6XOX

cryo-EM of human GLP-1R bound to non-peptide agonist LY3502970


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for GLP-1 receptor activation by LY3502970, an orally active nonpeptide agonist.

Kawai, T.Sun, B.Yoshino, H.Feng, D.Suzuki, Y.Fukazawa, M.Nagao, S.Wainscott, D.B.Showalter, A.D.Droz, B.A.Kobilka, T.S.Coghlan, M.P.Willard, F.S.Kawabe, Y.Kobilka, B.K.Sloop, K.W.

(2020) Proc Natl Acad Sci U S A 117: 29959-29967

  • DOI: https://doi.org/10.1073/pnas.2014879117
  • Primary Citation of Related Structures:  
    6XOX

  • PubMed Abstract: 

    Glucagon-like peptide-1 receptor (GLP-1R) agonists are efficacious antidiabetic medications that work by enhancing glucose-dependent insulin secretion and improving energy balance. Currently approved GLP-1R agonists are peptide based, and it has proven difficult to obtain small-molecule activators possessing optimal pharmaceutical properties. We report the discovery and mechanism of action of LY3502970 (OWL833), a nonpeptide GLP-1R agonist. LY3502970 is a partial agonist, biased toward G protein activation over β-arrestin recruitment at the GLP-1R. The molecule is highly potent and selective against other class B G protein-coupled receptors (GPCRs) with a pharmacokinetic profile favorable for oral administration. A high-resolution structure of LY3502970 in complex with active-state GLP-1R revealed a unique binding pocket in the upper helical bundle where the compound is bound by the extracellular domain (ECD), extracellular loop 2, and transmembrane helices 1, 2, 3, and 7. This mechanism creates a distinct receptor conformation that may explain the partial agonism and biased signaling of the compound. Further, interaction between LY3502970 and the primate-specific Trp33 of the ECD informs species selective activity for the molecule. In efficacy studies, oral administration of LY3502970 resulted in glucose lowering in humanized GLP-1R transgenic mice and insulinotropic and hypophagic effects in nonhuman primates, demonstrating an effect size in both models comparable to injectable exenatide. Together, this work determined the molecular basis for the activity of an oral agent being developed for the treatment of type 2 diabetes mellitus, offering insights into the activation of class B GPCRs by nonpeptide ligands.


  • Organizational Affiliation

    Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka 412-8513, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha subunit of Gs with N-terminus swapped with equivalent residues in Gi,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas373Homo sapiensMutation(s): 0 
Gene Names: GNASGNAS1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
Find proteins for Q5JWF2 (Homo sapiens)
Explore Q5JWF2 
Go to UniProtKB:  Q5JWF2
PHAROS:  Q5JWF2
GTEx:  ENSG00000087460 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP63092Q5JWF2
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
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
single-chain variable fragment scFv16C [auth E]259Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [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 
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UniProt GroupP59768
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 35E [auth N]160Lama glamaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptorF [auth R]445Homo sapiensMutation(s): 1 
Gene Names: GLP1R
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P43220 (Homo sapiens)
Explore P43220 
Go to UniProtKB:  P43220
PHAROS:  P43220
GTEx:  ENSG00000112164 
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UniProt GroupP43220
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V6G (Subject of Investigation/LOI)
Query on V6G

Download Ideal Coordinates CCD File 
G [auth R]3-[(1S,2S)-1-(5-[(4S)-2,2-dimethyloxan-4-yl]-2-{(4S)-2-(4-fluoro-3,5-dimethylphenyl)-3-[3-(4-fluoro-1-methyl-1H-indazol-5-yl)-2-oxo-2,3-dihydro-1H-imidazol-1-yl]-4-methyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carbonyl}-1H-indol-1-yl)-2-methylcyclopropyl]-1,2,4-oxadiazol-5(4H)-one
C48 H48 F2 N10 O5
USUWIEBBBWHKNI-KHIFEHGGSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
V6G BindingDB:  6XOX EC50: min: 1.2, max: 600 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2020-12-09
    Changes: Database references
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Refinement description, Structure summary