Crystal structure of the human glucagon receptor (GCGR) in complex with the antagonist MK-0893

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

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This is version 1.3 of the entry. See complete history


Extra-helical binding site of a glucagon receptor antagonist.

Jazayeri, A.Dore, A.S.Lamb, D.Krishnamurthy, H.Southall, S.M.Baig, A.H.Bortolato, A.Koglin, M.Robertson, N.J.Errey, J.C.Andrews, S.P.Teobald, I.Brown, A.J.Cooke, R.M.Weir, M.Marshall, F.H.

(2016) Nature 533: 274-277

  • DOI: https://doi.org/10.1038/nature17414
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Glucagon is a 29-amino-acid peptide released from the α-cells of the islet of Langerhans, which has a key role in glucose homeostasis. Glucagon action is transduced by the class B G-protein-coupled glucagon receptor (GCGR), which is located on liver, kidney, intestinal smooth muscle, brain, adipose tissue, heart and pancreas cells, and this receptor has been considered an important drug target in the treatment of diabetes. Administration of recently identified small-molecule GCGR antagonists in patients with type 2 diabetes results in a substantial reduction of fasting and postprandial glucose concentrations. Although an X-ray structure of the transmembrane domain of the GCGR has previously been solved, the ligand (NNC0640) was not resolved. Here we report the 2.5 Å structure of human GCGR in complex with the antagonist MK-0893 (ref. 4), which is found to bind to an allosteric site outside the seven transmembrane (7TM) helical bundle in a position between TM6 and TM7 extending into the lipid bilayer. Mutagenesis of key residues identified in the X-ray structure confirms their role in the binding of MK-0893 to the receptor. The unexpected position of the binding site for MK-0893, which is structurally similar to other GCGR antagonists, suggests that glucagon activation of the receptor is prevented by restriction of the outward helical movement of TM6 required for G-protein coupling. Structural knowledge of class B receptors is limited, with only one other ligand-binding site defined--for the corticotropin-releasing hormone receptor 1 (CRF1R)--which was located deep within the 7TM bundle. We describe a completely novel allosteric binding site for class B receptors, providing an opportunity for structure-based drug design for this receptor class and furthering our understanding of the mechanisms of activation of these receptors.

  • Organizational Affiliation

    Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucagon receptor,Endolysin,Glucagon receptor452Homo sapiensTequatrovirus T4Mutation(s): 16 
Gene Names: GCGR
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P47871 (Homo sapiens)
Explore P47871 
Go to UniProtKB:  P47871
PHAROS:  P47871
GTEx:  ENSG00000215644 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P47871
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5MV

Download Ideal Coordinates CCD File 
B [auth A]3-[[4-[(1~{S})-1-[3-[3,5-bis(chloranyl)phenyl]-5-(6-methoxynaphthalen-2-yl)pyrazol-1-yl]ethyl]phenyl]carbonylamino]propanoic acid
C32 H27 Cl2 N3 O4
Query on PE5

Download Ideal Coordinates CCD File 
Q [auth A]3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
C18 H38 O9
Query on OLA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
C18 H34 O2
Query on TLA

Download Ideal Coordinates CCD File 
C4 H6 O6
Binding Affinity Annotations 
IDSourceBinding Affinity
5MV BindingDB:  5EE7 Ki: 70 (nM) from 1 assay(s)
IC50: min: 6.6, max: 600 (nM) from 9 assay(s)
Binding MOAD:  5EE7 Kd: 0.62 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.583α = 90
b = 71.476β = 90
c = 183.108γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2016-05-18
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary