Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.73 kDa 
• Atom Count: 3503 
• Modelled Residue Count: 434 
• Deposited Residue Count: 491 
• Unique protein chains: 1

4PHU

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

• DOI: 10.2210/pdb4PHU/pdb

• Classification: Fatty acid binding protein/Hydrolase
• Organism(s): Homo sapiens, Escherichia virus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-05-07 Released: 2014-07-16 
• Deposition Author(s): Srivastava, A., Yano, J.K., Hirozane, Y., Kefala, G., Snell, G., Lane, W., Gruswitz, F., Ivetac, A., Aertgeerts, K., Nguyen, J., Jennings, A., Okada, K.

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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 

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

• PubMed: 25043059 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Free fatty acid receptor 1,Lysozyme	A	491	Homo sapiens, Escherichia virus T4	Mutation(s): 6  Gene Names: FFAR1, GPR40, E EC: 3.2.1.17
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors: 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
GTEx:  ENSG00000126266

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2YB	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 BZCALJIHZVNMGJ-HSZRJFAPSA-N
OLC	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 RZRNAYUHWVFMIP-GDCKJWNLSA-N
1PE	H [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
DMS	I [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
2YB	EC50:  58   nM  BindingDB
2YB	EC50:  14   nM  BindingDB
2YB	EC50:  21.8799991607666   nM  BindingDB
2YB	EC50:  16   nM  BindingDB
2YB	EC50:  42   nM  BindingDB
2YB	EC50:  45   nM  BindingDB
2YB	EC50:  39   nM  BindingDB
2YB	Ki:  29   nM  BindingDB
2YB	EC50:  1.899999976158142   nM  BindingDB
2YB	EC50:  25.700000762939453   nM  BindingDB
2YB	EC50:  14.130000114440918   nM  BindingDB
2YB	EC50:  30   nM  BindingDB
2YB	EC50:  27   nM  BindingDB
2YB	EC50:  28   nM  BindingDB
2YB	EC50:  34   nM  BindingDB
2YB	Ki:  38   nM  BindingDB
2YB	EC50:  32   nM  BindingDB
2YB	EC50:  33   nM  BindingDB
2YB	Kd:  12.039999961853027   nM  Binding MOAD
2YB	EC50:  80   nM  BindingDB
2YB	EC50:  5100   nM  BindingDB
2YB	EC50:  9.300000190734863   nM  BindingDB
2YB	EC50:  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 = 101	α = 90
b = 61.74	β = 108.9
c = 105.7	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-07 
• Released Date: 2014-07-16 
Deposition Author(s): Srivastava, A., Yano, J.K., Hirozane, Y., Kefala, G., Snell, G., Lane, W., Gruswitz, F., Ivetac, A., Aertgeerts, K., Nguyen, J., Jennings, A., Okada, K.

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