6YZ0

Full length Open-form Sodium Channel NavMs F208L in complex with Cannabidiol (CBD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report



Literature

Cannabidiol interactions with voltage-gated sodium channels.

Sait, L.G.Sula, A.Ghovanloo, M.R.Hollingworth, D.Ruben, P.C.Wallace, B.A.

(2020) Elife 9

  • DOI: 10.7554/eLife.58593
  • Primary Citation of Related Structures:  
    6YZ0, 6YZ2

  • PubMed Abstract: 
  • Voltage-gated sodium channels are targets for a range of pharmaceutical drugs developed for the treatment of neurological diseases. Cannabidiol (CBD), the non-psychoactive compound isolated from cannabis plants, was recently approved for treatment of two ...

    Voltage-gated sodium channels are targets for a range of pharmaceutical drugs developed for the treatment of neurological diseases. Cannabidiol (CBD), the non-psychoactive compound isolated from cannabis plants, was recently approved for treatment of two types of epilepsy associated with sodium channel mutations. This study used high-resolution X-ray crystallography to demonstrate the detailed nature of the interactions between CBD and the NavMs voltage-gated sodium channel, and electrophysiology to show the functional effects of binding CBD to these channels. CBD binds at a novel site at the interface of the fenestrations and the central hydrophobic cavity of the channel. Binding at this site blocks the transmembrane-spanning sodium ion translocation pathway, providing a molecular mechanism for channel inhibition. Modelling studies suggest why the closely-related psychoactive compound tetrahydrocannabinol may not have the same effects on these channels. Finally, comparisons are made with the TRPV2 channel, also recently proposed as a target site for CBD. In summary, this study provides novel insight into a possible mechanism for CBD interactions with sodium channels.


    Organizational Affiliation

    Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ion transport protein A277Magnetococcus marinus MC-1Mutation(s): 1 
Gene Names: Mmc1_0798
Find proteins for A0L5S6 (Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1))
Explore A0L5S6 
Go to UniProtKB:  A0L5S6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
12P
Query on 12P

Download Ideal Coordinates CCD File 
A
DODECAETHYLENE GLYCOL
C24 H50 O13
WRZXKWFJEFFURH-UHFFFAOYSA-N
 Ligand Interaction
2CV
Query on 2CV

Download Ideal Coordinates CCD File 
A
HEGA-10
C18 H37 N O7
ITEIKACYSCODFV-ATLSCFEFSA-N
 Ligand Interaction
CD0
Query on CD0

Download Ideal Coordinates CCD File 
A
2-[(1R,2R,5S)-5-methyl-2-(prop-1-en-2-yl)cyclohexyl]-5-pentylbenzene-1,3-diol
C21 H32 O2
CODIXLGYYWMJFS-RYQLBKOJSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.328α = 90
b = 110.328β = 90
c = 207.876γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L006790, BB/N012763 and BB/R001294

Revision History 

  • Version 1.0: 2020-11-11
    Type: Initial release