5TZR

GPR40 in complex with partial agonist MK-8666


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40.

Lu, J.Byrne, N.Wang, J.Bricogne, G.Brown, F.K.Chobanian, H.R.Colletti, S.L.Di Salvo, J.Thomas-Fowlkes, B.Guo, Y.Hall, D.L.Hadix, J.Hastings, N.B.Hermes, J.D.Ho, T.Howard, A.D.Josien, H.Kornienko, M.Lumb, K.J.Miller, M.W.Patel, S.B.Pio, B.Plummer, C.W.Sherborne, B.S.Sheth, P.Souza, S.Tummala, S.Vonrhein, C.Webb, M.Allen, S.J.Johnston, J.M.Weinglass, A.B.Sharma, S.Soisson, S.M.

(2017) Nat. Struct. Mol. Biol. 24: 570-577

  • DOI: 10.1038/nsmb.3417
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clinical studies indicate that partial agonists of the G-protein-coupled, free fatty acid receptor 1 GPR40 enhance glucose-dependent insulin secretion and represent a potential mechanism for the treatment of type 2 diabetes mellitus. Full allosteric ...

    Clinical studies indicate that partial agonists of the G-protein-coupled, free fatty acid receptor 1 GPR40 enhance glucose-dependent insulin secretion and represent a potential mechanism for the treatment of type 2 diabetes mellitus. Full allosteric agonists (AgoPAMs) of GPR40 bind to a site distinct from partial agonists and can provide additional efficacy. We report the 3.2-Å crystal structure of human GPR40 (hGPR40) in complex with both the partial agonist MK-8666 and an AgoPAM, which exposes a novel lipid-facing AgoPAM-binding pocket outside the transmembrane helical bundle. Comparison with an additional 2.2-Å structure of the hGPR40-MK-8666 binary complex reveals an induced-fit conformational coupling between the partial agonist and AgoPAM binding sites, involving rearrangements of the transmembrane helices 4 and 5 (TM4 and TM5) and transition of the intracellular loop 2 (ICL2) into a short helix. These conformational changes likely prime GPR40 to a more active-like state and explain the binding cooperativity between these ligands.


    Organizational Affiliation

    Global Phasing Limited, Cambridge, UK.,Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA.,Department of Cardiometabolic Disease, Merck Research Laboratories, West Point, Pennsylvania, USA.,Department of In vitro Pharmacology, Merck Research Laboratories, West Point, Pennsylvania, USA.,Department of Screening and Protein Science, Merck Research Laboratories, West Point, Pennsylvania, USA.,Department of Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Free fatty acid receptor 1,Endolysin,Free fatty acid receptor 1
A
491Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 8 
Gene Names: FFAR1 (GPR40), E
EC: 3.2.1.17
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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
MK6
Query on MK6

Download SDF File 
Download CCD File 
A
(5aR,6S,6aS)-3-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy][1,1'-biphenyl]-3-yl}methoxy)-5,5a,6,6a-tetrahydrocyclopropa[4,5]cyclopenta[1,2-c]pyridine-6-carboxylic acid
C29 H31 N O6 S
CODQKEMYZZKQAE-QPVYNBJUSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MLI
Query on MLI

Download SDF File 
Download CCD File 
A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.620α = 90.00
b = 62.600β = 108.93
c = 106.150γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
BUSTERrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-21
    Type: Database references
  • Version 1.2: 2017-07-19
    Type: Database references