2YFE

Ligand binding domain of human PPAR gamma in complex with amorfrutin 1

Structural Biology Knowledgebase: 2YFE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YFE

Classification: RECEPTOR

Total Structure Weight: 66069.04

Macromolecule Entities
Molecule Chains Length Organism Details
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA A, B 287 Homo sapiens Fragment: LIGAND BINDING DOMAIN, RESIDUES 195-477
Gene Name(s): PPARG Gene View NR1C3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
YFE
Query on YFE

A, B Amorfrutin 1
C21 H24 O4
CTNFTPUIYFUXBE-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
YFE EC50: 458 nM (99) BindingDB
Kd: 236 nM (99) BindingDB

Ki: 236 nM  BindingMOAD
Ki: 236 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.204
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 92.81 α = 90.00
b = 61.10 β = 102.78
c = 118.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-05
  • Released Date: 2012-04-11
  • Deposition author(s): De Groot, J.C., Buessow, K.

Revision History

  • 2012-05-23
    Type: Other | Details: Citation
  • 2012-05-02
    Type: Other | Details: Citation
  • 2012-04-25
    Type: Other | Details: Citation