6ORV

Non-peptide agonist (TT-OAD2) bound to the Glucagon-Like peptide-1 (GLP-1) Receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Activation of the GLP-1 receptor by a non-peptidic agonist.

Zhao, P.Liang, Y.L.Belousoff, M.J.Deganutti, G.Fletcher, M.M.Willard, F.S.Bell, M.G.Christe, M.E.Sloop, K.W.Inoue, A.Truong, T.T.Clydesdale, L.Furness, S.G.B.Christopoulos, A.Wang, M.W.Miller, L.J.Reynolds, C.A.Danev, R.Sexton, P.M.Wootten, D.

(2020) Nature --: --

  • DOI: 10.1038/s41586-019-1902-z

  • PubMed Abstract: 
  • Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, including diabetes and obesity <sup>1 </sup>. Structures of active receptors reveal peptide agonists engage deep within the receptor core, leading to an outw ...

    Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, including diabetes and obesity 1 . Structures of active receptors reveal peptide agonists engage deep within the receptor core, leading to an outward movement of extracellular loop 3 and the tops of transmembrane helices 6 and 7, an inward movement of transmembrane helix 1, reorganization of extracellular loop 2 and outward movement of the intracellular side of transmembrane helix 6, resulting in G-protein interaction and activation 2-6 . Here we solved the structure of a non-peptide agonist, TT-OAD2, bound to the glucagon-like peptide-1 (GLP-1) receptor. Our structure identified an unpredicted non-peptide agonist-binding pocket in which reorganization of extracellular loop 3 and transmembrane helices 6 and 7 manifests independently of direct ligand interaction within the deep transmembrane domain pocket. TT-OAD2 exhibits biased agonism, and kinetics of G-protein activation and signalling that are distinct from peptide agonists. Within the structure, TT-OAD2 protrudes beyond the receptor core to interact with the lipid or detergent, providing an explanation for the distinct activation kinetics that may contribute to the clinical efficacy of this compound series. This work alters our understanding of the events that drive the activation of class B receptors.


    Organizational Affiliation

    Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA.,The National Center for Drug Screening and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Biological Sciences, University of Essex, Colchester, UK.,School of Pharmacy, Fudan University, Shanghai, China. patrick.sexton@monash.edu.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia. denise.wootten@monash.edu.,Graduate School of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan. rado@m.u-tokyo.ac.jp.,School of Pharmacy, Fudan University, Shanghai, China. denise.wootten@monash.edu.,School of Pharmacy, Fudan University, Shanghai, China.,Mayo Clinic, Scottsdale, AZ, USA.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia. patrick.sexton@monash.edu.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
AP
394Homo sapiensMutation(s): 0 
Gene Names: GNAS (GNAS1, GSP)
Find proteins for P63092 (Homo sapiens)
Go to Gene View: GNAS
Go to UniProtKB:  P63092
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
BP
350Homo sapiensMutation(s): 0 
Gene Names: GNB1
Find proteins for P62873 (Homo sapiens)
Go to Gene View: GNB1
Go to UniProtKB:  P62873
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
GP
71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Find proteins for P59768 (Homo sapiens)
Go to Gene View: GNG2
Go to UniProtKB:  P59768
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Nanobody 35
NP
138N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Glucagon-like peptide 1 receptor
RP
491Homo sapiensMutation(s): 0 
Gene Names: GLP1R
Find proteins for P43220 (Homo sapiens)
Go to Gene View: GLP1R
Go to UniProtKB:  P43220
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N2V
Query on N2V

Download SDF File 
Download CCD File 
RP
N-{(3S,8S)-3-{4-[(3,4-dichlorophenyl)methoxy]phenyl}-7-[(1S)-1-phenylpropyl]-2,3,6,7,8,9-hexahydro[1,4]dioxino[2,3-g]isoquinoline-8-carbonyl}-4-(2,3-dimethylpyridin-4-yl)-L-phenylalanine
C50 H47 Cl2 N3 O6
DEDPYBWOUXWMOX-ZTAAISNPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2020-01-22
    Type: Database references