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 
  • R-Value Observed: 0.233 

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
  • Primary Citation of Related Structures:  
    5KW2

  • 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 Research Laboratories, Lilly Corporate Center, 355 East Merrill Street, Indianapolis, IN, 46285, USA. hamdouchi_chafiq@lilly.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Free fatty acid receptor 1,Lysozyme,Free fatty acid receptor 1A491Homo sapiensEscherichia virus T4Mutation(s): 6 
Gene Names: FFAR1GPR40
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for O14842 (Homo sapiens)
Explore O14842 
Go to UniProtKB:  O14842
NIH Common Fund Data Resources
PHAROS  O14842
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XQ
Query on 6XQ

Download Ideal Coordinates 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 
  • R-Value Observed: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.654α = 90
b = 55.95β = 93.77
c = 80.313γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

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