2F4B

Crystal structure of the ligand binding domain of human PPAR-gamma in complex with an agonist

Structural Biology Knowledgebase: 2F4B SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.219

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2F4B

Classification: TRANSCRIPTION ACTIVATOR

Total Structure Weight: 62516.16

Macromolecule Entities
Molecule Chains Length Organism Details
Peroxisome proliferator-activated receptor gamma A, B 271 Homo sapiens Fragment: LIGAND BINDING DOMAIN
Gene Name(s): PPARG Gene View NR1C3

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

A (5-{3-[(6-BENZOYL-1-PROPYL-2-NAPHTHYL)OXY]PROPOXY}- 1H-INDOL-1-YL)ACETIC ACID
2-{5-[3-(6-BENZOYL-1-PROPYLNAPHTHALEN-2-YLOXY)PROPOXY]INDOL- 1-YL}ETHANOIC ACID (Synonym)
C33 H31 N O5
ZXWVCCFKIRBLDP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
EHA EC50: 70 nM (100) BindingDB
IC50: 50 nM (100) BindingDB

IC50: 50 nM  BindingMOAD
IC50: 50 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.219
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 55.97 α = 90.00
b = 88.64 β = 90.01
c = 57.88 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-23
  • Released Date: 2006-02-14
  • Deposition author(s): Lu, I.L., Peng, Y.H., Mahindroo, N., Hsieh, H.P., Wu, S.Y.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4