Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35382.64 
• Atom Count: 2297 
• Residue Count: 306 
• Unique protein chains: 2

1WM0

PPARgamma in complex with a 2-BABA compound

• DOI: 10.2210/pdb1WM0/pdb

• Classification: TRANSCRIPTION/SIGNALING PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2004-07-01 Released: 2004-09-07 
• Deposition Author(s): Svensson, S., Selen, G., Uppenberg, J., Thor, M., Sundbom, M., Sydow-Backman, M., Gustavsson, A.L., Jendeberg, L., Ostberg, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.295 
• R-Value Work: 0.191 

Literature

A new class of peroxisome proliferator-activated receptor agonists with a novel binding epitope shows antidiabetic effects

Ostberg, T., Svensson, S., Selen, G., Uppenberg, J., Thor, M., Sundbom, M., Sydow-Backman, M., Gustavsson, A.L., Jendeberg, L.

(2004) J.Biol.Chem. 279: 41124-41130

• PubMed: 15258145 
• DOI: 10.1074/jbc.M401552200


• PubMed Abstract: 
  

The peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors belonging to the NR1 subfamily of nuclear receptors. The PPARs play key roles in the control of glucose and lipid homeostasis, and the synthetic isoform-specific PPAR agonists are used clinically to improve insulin sensitivity and to lower serum triglyceride levels. All of the previously reported PPAR agonists form the same characteristic interactions with the receptor, which have been postulated to be important for the induction of agonistic activity. Here we describe a new class of PPARalpha/gamma modulators, the 5-substituted 2-benzoylaminobenzoic acids (2-BABAs). As shown by x-ray crystallography, the representative compounds BVT.13, BVT.762, and BVT.763, utilize a novel binding epitope and lack the agonist-characteristic interactions. Despite this, some compounds within the 2-BABA family are potent agonists in a cell-based reporter gene assay. Furthermore, BVT.13 displays antidiabetic effects in ob/ob mice. We concluded that the 2-BABA binding mode can be used to design isoform-specific PPAR modulators with biological activity in vivo.

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Organizational Affiliation: 

Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, SE-171 77 Stockholm, Sweden.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Peroxisome proliferator activated receptor gamma	X	292	Homo sapiens	Mutation(s): 0  Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens) Go to Gene View: PPARG Go to UniProtKB:  P37231

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
14-mer from Nuclear receptor coactivator 2	Y	14	Mus musculus	Mutation(s): 0  Gene Names: Ncoa2 (Grip1, Src2, Tif2)
Find proteins for Q61026 (Mus musculus) Go to UniProtKB:  Q61026

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PLB	X	2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID 5-(2-PYRIMIDINYLOXY)-2-BENZOYLAMINOBENZOIC ACID C18 H11 Cl2 N3 O4 VNDRRWBKNSHALL-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PLB	EC50: 1300 nM (99) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.295 
• R-Value Work: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 49.166	α = 90.00
b = 66.324	β = 90.00
c = 122.671	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-01 
• Released Date: 2004-09-07 
• Deposition Author(s): Svensson, S., Selen, G., Uppenberg, J., Thor, M., Sundbom, M., Sydow-Backman, M., Gustavsson, A.L., Jendeberg, L., Ostberg, T.

Revision History 

• Version 1.0: 2004-09-07
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance