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 8PJK | pdb_00008pjk

ST171-bound serotonin 5-HT1A receptor - Gi Protein Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8PJK

This is version 1.3 of the entry. See complete history. 

Literature

Discovery of a functionally selective serotonin receptor (5-HT 1A R) agonist for the treatment of pain.

Ullrich, A., Schneider, J., Braz, J.M., Neu, E., Staffen, N., Stanek, M., Blahova, J., Hove, T., Albert, T., Allikalt, A., Lober, S., Bhardwaj, K., Rodriguez-Rosado, S., Fink, E., Rasmussen, T., Hubner, H., Inoue, A., Shoichet, B.K., Basbaum, A.I., Bottcher, B., Weikert, D., Gmeiner, P.

(2025) Sci Adv 11: eadv9267-eadv9267

  • DOI: https://doi.org/10.1126/sciadv.adv9267
  • Primary Citation Related Structures: 
    8PJK, 8PKM, 9GL2

  • PubMed Abstract: 

    The heterotrimeric G protein-coupled serotonin receptor 5-HT 1A receptor (5-HT 1A R) mediates antinociception and may serve as a valuable target for the treatment of pain. Starting from a chemical library, we evolved ST171, a bitopic 5-HT 1A R agonist that revealed highly potent and functionally selective G i/o signaling without G s activation and marginal β-arrestin recruitment. ST171 is effective in acute and chronic pain models. Cryo-electron microscopy structures of ST171 bound to 5-HT 1A R in complex with the G i protein compared to the canonical agonist befiradol bound to complexes of 5-HT 1A R with G i or G s revealed that the ligands occupy different exo-sites. The individual binding poses are associated with ligand-specific receptor conformations that were further studied by molecular dynamics simulations, allowing us to better understand ligand bias, a phenomenon that may be crucial to the discovery of more effective and safe G protein-coupled receptor drugs.


  • Organizational Affiliation: 
    • Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.

Macromolecule Content 

  • Total Structure Weight: 140.62 kDa 
  • Atom Count: 7,227 
  • Modeled Residue Count: 902 
  • Deposited Residue Count: 1,243 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63096
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1352Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62873
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
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UniProt GroupP59768
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 1AD [auth R]466Homo sapiensMutation(s): 0 
Gene Names: HTR1A, ADRB2RL1, ADRBRL1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P08908 (Homo sapiens)
Explore P08908 
Go to UniProtKB:  P08908
PHAROS:  P08908
GTEx:  ENSG00000178394 
Entity Groups
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UniProt GroupP08908
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T7M

Query on T7M



Download:Ideal Coordinates CCD File
H [auth R](2R)-1-(heptadecanoyloxy)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate
C46 H82 O16 P2
WSLBJQQQZZTFBA-NPJVAJNNSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
E [auth R],
F [auth R]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
ZL9
(Subject of Investigation/LOI)

Query on ZL9



Download:Ideal Coordinates CCD File
G [auth R]6-[3-[2-(2-methoxyphenoxy)ethylamino]propoxy]-4~{H}-1,4-benzoxazin-3-one
C20 H24 N2 O5
JIDGHQZPZOREIN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
iNEXT-DiscoveryEuropean Union20311
German Research Foundation (DFG)GermanyINST 93/903-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-12-18
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-02
    Changes: Data collection, Database references