1NYX

Ligand binding domain of the human peroxisome proliferator activated receptor gamma in complex with an agonist

Structural Biology Knowledgebase: 1NYX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.237

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1NYX

Classification: Transcription

Total Structure Weight: 63549.22

Macromolecule Entities
Molecule Chains Length Organism Details
peroxisome proliferator activated receptor gamma A, B 276 Homo sapiens Fragment: Ligand binding domain
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
DRF
Query on DRF

A (2S)-2-ETHOXY-3-{4-[2-(10H-PHENOXAZIN-10- YL)ETHOXY]PHENYL}PROPANOIC ACID
RAGAGLITAZAR (Synonym)
C25 H25 N O5
WMUIIGVAWPWQAW-DEOSSOPVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DRF EC50: 570 - 600 nM (100) BindingDB
IC50: 92 nM (100) BindingDB
Ki: 90 nM (100) BindingDB

N/A in BindingMoad
IC50: 92 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.237
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 91.55 α = 90.00
b = 62.09 β = 102.91
c = 117.74 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-14
  • Released Date: 2003-07-15
  • Deposition author(s): Ebdrup, S., Pettersson, I., Rasmussen, H.B., Deussen, H.-J., Frost Jensen, A., Mortensen, S.B., Fleckner, J., Pridal, L., Nygaard, L., Sauerberg, P.

Revision History

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