

Revision History

  • 2008-04-28
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance