Structure of the human GLP-1 receptor complex with NNC0640

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

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Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators.

Song, G.Yang, D.Wang, Y.de Graaf, C.Zhou, Q.Jiang, S.Liu, K.Cai, X.Dai, A.Lin, G.Liu, D.Wu, F.Wu, Y.Zhao, S.Ye, L.Han, G.W.Lau, J.Wu, B.Hanson, M.A.Liu, Z.J.Wang, M.W.Stevens, R.C.

(2017) Nature 546: 312-315

  • DOI: https://doi.org/10.1038/nature22378
  • Primary Citation of Related Structures:  
    5VEW, 5VEX

  • PubMed Abstract: 

    The glucagon-like peptide-1 receptor (GLP-1R) and the glucagon receptor (GCGR) are members of the secretin-like class B family of G-protein-coupled receptors (GPCRs) and have opposing physiological roles in insulin release and glucose homeostasis. The treatment of type 2 diabetes requires positive modulation of GLP-1R to inhibit glucagon secretion and stimulate insulin secretion in a glucose-dependent manner. Here we report crystal structures of the human GLP-1R transmembrane domain in complex with two different negative allosteric modulators, PF-06372222 and NNC0640, at 2.7 and 3.0 Å resolution, respectively. The structures reveal a common binding pocket for negative allosteric modulators, present in both GLP-1R and GCGR and located outside helices V-VII near the intracellular half of the receptor. The receptor is in an inactive conformation with compounds that restrict movement of the intracellular tip of helix VI, a movement that is generally associated with activation mechanisms in class A GPCRs. Molecular modelling and mutagenesis studies indicate that agonist positive allosteric modulators target the same general region, but in a distinct sub-pocket at the interface between helices V and VI, which may facilitate the formation of an intracellular binding site that enhances G-protein coupling.

  • Organizational Affiliation

    iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptor, Endolysin chimera
A, B
455Homo sapiensTequatrovirus T4Mutation(s): 14 
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 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P43220
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 97V

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C29 H31 N7 O4 S
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CSD
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.81α = 91.55
b = 67.51β = 89.88
c = 83.66γ = 107.56
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references
  • Version 1.2: 2017-06-14
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description