5CDB

Structure of the complex of a bimolecular human telomeric DNA with a 13-diphenylalkyl Berberine derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

wwPDB Validation 3D Report Full Report



Literature

Solution and Solid-State Analysis of Binding of 13-Substituted Berberine Analogues to Human Telomeric G-quadruplexes.

Ferraroni, M.Bazzicalupi, C.Papi, F.Fiorillo, G.Guaman-Ortiz, L.M.Nocentini, A.Scovassi, A.I.Lombardi, P.Gratteri, P.

(2016) Chem Asian J 11: 1107-1115

  • DOI: 10.1002/asia.201600116
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The interaction between 13-phenylalkyl and 13-diphenylalkyl berberine derivatives (NAX) and human telomeric DNA G4 structures has been investigated by both spectroscopic and crystallographic methods. NAX042 and NAX053 are the best compounds improving ...

    The interaction between 13-phenylalkyl and 13-diphenylalkyl berberine derivatives (NAX) and human telomeric DNA G4 structures has been investigated by both spectroscopic and crystallographic methods. NAX042 and NAX053 are the best compounds improving the performance of the natural precursor berberine. This finding is in agreement with the X-ray diffraction result for the NAX053-Tel12 adduct, showing the ligand which interacts via π-stacking, sandwiched at the interface of two symmetry-related quadruplex units, with its benzhydryl group contributing to the overall stability of the adduct by means of additional π-stacking interactions with the DNA residues. The berberine derivatives were also investigated for their cytotoxic activity towards a panel of human cancer cell lines. Compounds NAX042 and NAX053 affect the viability of cancer cell lines in a dose-dependent manner.


    Organizational Affiliation

    Department NEUROFARBA-Pharmaceutical and nutraceutical section, Laboratory of Molecular Modeling Cheminformatics&QSAR, University of Firenze, via Ugo Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy. paola.gratteri@unifi.it.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
human telomeric DNAA, B12Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
50B
Query on 50B

Download CCD File 
A
13-diphenylalkyl Berberine
C36 H34 N O4
GTWMZDSMZWCFBR-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.132α = 90
b = 41.132β = 90
c = 71.204γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release