4MNB

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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.253 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

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 of 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.

---

Organizational Affiliation: 

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 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 
• Modelled 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 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• 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