6AST

NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA Sequence


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 11 
  • Conformers Submitted: 11 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences.

Harika, N.K.Germann, M.W.Wilson, W.D.

(2017) Chemistry 23: 17612-17620

  • DOI: 10.1002/chem.201704563
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The high-resolution NMR structure of the first heterocyclic, non-amide, organic cation that strongly and selectively recognizes mixed AT/GC bp (bp=base pair) sequences of DNA in a 1:1 complex is described. Compound designs of this type provide essent ...

    The high-resolution NMR structure of the first heterocyclic, non-amide, organic cation that strongly and selectively recognizes mixed AT/GC bp (bp=base pair) sequences of DNA in a 1:1 complex is described. Compound designs of this type provide essential methods for control of functional, non-genomic DNA sequences and have broad cell uptake capability, based on studies from animals to humans. The high-resolution structural studies described in this report are essential for understanding the molecular basis for the sequence-specific binding as well as for new ideas for additional compound designs for sequence-specific recognition. The molecular features, in this report, explain the mechanism of recognition of both A⋅T and G⋅C bps and are an interesting molecular recognition story. Examination of the experimental structure and the NMR restrained molecular dynamics model suggests that recognition of the G⋅C base pair involves two specific H-bonds. The structure illustrates a wealth of information on different DNA interactions and illustrates an interfacial water molecule that is a key component of the complex.


    Organizational Affiliation

    Department of Chemistry, Georgia State University, Atlanta, GA, 30303-3083, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3')A9synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3')B9synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BVV
Query on BVV

Download SDF File 
Download CCD File 
B
amino(4-{[(2-{4-[amino(iminio)methyl]phenyl}-3H-imidazo[4,5-b]pyridin-5-yl)oxy]methyl}phenyl)methaniminium
C21 H21 N7 O
UDAHUTJVVAQSQI-UHFFFAOYSA-P
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 11 
  • Conformers Submitted: 11 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM111749

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release