7JOZ

Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 

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Literature

Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist.

Sun, B.Feng, D.Chu, M.L.Fish, I.Lovera, S.Sands, Z.A.Kelm, S.Valade, A.Wood, M.Ceska, T.Kobilka, T.S.Lebon, F.Kobilka, B.K.

(2021) Nat Commun 12: 3305-3305

  • DOI: https://doi.org/10.1038/s41467-021-23519-9
  • Primary Citation of Related Structures:  
    7JOZ

  • PubMed Abstract: 

    Dopamine D1 receptor (D1R) is an important drug target implicated in many psychiatric and neurological disorders. Selective agonism of D1R are sought to be the therapeutic strategy for these disorders. Most selective D1R agonists share a dopamine-like catechol moiety in their molecular structure, and their therapeutic potential is therefore limited by poor pharmacological properties in vivo. Recently, a class of non-catechol D1R selective agonists with a distinct scaffold and pharmacological properties were reported. Here, we report the crystal structure of D1R in complex with stimulatory G protein (Gs) and a non-catechol agonist Compound 1 at 3.8 Å resolution. The structure reveals the ligand bound to D1R in an extended conformation, spanning from the orthosteric site to extracellular loop 2 (ECL2). Structural analysis reveals that the unique features of D1R ligand binding pocket explains the remarkable selectivity of this scaffold for D1R over other aminergic receptors, and sheds light on the mechanism for D1R activation by the non-catechol agonist.


  • Organizational Affiliation

    ConfometRx, Inc., Santa Clara, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short380Homo sapiensMutation(s): 0 
Gene Names: GNASGNAS1GSP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
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PHAROS:  P63092
GTEx:  ENSG00000087460 
Entity Groups  
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UniProt GroupP63092
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1350Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 35D [auth N]160Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Endolysin,D(1A) dopamine receptorE [auth R]540Tequatrovirus T4Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: eT4Tp126DRD1
EC: 3.2.1.17
Membrane Entity: Yes 
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Find proteins for P21728 (Homo sapiens)
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PHAROS:  P21728
GTEx:  ENSG00000184845 
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UniProt GroupsP21728D9IEF7
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VFP (Subject of Investigation/LOI)
Query on VFP

Download Ideal Coordinates CCD File 
F [auth R]6-{4-[(furo[3,2-c]pyridin-4-yl)oxy]-2-methylphenyl}-1,5-dimethylpyrimidine-2,4(1H,3H)-dione
C20 H17 N3 O4
CKMFOKUQUOYIOR-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
G [auth R]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.194α = 90
b = 144.305β = 90
c = 147.069γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description