9BS9 | pdb_00009bs9

Local refinement of DRD2 bound to LSD in complex with a mini-GoA and scFv16 obtained by cryo-electron microscopy (cryoEM)

• PDB DOI: https://doi.org/10.2210/pdb9BS9/pdb
• EM Map EMD-44865: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-05-13 Released: 2025-09-17 
• Deposition Author(s): Kim, K., Gumpper, R.H., Fay, J.F., Roth, B.L.
• Funding Organization(s): Defense Advanced Research Projects Agency (DARPA)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The polypharmacology of psychedelics reveals multiple targets for potential therapeutics.

Jain, M.K., Gumpper, R.H., Slocum, S.T., Schmitz, G.P., Madsen, J.S., Tummino, T.A., Suomivuori, C.M., Huang, X.P., Shub, L., DiBerto, J.F., Kim, K., DeLeon, C., Krumm, B.E., Fay, J.F., Keiser, M., Hauser, A.S., Dror, R.O., Shoichet, B., Gloriam, D.E., Nichols, D.E., Roth, B.L.

(2025) Neuron 113: 3129-3142.e9

• PubMed: 40683247 
• DOI: https://doi.org/10.1016/j.neuron.2025.06.012
• Primary Citation of Related Structures:  
  9BS9, 9BSB


• PubMed Abstract: 
  

  The classical psychedelics (+)-lysergic acid diethylamide (LSD), psilocybin, and mescaline exert their psychedelic effects via activation of the 5-HT _2A serotonin receptor (5-HT _2A R). Recent clinical studies have suggested that classical psychedelics may additionally have therapeutic potential for many neuropsychiatric conditions including depression, anxiety, migraine and cluster headaches, drug abuse, and post-traumatic stress disorder. In this study, we investigated the pharmacology of 41 classical psychedelics from the tryptamine, phenethylamine, and lysergamide chemical classes. We profiled these compounds against 318 human G-protein-coupled receptors (GPCRs) to elucidate their target profiles, and in the case of LSD, against more than 450 human kinases. We found that psychedelics have potent and efficacious actions at nearly every serotonin, dopamine, and adrenergic receptor. We quantified their activation for multiple transducers and found that psychedelics stimulate multiple 5-HT _2A R transducers, each of which correlates with psychedelic drug-like actions in vivo. Our results suggest that multiple molecular targets likely contribute to the actions of psychedelics.

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Organizational Affiliation: 
• Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA.
Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark.
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94304, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.
National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA.
Institute of Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA 94158, USA.
Department of System Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea.
Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA.
Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA; National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA; Divison of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360, USA. Electronic address: [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: 67.56 kDa 
• Atom Count: 2,008 
• Modeled Residue Count: 263 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,D(2) dopamine receptor	A [auth R]	588	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: cybC, DRD2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P14416 (Homo sapiens) Explore P14416  Go to UniProtKB:  P14416
PHAROS:  P14416 GTEx:  ENSG00000149295

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7LD (Subject of Investigation/LOI)	B [auth R]	(8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide C20 H25 N3 O VAYOSLLFUXYJDT-RDTXWAMCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Kim, K., Gumpper, R.H., Fay, J.F., Roth, B.L.

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Funding Organization	Location	Grant Number
Defense Advanced Research Projects Agency (DARPA)	United States	HR0011-20-2-0029

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release
  
• Version 1.1: 2025-10-15
  Changes: Data collection, Database references