4PHU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.332 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 

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

  • 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

    1] Department of Structural Biology and Core Sciences &Technology, Takeda California, 10410 Science Center Drive, San Diego, California 92121, USA [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Free fatty acid receptor 1,Lysozyme
A
491Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 6 
Gene Names: FFAR1 (GPR40), E
EC: 3.2.1.17
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
GPR40 free fatty-acid receptor 1 (FFAR1) bound to TAK-875
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
2YB
Query on 2YB

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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
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2YBEC50: 1.9 - 58 nM (96) BINDINGDB
2YBKi: 29 - 38 nM (96) BINDINGDB
2YBKd: 16 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.332 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.000α = 90.00
b = 61.740β = 108.90
c = 105.700γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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