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

Literature

Macromolecules
Sequence Display for 5TZR

Classification: FATTY ACID BINDING PROTEIN / HYDROLASE

Total Structure Weight: 57077.73

Macromolecule Entities
Molecule Chains Length Organism Details
Free fatty acid receptor 1,Endolysin,Free fatty acid receptor 1 A 491 Homo sapiens Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Mutation: L42A, F88A, G103A, Y202F, R1012G, C1054T, C1097A, I1137R
Gene Name(s): FFAR1 Gene View GPR40 E
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: GPR40 free fatty-acid receptor 1 (FFAR1) bound to TAK-875


Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MK6
Query on MK6

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 Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OLC
Query on OLC

A (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol (Synonym)
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1PE
Query on 1PE

A PENTAETHYLENE GLYCOL
PEG400 (Synonym)
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MLI
Query on MLI

A MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

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 = 100.62 α = 90.00
b = 62.60 β = 108.93
c = 106.15 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-11-22
  • Released Date: 2017-06-07
  • Deposition author(s): Lu, J., Byrne, N., Patel, S., Sharma, S., Soisson, S.M.

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