4ZGM | pdb_00004zgm

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.193 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.5b00726
  • Primary Citation Related Structures: 
    4ZGM

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 18.52 kDa 
  • Atom Count: 1,195 
  • Modeled Residue Count: 128 
  • Deposited Residue Count: 153 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptor122Homo sapiensMutation(s): 0 
Gene Names: GLP1R
UniProt & NIH Common Fund Data Resources
Find proteins for P43220 (Homo sapiens)
Explore P43220 
Go to UniProtKB:  P43220
PHAROS:  P43220
GTEx:  ENSG00000112164 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43220
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Semaglutide peptide backbone; 8Aib,34R-GLP-1(7-37)-OH31Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01275 (Homo sapiens)
Explore P01275 
Go to UniProtKB:  P01275
PHAROS:  P01275
GTEx:  ENSG00000115263 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01275
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AIB
Query on AIB
B
L-PEPTIDE LINKINGC4 H9 N O2ALA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.193 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.61α = 90
b = 35.79β = 90
c = 42.68γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Database references
  • Version 1.2: 2015-10-07
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description