5KW2

The extra-helical binding site of GPR40 and the structural basis for allosteric agonism and incretin stimulation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for GPR40 allosteric agonism and incretin stimulation.

Ho, J.D.Chau, B.Rodgers, L.Lu, F.Wilbur, K.L.Otto, K.A.Chen, Y.Song, M.Riley, J.P.Yang, H.C.Reynolds, N.A.Kahl, S.D.Lewis, A.P.Groshong, C.Madsen, R.E.Conners, K.Lineswala, J.P.Gheyi, T.Saflor, M.D.Lee, M.R.Benach, J.Baker, K.A.Montrose-Rafizadeh, C.Genin, M.J.Miller, A.R.Hamdouchi, C.

(2018) Nat Commun 9: 1645-1645

  • DOI: 10.1038/s41467-017-01240-w

  • PubMed Abstract: 
  • Activation of free fatty acid receptor 1 (GPR40) by synthetic partial and full agonists occur via distinct allosteric sites. A crystal structure of GPR40-TAK-875 complex revealed the allosteric site for the partial agonist. Here we report the 2.76-Å ...

    Activation of free fatty acid receptor 1 (GPR40) by synthetic partial and full agonists occur via distinct allosteric sites. A crystal structure of GPR40-TAK-875 complex revealed the allosteric site for the partial agonist. Here we report the 2.76-Å crystal structure of human GPR40 in complex with a synthetic full agonist, compound 1, bound to the second allosteric site. Unlike TAK-875, which acts as a Gα q -coupled partial agonist, compound 1 is a dual Gα q and Gα s -coupled full agonist. compound 1 binds in the lipid-rich region of the receptor near intracellular loop 2 (ICL2), in which the stabilization of ICL2 by the ligand is likely the primary mechanism for the enhanced G protein activities. The endogenous free fatty acid (FFA), γ-linolenic acid, can be computationally modeled in this site. Both γ-linolenic acid and compound 1 exhibit positive cooperativity with TAK-875, suggesting that this site could also serve as a FFA binding site.


    Organizational Affiliation

    Lilly Biotechnology Center San Diego, 10290 Campus Point Drive, San Diego, CA, 92121, USA.,Lilly Research Laboratories, Lilly Corporate Center, 355 East Merrill Street, Indianapolis, IN, 46285, USA.,Lilly Research Laboratories, Lilly Corporate Center, 355 East Merrill Street, Indianapolis, IN, 46285, USA. hamdouchi_chafiq@lilly.com.,Lilly Research Laboratories Collaborative Access Team, Advanced Photon Source, Argonne National Laboratory, Building 438A, 9700 S. Cass Avenue, Lemont, IL, 60439, USA.,Lilly Biotechnology Center San Diego, 10290 Campus Point Drive, San Diego, CA, 92121, USA. ho_joseph_d@lilly.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Free fatty acid receptor 1,Lysozyme,Free fatty acid receptor 1
A
491Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 6 
Gene Names: FFAR1 (GPR40), E
EC: 3.2.1.17
Find proteins for O14842 (Homo sapiens)
Go to Gene View: FFAR1
Go to UniProtKB:  O14842
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XQ
Query on 6XQ

Download SDF File 
Download CCD File 
A
(3~{S})-3-cyclopropyl-3-[2-[1-[2-[2,2-dimethylpropyl-(6-methylpyridin-2-yl)carbamoyl]-5-methoxy-phenyl]piperidin-4-yl]-1-benzofuran-6-yl]propanoic acid
C38 H45 N3 O5
RJZJYKXHTPUHAO-HKBQPEDESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 147.654α = 90.00
b = 55.950β = 93.77
c = 80.313γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-09
    Type: Data collection, Database references