7S15

GLP-1 receptor bound with Pfizer small molecule agonist


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Small-Molecule Oral Agonist of the Human Glucagon-like Peptide-1 Receptor.

Griffith, D.A.Edmonds, D.J.Fortin, J.P.Kalgutkar, A.S.Kuzmiski, J.B.Loria, P.M.Saxena, A.R.Bagley, S.W.Buckeridge, C.Curto, J.M.Derksen, D.R.Dias, J.M.Griffor, M.C.Han, S.Jackson, V.M.Landis, M.S.Lettiere, D.Limberakis, C.Liu, Y.Mathiowetz, A.M.Patel, J.C.Piotrowski, D.W.Price, D.A.Ruggeri, R.B.Tess, D.A.

(2022) J Med Chem 65: 8208-8226

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01856
  • Primary Citation of Related Structures:  
    7S15

  • PubMed Abstract: 

    Peptide agonists of the glucagon-like peptide-1 receptor (GLP-1R) have revolutionized diabetes therapy, but their use has been limited because they require injection. Herein, we describe the discovery of the orally bioavailable, small-molecule, GLP-1R agonist PF-06882961 (danuglipron). A sensitized high-throughput screen was used to identify 5-fluoropyrimidine-based GLP-1R agonists that were optimized to promote endogenous GLP-1R signaling with nanomolar potency. Incorporation of a carboxylic acid moiety provided considerable GLP-1R potency gains with improved off-target pharmacology and reduced metabolic clearance, ultimately resulting in the identification of danuglipron. Danuglipron increased insulin levels in primates but not rodents, which was explained by receptor mutagensis studies and a cryogenic electron microscope structure that revealed a binding pocket requiring a primate-specific tryptophan 33 residue. Oral administration of danuglipron to healthy humans produced dose-proportional increases in systemic exposure (NCT03309241). This opens an opportunity for oral small-molecule therapies that target the well-validated GLP-1R for metabolic health.


  • Organizational Affiliation

    Pfizer Worldwide Research, Development, and Medical, Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptorA [auth R]399Homo sapiensMutation(s): 8 
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43220
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
82L (Subject of Investigation/LOI)
Query on 82L

Download Ideal Coordinates CCD File 
B [auth R]2-[(4-{6-[(2,4-difluorophenyl)methoxy]pyridin-2-yl}piperidin-1-yl)methyl]-1-[(1-ethyl-1H-imidazol-5-yl)methyl]-1H-benzimidazole-6-carboxylic acid
C32 H32 F2 N6 O3
IFXPEJAGKQFBER-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2022-07-06
    Changes: Database references