8ZMF | pdb_00008zmf

Crystal structure of an inverse agonist antipsychotic drug derivative-bound 5-HT2C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.285 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.263 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 
    0.265 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8ZMF

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • Laboratory for Medicinal Chemistry Research, Shionogi Pharmaceutical Research Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.

Macromolecule Content 

  • Total Structure Weight: 50.22 kDa 
  • Atom Count: 2,685 
  • Modeled Residue Count: 331 
  • Deposited Residue Count: 439 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 2C,Soluble cytochrome b562439Homo sapiensEscherichia coliMutation(s): 4 
Gene Names: HTR2CHTR1CcybC
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P28335 (Homo sapiens)
Explore P28335 
Go to UniProtKB:  P28335
PHAROS:  P28335
GTEx:  ENSG00000147246 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P28335
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L10
(Subject of Investigation/LOI)

Query on A1L10



Download:Ideal Coordinates CCD File
B [auth A]1-[(4-fluorophenyl)methyl]-1-[(8~{S})-5-methyl-5-azaspiro[2.5]octan-8-yl]-3-[[4-(2-methylpropoxy)phenyl]methyl]urea
C27 H36 F N3 O2
KQRKHYJZSCKWTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.285 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.263 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 0.265 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.84α = 90
b = 96.01β = 90
c = 149γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan22KK0099

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Structure summary