3NP6

Deposited: 2010-06-28 Released: 2011-05-04
Deposition Author(s): Ferraroni, M., Bazzicalupi, C., Gratteri, P., Bilia, A.R.

Experimental Data Snapshot

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

(2011) Chem Commun (Camb) 47: 4917-4919

PubMed Abstract:
The first crystal structures of Berberine and Sanguinarine intercalated with a d(CGTACG)(2) DNA sequence were obtained by X-ray diffraction analysis at 2.3 ? resolution. Both drugs join the end of two "two-molecules" DNA units, stacked in a non-classic intercalation site formed by six bases. Sanguinarine interacts with d(CGTACG)(2) DNA in its iminium form.

Organizational Affiliation

Department of Chemistry Ugo Schiff, University of Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Firenze, Italy.

Macromolecule Content

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(CPGPTPAPCPG)-3'	A, B, C, D	6	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BER Query on BER Download Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	BERBERINE C₂₀ H₁₈ N O₄ YBHILYKTIRIUTE-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Unit Cell:

Software Package:

Entry History

Deposition Author(s):

Ferraroni, M.

Version 1.0: 2011-05-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description