8ZMG | pdb_00008zmg

Crystal structure of an inverse agonist antipsychotic drug pimavanserin-bound 5-HT2A

• PDB DOI: https://doi.org/10.2210/pdb8ZMG/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-05-23 Released: 2024-08-28 
• Deposition Author(s): Oguma, T., Asada, H., Sekiguchi, Y., Imono, M., Iwata, S., Kusakabe, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.328 (Depositor), 0.326 (DCC) 
• R-Value Work: 
  0.291 (Depositor), 0.291 (DCC) 
• R-Value Observed: 
  0.294 (Depositor) 

Starting Model: experimental

Literature

Dual 5-HT 2A and 5-HT 2C Receptor Inverse Agonist That Affords In Vivo Antipsychotic Efficacy with Minimal hERG Inhibition for the Treatment of Dementia-Related Psychosis.

Oguma, T., Jino, K., Nakahara, K., Asada, H., Fuchino, K., Nagatani, K., Kouki, K., Okamoto, R., Takai, N., Koda, K., Fujita, S., Sekiguchi, Y., Yasuo, K., Mayumi, K., Abe, A., Imono, M., Horiguchi, N., Iwata, S., Kusakabe, K.I.

(2024) J Med Chem 67: 14478-14492

• PubMed: 39137033 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c01244
• Primary Citation Related Structures: 
  8ZMF, 8ZMG


• PubMed Abstract: 
  

  Psychosis is a distressing symptom commonly occurring in people with dementia. To treat Parkinson's disease psychosis, pimavanserin ( 1 ), a 5-HT _2A receptor inverse agonist having minimal 5-HT _2C receptor affinity and no dopamine D ₂ receptor affinity, was approved in the United States, but not for dementia-related psychosis due to limited efficacy issues. Herein, we report on the identification of a potent and dual 5-HT _2A and 5-HT _2C receptor inverse agonist 8 having minimal hERG inhibition, after having demonstrated the involvement of both 5-HT _2A and 5-HT _2C receptors to deliver antipsychotic efficacy in an MK-801-induced locomotor model and having conducted 5-HT _2A and 5-HT _2C occupancy studies including a surrogate method. The introduction of a spirocyclopropyl group boosting 5-HT _2C affinity in 1 followed by further optimization to control lipophilicity resulted in balanced dual potency and metabolic stability, and mitigating hERG inhibition led to 8 that showed significant antipsychotic efficacy due to the involvement of both receptors.

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Organizational Affiliation: 
• Laboratory for Medicinal Chemistry Research, Shionogi Pharmaceutical Research Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.
Laboratory for Drug Discovery & Disease Research, Shionogi Pharmaceutical Research Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo-yu, Kyoto 606-8501, Japan.
Laboratory for Bio-Modality Research, Shionogi Pharmaceutical Research Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.
Laboratory for Drug Discovery & Development, Shionogi Pharmaceutical Research Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.07 kDa 
• Atom Count: 5,769 
• Modeled Residue Count: 726 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 2A,Soluble cytochrome b562	A, B	414	Homo sapiens, Escherichia coli	Mutation(s): 6  Gene Names: HTR2A, HTR2, cybC
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P28223 (Homo sapiens) Explore P28223  Go to UniProtKB:  P28223
PHAROS:  P28223 GTEx:  ENSG00000102468
UniProt Groups	P28223P0ABE7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L11 (Subject of Investigation/LOI)	C [auth A], D [auth B]	Pimavanserin C25 H34 F N3 O2 RKEWSXXUOLRFBX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.328 (Depositor), 0.326 (DCC) 
• R-Value Work:  0.291 (Depositor), 0.291 (DCC) 
• R-Value Observed: 0.294 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 276.26	α = 90
b = 42.04	β = 93.147
c = 90.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Oguma, T., Asada, H., Sekiguchi, Y., Imono, M., Iwata, S., Kusakabe, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22KK0099

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release
  
• Version 1.1: 2024-09-04
  Changes: Database references, Structure summary
• Version 1.2: 2024-10-09
  Changes: Structure summary