8PKM | pdb_00008pkm

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
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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  
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UniProt GroupP62873
Sequence Annotations
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  • Reference Sequence
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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 
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 1AD [auth R]466Homo sapiensMutation(s): 0 
Gene Names: HTR1AADRB2RL1ADRBRL1
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 
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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 
F [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
ZKV (Subject of Investigation/LOI)
Query on ZKV

Download Ideal Coordinates CCD File 
G [auth R](3-chloranyl-4-fluoranyl-phenyl)-[4-fluoranyl-4-[[(5-methylpyridin-2-yl)methylamino]methyl]piperidin-1-yl]methanone
C20 H22 Cl F2 N3 O
PKZXLMVXBZICTF-UHFFFAOYSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
E [auth R]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ZKV BindingDB:  8PKM Ki: min: 0.4, max: 1 (nM) from 3 assay(s)
EC50: min: 23, max: 26 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
iNEXT-DiscoveryEuropean Union24759
German Research Foundation (DFG)GermanyINST 93/903-1
German Research Foundation (DFG)GermanyINST 93/1042-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-10-16
    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