Crystal structure of 5-HT2AR in complex with cariprazine

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structure-based design of a novel third-generation antipsychotic drug lead with potential antidepressant properties.

Chen, Z.Fan, L.Wang, H.Yu, J.Lu, D.Qi, J.Nie, F.Luo, Z.Liu, Z.Cheng, J.Wang, S.

(2022) Nat Neurosci 25: 39-49

  • DOI: https://doi.org/10.1038/s41593-021-00971-w
  • Primary Citation of Related Structures:  
    7VOD, 7VOE

  • PubMed Abstract: 

    Partial agonist activity at the dopamine D 2 receptor (DRD2) is a key feature of third-generation antipsychotics (TGAs). However, TGAs also act as antagonists or weak partial agonists to the serotonin (5-hydroxytryptamine; 5-HT) 2A receptor (5-HT 2A R). Here we present the crystal structures of aripiprazole- and cariprazine-bound human 5-HT 2A R. Both TGAs adopt an unexpected 'upside-down' pose in the 5-HT 2A R binding pocket, with secondary pharmacophores inserted in a similar way to a 'bolt'. This insight into the binding modes of TGAs offered a structural mechanism underlying their varied partial efficacies at 5-HT 2A R and DRD2. These structures enabled the design of a partial agonist at DRD2/3 and 5-HT 1A R with negligible 5-HT 2A R binding that displayed potent antipsychotic-like activity without motor side effects in mice. This TGA lead also had antidepressant-like effects and improved cognitive performance in mouse models via 5-HT 1A R. This work indicates that 5-HT 2A R affinity is a dispensable contributor to the therapeutic actions of TGAs.

  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 2A,Soluble cytochrome b562376Homo sapiensMutation(s): 7 
Gene Names: HTR2AHTR2cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P28223 (Homo sapiens)
Explore P28223 
Go to UniProtKB:  P28223
PHAROS:  P28223
GTEx:  ENSG00000102468 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP28223P0ABE7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7RU (Subject of Investigation/LOI)
Query on 7RU

Download Ideal Coordinates CCD File 
I [auth A]3-[4-[2-[4-[2,3-bis(chloranyl)phenyl]piperazin-1-yl]ethyl]cyclohexyl]-1,1-dimethyl-urea
C21 H32 Cl2 N4 O
Query on CLR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth A]
C27 H46 O
Query on OLC

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.27α = 90
b = 55.04β = 90
c = 180.29γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB19020111
Ministry of Science and Technology (MoST, China)China2020YFA0509600
National Natural Science Foundation of China (NSFC)China32071197

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Data collection, Structure summary
  • Version 1.2: 2022-02-16
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description