7FEE

Crystal structure of the allosteric modulator ZCZ011 binding to CP55940-bound cannabinoid receptor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.293 
  • R-Value Observed: 0.295 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Molecular mechanism of allosteric modulation for the cannabinoid receptor CB1.

Yang, X.Wang, X.Xu, Z.Wu, C.Zhou, Y.Wang, Y.Lin, G.Li, K.Wu, M.Xia, A.Liu, J.Cheng, L.Zou, J.Yan, W.Shao, Z.Yang, S.

(2022) Nat Chem Biol 18: 831-840

  • DOI: https://doi.org/10.1038/s41589-022-01038-y
  • Primary Citation of Related Structures:  
    7FEE, 7WV9

  • PubMed Abstract: 

    Given the promising clinical value of allosteric modulators of G protein-coupled-receptors (GPCRs), mechanistic understanding of how these modulators alter GPCR function is of significance. Here, we report the crystallographic and cryo-electron microscopy structures of the cannabinoid receptor CB1 bound to the positive allosteric modulator (PAM) ZCZ011. These structures show that ZCZ011 binds to an extrahelical site in the transmembrane 2 (TM2)-TM3-TM4 surface. Through (un)biased molecular dynamics simulations and mutagenesis experiments, we show that TM2 rearrangement is critical for the propagation of allosteric signals. ZCZ011 exerts a PAM effect by promoting TM2 rearrangement in favor of receptor activation and increasing the population of receptors that adopt an active conformation. In contrast, ORG27569, a negative allosteric modulator (NAM) of CB1, also binds to the TM2-TM3-TM4 surface and exerts a NAM effect by impeding the TM2 rearrangement. Our findings fill a gap in the understanding of CB1 allosteric regulation and could guide the rational design of CB1 allosteric modulators.


  • Organizational Affiliation

    State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cannabinoid receptor 1,GlgA glycogen synthase559Homo sapiensPyrococcus abyssi GE5Mutation(s): 6 
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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
9GF
Query on 9GF

Download Ideal Coordinates CCD File 
D [auth A]2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol
C24 H40 O3
YNZFFALZMRAPHQ-SYYKKAFVSA-N
7IC
Query on 7IC

Download Ideal Coordinates CCD File 
E [auth A]6-methyl-3-[(1S)-2-nitro-1-thiophen-2-yl-ethyl]-2-phenyl-1H-indole
C21 H18 N2 O2 S
RJSPNRDBWHHFMH-KRWDZBQOSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
L [auth A],
M [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 
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.293 
  • R-Value Observed: 0.295 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.79α = 90
b = 74.33β = 90
c = 184.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-04-03
    Changes: Structure summary