7VOE

Crystal structure of 5-HT2AR in complex with aripiprazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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: 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) ...

    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. wangsheng@sibcb.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 2A,Soluble cytochrome b562A376Homo 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
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P28223
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9SC (Subject of Investigation/LOI)
Query on 9SC

Download Ideal Coordinates CCD File 
J [auth A]7-[4-[4-[2,3-bis(chloranyl)phenyl]piperazin-1-yl]butoxy]-3,4-dihydro-1H-quinolin-2-one
C23 H27 Cl2 N3 O2
CEUORZQYGODEFX-UHFFFAOYSA-N
 Ligand Interaction
CLR
Query on CLR

Download Ideal Coordinates CCD File 
B [auth A],
G [auth A],
I [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
OLC
Query on OLC

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
H [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
C [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.27α = 90
b = 54.28β = 90
c = 179.55γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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