4PHU

Crystal structure of Human GPR40 bound to allosteric agonist TAK-875

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

High-resolution structure of the human GPR40 receptor bound to allosteric agonist TAK-875.

Srivastava, A., Yano, J., Hirozane, Y., Kefala, G., Gruswitz, F., Snell, G., Lane, W., Ivetac, A., Aertgeerts, K., Nguyen, J., Jennings, A., Okada, K.

(2014) Nature 513: 124-127

  • DOI: 10.1038/nature13494
  • Primary Citation of Related Structures:  
    4PHU

  • PubMed Abstract: 

    • Human GPR40 receptor (hGPR40), also known as free fatty-acid receptor 1 (FFAR1), is a G-protein-coupled receptor that binds long-chain free fatty acids to enhance glucose-dependent insulin secretion. Novel treatments for type-2 diabetes mellitus are ...

    Human GPR40 receptor (hGPR40), also known as free fatty-acid receptor 1 (FFAR1), is a G-protein-coupled receptor that binds long-chain free fatty acids to enhance glucose-dependent insulin secretion. Novel treatments for type-2 diabetes mellitus are therefore possible by targeting hGPR40 with partial or full agonists. TAK-875, or fasiglifam, is an orally available, potent and selective partial agonist of hGPR40 receptor, which reached phase III clinical trials for the potential treatment of type-2 diabetes mellitus. Data from clinical studies indicate that TAK-875, which is an ago-allosteric modulator of hGPR40 (ref. 3), demonstrates improved glycaemic control and low hypoglycaemic risk in diabetic patients. Here we report the crystal structure of hGPR40 receptor bound to TAK-875 at 2.3 Å resolution. The co-complex structure reveals a unique binding mode of TAK-875 and suggests that entry to the non-canonical binding pocket most probably occurs via the lipid bilayer. The atomic details of the extensive charge network in the ligand binding pocket reveal additional interactions not identified in previous studies and contribute to a clear understanding of TAK-875 binding to the receptor. The hGPR40-TAK-875 structure also provides insights into the plausible binding of multiple ligands to the receptor, which has been observed in radioligand binding and Ca(2+) influx assay studies. Comparison of the transmembrane helix architecture with other G-protein-coupled receptors suggests that the crystallized TAK-875-bound hGPR40 complex is in an inactive-like state.

    Organizational Affiliation: 

    Biomolecular Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Free fatty acid receptor 1,LysozymeA491Homo sapiens, Escherichia virus T4Mutation(s): 6 
Gene Names: FFAR1, GPR40
EC: 3.2.1.17
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A		Protein: 
GPR40 free fatty-acid receptor 1 (FFAR1) bound to TAK-875
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
GTEx  ENSG00000126266
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2YB
Query on 2YB
Download CCD File 
A
[(3S)-6-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy]biphenyl-3-yl}methoxy)-2,3-dihydro-1-benzofuran-3-yl]acetic acid
C29 H32 O7 S
BZCALJIHZVNMGJ-HSZRJFAPSA-N		 Ligand Interaction
OLC
Query on OLC
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N		 Ligand Interaction
1PE
Query on 1PE
Download CCD File 
A
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2YBEC50:  58   nM  BindingDB
2YBEC50:  14   nM  BindingDB
2YBEC50:  21.8799991607666   nM  BindingDB
2YBEC50:  16   nM  BindingDB
2YBEC50:  42   nM  BindingDB
2YBEC50:  45   nM  BindingDB
2YBEC50:  39   nM  BindingDB
2YBKi:  29   nM  BindingDB
2YBEC50:  1.899999976158142   nM  BindingDB
2YBEC50:  25.700000762939453   nM  BindingDB
2YBKd:  16   nM  Binding MOAD
2YBEC50:  14.130000114440918   nM  BindingDB
2YBEC50:  30   nM  BindingDB
2YBEC50:  27   nM  BindingDB
2YBEC50:  28   nM  BindingDB
2YBEC50:  34   nM  BindingDB
2YBKi:  38   nM  BindingDB
2YBEC50:  32   nM  BindingDB
2YBEC50:  33   nM  BindingDB
2YBEC50:  80   nM  BindingDB
2YBEC50:  5100   nM  BindingDB
2YBEC50:  9.300000190734863   nM  BindingDB
2YBEC50:  26   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101α = 90
b = 61.74β = 108.9
c = 105.7γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2014-08-06
    Changes: Database references
  • Version 1.3: 2014-10-01
    Changes: Database references
  • Version 1.4: 2015-02-04
    Changes: Derived calculations
  • Version 1.5: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy