6X19

Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Differential GLP-1R Binding and Activation by Peptide and Non-peptide Agonists.

Zhang, X.Belousoff, M.J.Zhao, P.Kooistra, A.J.Truong, T.T.Ang, S.Y.Underwood, C.R.Egebjerg, T.Senel, P.Stewart, G.D.Liang, Y.L.Glukhova, A.Venugopal, H.Christopoulos, A.Furness, S.G.B.Miller, L.J.Reedtz-Runge, S.Langmead, C.J.Gloriam, D.E.Danev, R.Sexton, P.M.Wootten, D.

(2020) Mol Cell 80: 485

  • DOI: https://doi.org/10.1016/j.molcel.2020.09.020
  • Primary Citation of Related Structures:  
    6X18, 6X19, 6X1A

  • PubMed Abstract: 

    Peptide drugs targeting class B1 G-protein-coupled receptors (GPCRs) can treat multiple diseases; however, there remains substantial interest in the development of orally delivered non-peptide drugs. Here, we reveal unexpected overlap between signaling and regulation of the glucagon-like peptide-1 (GLP-1) receptor by the non-peptide agonist PF 06882961 and GLP-1 that was not observed for another compound, CHU-128. Compounds from these patent series, including PF 06882961, are currently in clinical trials for treatment of type 2 diabetes. High-resolution cryoelectron microscopy (cryo-EM) structures reveal that the binding sites for PF 06882961 and GLP-1 substantially overlap, whereas CHU-128 adopts a unique binding mode with a more open receptor conformation at the extracellular face. Structural differences involving extensive water-mediated hydrogen bond networks could be correlated to functional data to understand how PF 06882961, but not CHU-128, can closely mimic the pharmacological properties of GLP-1. These findings will facilitate rational structure-based discovery of non-peptide agonists targeting class B GPCRs.


  • Organizational Affiliation

    Apigenex, Poděbradská 173/5, Prague 9 190 00, Czech Republic.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short394Homo sapiensMutation(s): 0 
Gene Names: GNASGNAS1GSP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
GTEx:  ENSG00000087460 
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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-1340Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  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]58Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody35D [auth N]128Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptorE [auth R]491Homo sapiensMutation(s): 0 
Gene Names: GLP1R
Membrane Entity: Yes 
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Find proteins for P43220 (Homo sapiens)
Explore P43220 
Go to UniProtKB:  P43220
GTEx:  ENSG00000112164 
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UniProt GroupP43220
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UK1 (Subject of Investigation/LOI)
Query on UK1

Download Ideal Coordinates CCD File 
F [auth R]3-{(1S)-1-[5-(2,2-dimethylmorpholin-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]butyl}-1,2,4-oxadiazol-5(4H)-one
C47 H49 F2 N11 O5
WUVYFHGOFAAJMK-AIJWEMPKSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1061044
National Health and Medical Research Council (NHMRC, Australia)Australia1065410
National Health and Medical Research Council (NHMRC, Australia)Australia1120919
National Health and Medical Research Council (NHMRC, Australia)Australia1126857
National Health and Medical Research Council (NHMRC, Australia)Australia1055134

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-10-21
    Changes: Database references
  • Version 1.2: 2020-11-18
    Changes: Database references