6KQI

Crystal Structure of protein1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.245 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 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. --: --

  • DOI: 10.1038/s41589-019-0387-2

  • 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 mechan ...

    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

    GM/CA, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA. dan.rosenbaum@utsouthwestern.edu.,Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1
A
492Pyrococcus abyssi (strain GE5 / Orsay)Homo sapiens
This entity is chimeric
Mutation(s): 5 
Gene Names: CNR1 (CNR)
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V2J8
Find proteins for P21554 (Homo sapiens)
Go to Gene View: CNR1
Go to UniProtKB:  P21554
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
OLA
Query on OLA

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Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
9GL
Query on 9GL

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Download CCD File 
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
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
9GF
Query on 9GF

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Download CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.245 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.342α = 90.00
b = 167.940β = 91.39
c = 41.526γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-11-13
    Type: Database references