4MNB | pdb_00004mnb

Crystal Structure of a complex between the marine anticancer drug Variolin B and DNA

• PDB DOI: https://doi.org/10.2210/pdb4MNB/pdb
• NAKB: 4MNB

• Classification: DNA
• Mutation(s): No 


• Deposited: 2013-09-10 Released: 2015-03-11 
• Deposition Author(s): Canals, A., Arribas-Bosacoma, R., Alvarez, M., Albericio, F., Aymami, J., Coll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Intercalative DNA binding of the marine anticancer drug variolin B.

Canals, A., Arribas-Bosacoma, R., Albericio, F., Alvarez, M., Aymami, J., Coll, M.

(2017) Sci Rep 7: 39680-39680

• PubMed: 28051169 
• DOI: https://doi.org/10.1038/srep39680
• Primary Citation Related Structures: 
  4MNB


• PubMed Abstract: 
  

  Variolin B is a rare marine alkaloid that showed promising anti-cancer activity soon after its isolation. It acts as a cyclin-dependent kinase inhibitor, although the precise mechanism through which it exerts the cytotoxic effects is still unknown. The crystal structure of a variolin B bound to a DNA forming a pseudo-Holliday junction shows that this compound can also contribute, through intercalative binding, to either the formation or stabilization of multi-stranded DNA forms.

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Organizational Affiliation: 
• Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.
Institut de Biologia Molecular de Barcelona (CSIC), Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain.
CIBER-BBN, Networking Centre on Bioengineering Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain.
Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain.
School of Chemistry, University of KwaZulu-Natal, 4001 Durban, South Africa.
Laboratory of Organic Chemistry, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain.
Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 4.77 kDa 
• Atom Count: 309 
• Modeled Residue Count: 11 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*TP*AP*CP*G)-3'	A, B	6	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VAR	C [auth A], D [auth A]	9-amino-5-(2-aminopyrimidin-4-yl)pyrido[3',2':4,5]pyrrolo[1,2-c]pyrimidin-4-ol C14 H11 N7 O RTHKPHCVZVYDFN-UHFFFAOYSA-N
NCO	E [auth A], G [auth B], H [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
CO	F [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
NA	I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.7	α = 90
b = 53.4	β = 90
c = 40.8	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-11 
Deposition Author(s): Canals, A., Arribas-Bosacoma, R., Alvarez, M., Albericio, F., Aymami, J., Coll, M.

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2017-02-22
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations