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


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/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 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

    Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1492Homo sapiensPyrococcus abyssi GE5Mutation(s): 5 
Gene Names: CNR1CNRPAB2292
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
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
PHAROS:  P21554
GTEx:  ENSG00000118432 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9V2J8P21554
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9GL (Subject of Investigation/LOI)
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
9GF (Subject of Investigation/LOI)
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
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
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
PEG
Query on PEG

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9GF BindingDB:  6KQI Ki: min: 0.32, max: 13 (nM) from 25 assay(s)
Kd: min: 0.5, max: 3.3 (nM) from 10 assay(s)
IC50: min: 0.13, max: 28 (nM) from 9 assay(s)
EC50: min: 0.14, max: 100 (nM) from 37 assay(s)
9GL BindingDB:  6KQI IC50: min: 0.29, max: 853 (nM) from 3 assay(s)
EC50: min: 9.1, max: 1.06e+4 (nM) from 8 assay(s)
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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
  • Version 1.4: 2023-11-22
    Changes: Data collection, Database references, Refinement description