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

Experimental Data Snapshot

  • Resolution: 2.33 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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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: https://doi.org/10.1038/nature13494
  • Primary Citation of Related Structures:  

  • 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 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

    Department of Structural Biology and Core Sciences &Technology, Takeda California, 10410 Science Center Drive, San Diego, California 92121, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Free fatty acid receptor 1,Lysozyme491Homo sapiensTequatrovirus T4Mutation(s): 6 
Gene Names: FFAR1GPR40E
Membrane Entity: Yes 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720O14842
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2YB

Download Ideal Coordinates CCD File 
B [auth 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
Query on OLC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Query on 1PE

Download Ideal Coordinates CCD File 
C10 H22 O6
Query on DMS

Download Ideal Coordinates CCD File 
C2 H6 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
2YB BindingDB:  4PHU Ki: min: 7.7, max: 38 (nM) from 3 assay(s)
Kd: min: 4.5, max: 12 (nM) from 2 assay(s)
EC50: min: 0.35, max: 1000 (nM) from 26 assay(s)
Binding MOAD:  4PHU Kd: 12.04 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description