4PHU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 4PHU

Classification: Fatty acid binding protein / Hydrolase

Total Structure Weight: 55725.93

Macromolecule Entities
Molecule Chains Length Organism Details
Free fatty acid receptor 1,Lysozyme A 491 Homo sapiens Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Fragment: UNP O14842 residues 2-213, UNP P00720 residues 2-161, UNP O14842 residues 214-300
Mutation: L42A, F88A, G103A, Y202F, C1054T, C1097A
Details: Chimera
Gene Name(s): FFAR1 Gene View GPR40 E
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | 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 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
2YB
Query on 2YB

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 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)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
2YB EC50: 14 - 42 nM (96) BindingDB
Ki: 38 nM (96) BindingDB

Kd: 16 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.198
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 101.00 α = 90.00
b = 61.74 β = 108.90
c = 105.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



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

  • 2014-07-23
    Type: Database references
  • 2014-08-06
    Type: Database references
  • 2014-10-01
    Type: Database references
  • 2015-02-04
    Type: Derived calculations