9WQ5 | pdb_00009wq5

5-HT2AR bound to IHCH-6122 in complex with mini-Gq and scFv16 obtained by cryo-electron microscopy (cryoEM)

• PDB DOI: https://doi.org/10.2210/pdb9WQ5/pdb
• EM Map EMD-66159: EMDB EMDataResource

• Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-09-10 Released: 2026-09-16 
• Deposition Author(s): Li, H., Tang, L., Zhang, J., Meng, B., Cao, D., Chen, Y., Yu, J., Liu, Z., Wang, S., Cheng, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-based design of subtype-selective psychedelic analogs.

Li, H., Tang, L., Zhang, J., Meng, B., Cao, D., Chen, Y., Yu, J., Wang, H., Liu, Z.J., Wang, S., Cheng, J.

(2026) Nat Commun 17

• PubMed: 42754591 
• DOI: https://doi.org/10.1038/s41467-026-77658-y
• Primary Citation Related Structures: 
  9WPQ, 9WPX, 9WQ5, 9WQ6, 9WQA, 9WQB


• PubMed Abstract: 
  

  Classical psychedelics exert hallucinogenic and therapeutic effects primarily through activation of serotonin 2 A receptor (5-HT _2A R), offering promise as transformative treatments for neuropsychiatric disorders. However, their concurrent activation of 5-HT _2B R-associated with cardiac valvulopathy-raises serious safety concerns, underscoring the need for subtype-selective psychedelics. To address this, we determine the cryo-EM structure of 5-HT _2A R and perform a comparative structural analysis of the orthosteric binding pockets (OBPs) of 5-HT _2A R and 5-HT _2B R. Guided by key residue differences, we develop a trigonal pharmacophore model to inform the design of 5-HT _2A R-selective agonists that avoid 5-HT _2B R activation. Using this model, we design and synthesize two compound series that selectively activate 5-HT _2A R while antagonizing 5-HT _2B R. Molecular basis of subtype selectivity is confirmed by five additional cryo-EM structures of receptor-ligand complexes. Selected compounds also exhibit antidepressant-like efficacy in animal models. Our findings provide a strategy for the development of safer, subtype-selective psychedelic analogs with therapeutic potential.

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Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
iHuman Institute, ShanghaiTech University, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China. [e-mail].
Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China. [e-mail].
Shanghai Academy of Natural Sciences (SANS), Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China. [e-mail].
iHuman Institute, ShanghaiTech University, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 142.32 kDa 
• Atom Count: 7,708 
• Modeled Residue Count: 1,118 
• Deposited Residue Count: 1,282 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 2A	A	339	Homo sapiens	Mutation(s): 0  Gene Names: HTR2A, HTR2
UniProt & NIH Common Fund Data Resources
Find proteins for P28223 (Homo sapiens) Explore P28223  Go to UniProtKB:  P28223
PHAROS:  P28223 GTEx:  ENSG00000102468

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B [auth C]	340	Homo sapiens	Mutation(s): 0  Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873  Go to UniProtKB:  P62873
PHAROS:  P62873 GTEx:  ENSG00000078369

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
G protein subunit q (Gi2-mini-Gq chimera)	C [auth B]	246	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
single-chain variable fragment 16 (scFv16)	E	286	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EYD (Subject of Investigation/LOI)	F [auth A]	3-piperazin-1-yl-5,6,7,8-tetrahydroisoquinoline C13 H19 N3 IPQHEOUVJXLYMR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-16 
Deposition Author(s): Li, H., Tang, L., Zhang, J., Meng, B., Cao, D., Chen, Y., Yu, J., Liu, Z., Wang, S., Cheng, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-09-16
  Type: Initial release
  
• Version 1.1: 2026-09-30
  Changes: Data collection, Database references