7DFP

Human dopamine D2 receptor in complex with spiperone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of the dopamine D 2 receptor in complex with the antipsychotic drug spiperone.

Im, D.Inoue, A.Fujiwara, T.Nakane, T.Yamanaka, Y.Uemura, T.Mori, C.Shiimura, Y.Kimura, K.T.Asada, H.Nomura, N.Tanaka, T.Yamashita, A.Nango, E.Tono, K.Kadji, F.M.N.Aoki, J.Iwata, S.Shimamura, T.

(2020) Nat Commun 11: 6442-6442

  • DOI: https://doi.org/10.1038/s41467-020-20221-0
  • Primary Citation of Related Structures:  
    7DFP

  • PubMed Abstract: 

    In addition to the serotonin 5-HT 2A receptor (5-HT 2A R), the dopamine D 2 receptor (D 2 R) is a key therapeutic target of antipsychotics for the treatment of schizophrenia. The inactive state structures of D 2 R have been described in complex with the inverse agonists risperidone (D 2 R ris ) and haloperidol (D 2 R hal ). Here we describe the structure of human D 2 R in complex with spiperone (D 2 R spi ). In D 2 R spi , the conformation of the extracellular loop (ECL) 2, which composes the ligand-binding pocket, was substantially different from those in D 2 R ris and D 2 R hal , demonstrating that ECL2 in D 2 R is highly dynamic. Moreover, D 2 R spi exhibited an extended binding pocket to accommodate spiperone's phenyl ring, which probably contributes to the selectivity of spiperone to D 2 R and 5-HT 2A R. Together with D 2 R ris and D 2 R hal , the structural information of D 2 R spi should be of value for designing novel antipsychotics with improved safety and efficacy.


  • Organizational Affiliation

    Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D(2) dopamine receptor,Soluble cytochrome b562360Homo sapiensEscherichia coliMutation(s): 6 
Gene Names: DRD2cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P14416 (Homo sapiens)
Explore P14416 
Go to UniProtKB:  P14416
PHAROS:  P14416
GTEx:  ENSG00000149295 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P14416
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FabL215Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FabH220Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIP (Subject of Investigation/LOI)
Query on SIP

Download Ideal Coordinates CCD File 
D [auth A]8-[4-(4-fluorophenyl)-4-oxidanylidene-butyl]-1-phenyl-1,3,8-triazaspiro[4.5]decan-4-one
C23 H26 F N3 O2
DKGZKTPJOSAWFA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.9α = 90
b = 40.5β = 116.5
c = 165.9γ = 90
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-29
    Changes: Refinement description