4ZGM

Crystal structure of Semaglutide peptide backbone in complex with the GLP-1 receptor extracellular domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of the Once-Weekly Glucagon-Like Peptide-1 (GLP-1) Analogue Semaglutide.

Lau, J.Bloch, P.Schaffer, L.Pettersson, I.Spetzler, J.Kofoed, J.Madsen, K.Knudsen, L.B.McGuire, J.Steensgaard, D.B.Strauss, H.M.Gram, D.X.Knudsen, S.M.Nielsen, F.S.Thygesen, P.Reedtz-Runge, S.Kruse, T.

(2015) J.Med.Chem. 58: 7370-7380

  • DOI: 10.1021/acs.jmedchem.5b00726

  • PubMed Abstract: 
  • Liraglutide is an acylated glucagon-like peptide-1 (GLP-1) analogue that binds to serum albumin in vivo and is approved for once-daily treatment of diabetes as well as obesity. The aim of the present studies was to design a once weekly GLP-1 analogue ...

    Liraglutide is an acylated glucagon-like peptide-1 (GLP-1) analogue that binds to serum albumin in vivo and is approved for once-daily treatment of diabetes as well as obesity. The aim of the present studies was to design a once weekly GLP-1 analogue by increasing albumin affinity and secure full stability against metabolic degradation. The fatty acid moiety and the linking chemistry to GLP-1 were the key features to secure high albumin affinity and GLP-1 receptor (GLP-1R) potency and in obtaining a prolonged exposure and action of the GLP-1 analogue. Semaglutide was selected as the optimal once weekly candidate. Semaglutide has two amino acid substitutions compared to human GLP-1 (Aib(8), Arg(34)) and is derivatized at lysine 26. The GLP-1R affinity of semaglutide (0.38 ± 0.06 nM) was three-fold decreased compared to liraglutide, whereas the albumin affinity was increased. The plasma half-life was 46.1 h in mini-pigs following i.v. administration, and semaglutide has an MRT of 63.6 h after s.c. dosing to mini-pigs. Semaglutide is currently in phase 3 clinical testing.


    Organizational Affiliation

    Global Research, Novo Nordisk A/S , Novo Nordisk Park, DK-2760 Måløv, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucagon-like peptide 1 receptor
A
122Homo sapiensMutation(s): 0 
Gene Names: GLP1R
Find proteins for P43220 (Homo sapiens)
Go to Gene View: GLP1R
Go to UniProtKB:  P43220
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Semaglutide peptide backbone; 8Aib,34R-GLP-1(7-37)-OH
B
31Homo sapiensMutation(s): 0 
Gene Names: GCG
Find proteins for P01275 (Homo sapiens)
Go to Gene View: GCG
Go to UniProtKB:  P01275
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
32M
Query on 32M

Download SDF File 
Download CCD File 
A, B
3,6,9,12,15,18-hexaoxahexacosan-1-ol
HEXAETHYLENE GLYCOL MONOOCTYL ETHER
C20 H42 O7
VVSOZSGWKFPDFX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AIB
Query on AIB
B
L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.610α = 90.00
b = 35.790β = 90.00
c = 42.680γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-04-23 
  • Released Date: 2015-09-09 
  • Deposition Author(s): Reedtz-Runge, S.

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references
  • Version 1.2: 2015-10-07
    Type: Database references