6KQI

Structure of an allosteric modulator bound to the CB1 cannabinoid receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of an allosteric modulator bound to the CB1 cannabinoid receptor.

Shao, Z.Yan, W.Chapman, K.Ramesh, K.Ferrell, A.J.Yin, J.Wang, X.Xu, Q.Rosenbaum, D.M.

(2019) Nat Chem Biol 15: 1199-1205

  • DOI: 10.1038/s41589-019-0387-2
  • Primary Citation of Related Structures:  
    6KQI

  • PubMed Abstract: 
  • The CB1 receptor mediates the central nervous system response to cannabinoids, and is a drug target for pain, anxiety and seizures. CB1 also responds to allosteric modulators, which influence cannabinoid binding and efficacy. To understand the mechanism of these compounds, we solved the crystal structure of CB1 with the negative allosteric modulator (NAM) ORG27569 and the agonist CP55940 ...

    The CB1 receptor mediates the central nervous system response to cannabinoids, and is a drug target for pain, anxiety and seizures. CB1 also responds to allosteric modulators, which influence cannabinoid binding and efficacy. To understand the mechanism of these compounds, we solved the crystal structure of CB1 with the negative allosteric modulator (NAM) ORG27569 and the agonist CP55940. The structure reveals that the NAM binds to an extrahelical site within the inner leaflet of the membrane, which overlaps with a conserved site of cholesterol interaction in many G protein-coupled receptors (GPCRs). The ternary structure with ORG27569 and CP55940 captures an intermediate state of the receptor, in which aromatic residues at the base of the agonist-binding pocket adopt an inactive conformation despite the large contraction of the orthosteric pocket. The structure illustrates a potential strategy for drug modulation of CB1 and other class A GPCRs.


    Organizational Affiliation

    Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA. dan.rosenbaum@utsouthwestern.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1A492Homo sapiensPyrococcus abyssi GE5Mutation(s): 5 
Gene Names: CNR1CNRPAB2292
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors: Class A
Protein: 
CB1 cannabinoid receptor with bound ORG27569 (NAM) and CP55940 agonist
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2J8 
Go to UniProtKB:  Q9V2J8
Find proteins for P21554 (Homo sapiens)
Explore P21554 
Go to UniProtKB:  P21554
NIH Common Fund Data Resources
PHAROS:  P21554
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9GL
Query on 9GL

Download Ideal Coordinates CCD File 
C [auth A]5-chloro-3-ethyl-N-{2-[4-(piperidin-1-yl)phenyl]ethyl}-1H-indole-2-carboxamide
C24 H28 Cl N3 O
AHFZDNYNXFMRFQ-UHFFFAOYSA-N
 Ligand Interaction
9GF
Query on 9GF

Download Ideal Coordinates CCD File 
B [auth A]2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol
C24 H40 O3
YNZFFALZMRAPHQ-SYYKKAFVSA-N
 Ligand Interaction
OLC
Query on OLC

Download Ideal Coordinates CCD File 
H [auth A], I [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
OLA
Query on OLA

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], G [auth A]OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
J [auth A], K [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.342α = 90
b = 167.94β = 91.39
c = 41.526γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-08-17 
  • Released Date: 2019-10-23 
  • Deposition Author(s): Shao, Z.H., Yan, W.

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Database references
  • Version 1.3: 2020-10-28
    Changes: Structure summary