22WT | pdb_000022wt

local refinement of 5HT2BR-fab heterotrimer in complex with a novel antagonist IHCH-2330

• PDB DOI: https://doi.org/10.2210/pdb22WT/pdb
• EM Map EMD-68739: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2026-01-26 Released: 2026-09-16 
• Deposition Author(s): Tang, L., Ji, X., Cheng, J., Wang, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences, Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanistic Basis for 5-HT 2A R Over 5-HT 2B R Activation.

Tang, L., Ji, X., Wang, Y., Cao, D., Li, H., He, L., Cheng, J., Wang, S.

(2026) Nat Commun 17

• PubMed: 42754589 
• DOI: https://doi.org/10.1038/s41467-026-77659-x
• Primary Citation Related Structures: 
  22WP, 22WR, 22WT, 9WND, 9WNF, 9WNG


• PubMed Abstract: 
  

  Selective 5-HT _2A R agonism without 5-HT _2B R activation is critical for safe psychedelic-inspired therapeutics. Here, we systematically probe the ligand-binding pockets of 5-HT _2A R and 5-HT _2B R and identify steric and conformational constraints at the side-extended pocket (SEP) and extended binding pocket (EBP) that dictate ligand orientation and receptor signaling. Guided by these insights, we design derivatives across tryptamine and phenethylamine scaffolds that integrate SEP and EBP engagement with scaffold modification to reinforce 5-HT _2A R activation while limiting 5-HT _2B R activity. Cryo-EM structures of 5-HT _2A R and 5-HT _2B R bound to IHCH-2330, a selective 5-HT _2A R agonist and 5-HT _2B R antagonist, confirm the design principle. These findings show differential activation mechanisms between 5-HT _2A R and 5-HT _2B R and provide a rational framework for engineering safer, functionally selective serotonergic compounds, mitigating 5-HT _2B R-mediated side effects while preserving therapeutic efficacy.

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Organizational Affiliation: 
• 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.
School of Life Science and Technology, ShanghaiTech University, 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].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 32.19 kDa 
• Atom Count: 1,872 
• Modeled Residue Count: 252 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 2B	A [auth R]	280	Homo sapiens	Mutation(s): 0  Gene Names: HTR2B
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EXY (Subject of Investigation/LOI)	C [auth R]	3-[2-[2-[2,5-dimethoxy-4-(trifluoromethyl)phenyl]ethyl-methyl-amino]ethyl]-2-methyl-pyrido[1,2-a]pyrimidin-4-one C23 H26 F3 N3 O3 YRZLOPLPHUOJSL-UHFFFAOYSA-N
NAG (Subject of Investigation/LOI)	B [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	CCP4 package

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-16 
Deposition Author(s): Tang, L., Ji, X., Cheng, J., Wang, S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--
Chinese Academy of Sciences	China	--
Ministry of Science and Technology (MoST, China)	China	--

Revision History  

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