9DGI | pdb_00009dgi

Cannabinoid receptor 1-Gi complex with novel ligand

• PDB DOI: https://doi.org/10.2210/pdb9DGI/pdb
• EM Map EMD-46828: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
• Mutation(s): No 


• Deposited: 2024-09-02 Released: 2025-04-30 
• Deposition Author(s): Tummino, T.A., Iliopoulos-Tsoutsouvas, C., Braz, J.M., O'Brien, E.S., Krishna Kumar, K., Makriyannis, M., Basbaum, A.I., Shoichet, B.K.
• Funding Organization(s): Defense Advanced Research Projects Agency (DARPA)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Virtual library docking for cannabinoid-1 receptor agonists with reduced side effects.

Tummino, T.A., Iliopoulos-Tsoutsouvas, C., Braz, J.M., O'Brien, E.S., Stein, R.M., Craik, V., Tran, N.K., Ganapathy, S., Liu, F., Shiimura, Y., Tong, F., Ho, T.C., Radchenko, D.S., Moroz, Y.S., Rosado, S.R., Bhardwaj, K., Benitez, J., Liu, Y., Kandasamy, H., Normand, C., Semache, M., Sabbagh, L., Glenn, I., Irwin, J.J., Kumar, K.K., Makriyannis, A., Basbaum, A.I., Shoichet, B.K.

(2025) Nat Commun 16: 2237-2237

• PubMed: 40044644 
• DOI: https://doi.org/10.1038/s41467-025-57136-7
• Primary Citation of Related Structures:  
  9DGI, 9EGO


• PubMed Abstract: 
  

  Virtual library docking can reveal unexpected chemotypes that complement the structures of biological targets. Seeking agonists for the cannabinoid-1 receptor (CB1R), we dock 74 million tangible molecules and prioritize 46 high ranking ones for de novo synthesis and testing. Nine are active by radioligand competition, a 20% hit-rate. Structure-based optimization of one of the most potent of these (K _i = 0.7 µM) leads to '1350, a 0.95 nM ligand and a full CB1R agonist of G _i/o signaling. A cryo-EM structure of '1350 in complex with CB1R-G _i1 confirms its predicted docked pose. The lead agonist is strongly analgesic in male mice, with a 2-20-fold therapeutic window over hypolocomotion, sedation, and catalepsy and no observable conditioned place preference. These findings suggest that unique cannabinoid chemotypes may disentangle characteristic cannabinoid side-effects from analgesia, supporting the further development of cannabinoids as pain therapeutics.

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Organizational Affiliation: 
• Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA.
Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA, 94158, USA.
Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, 02115, USA.
Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94158, USA.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Division of Molecular Genetics, Institute of Life Science, Kurume University, Fukuoka, Japan.
Enamine Ltd., 67 Winston Churchill Street, Kyiv, 02094, Ukraine.
National Taras Shevchenko University of Kyiv, 60 Volodymyrska Stree, Kyiv, 01601, Ukraine.
Chemspace LLC, 85 Winston Churchill Street, Suite 1, Kyiv, 02094, Ukraine.
National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), School of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA.
Domain Therapeutics North America Inc., Montréal, Québec, H4S 1Z9, Canada.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA. [e-mail].
Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, 02115, USA. [e-mail].
Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA. [e-mail].
Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94158, USA. [e-mail].
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 56.12 kDa 
• Atom Count: 2,048 
• Modeled Residue Count: 265 
• Deposited Residue Count: 495 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cannabinoid receptor 1	A [auth R]	495	Homo sapiens	Mutation(s): 0  Gene Names: CNR1, CNR
UniProt & NIH Common Fund Data Resources
Find proteins for P21554 (Homo sapiens) Explore P21554  Go to UniProtKB:  P21554
PHAROS:  P21554 GTEx:  ENSG00000118432

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YVF (Subject of Investigation/LOI)	B [auth R]	methyl (2R)-2-({(1M)-5-methyl-1-[3-(trifluoromethyl)phenyl]-1H-pyrazole-3-carbonyl}amino)-2-(thiophen-2-yl)propanoate C20 H18 F3 N3 O3 S XCJKFSDARVULKK-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Tummino, T.A., Iliopoulos-Tsoutsouvas, C., Braz, J.M., O'Brien, E.S., Krishna Kumar, K., Makriyannis, M., Basbaum, A.I., Shoichet, B.K.

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Funding Organization	Location	Grant Number
Defense Advanced Research Projects Agency (DARPA)	United States	HR0011-19-2-0020

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release
  
• Version 1.1: 2025-05-07
  Changes: Data collection, Database references