2J14

3,4,5-Trisubstituted Isoxazoles as Novel PPARdelta Agonists: Part2

• PDB DOI: https://doi.org/10.2210/pdb2J14/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-08 Released: 2006-09-06 
• Deposition Author(s): Epple, R., Azimioara, M., Russo, R., Xie, Y., Wang, X., Cow, C., Wityak, J., Karanewsky, D., Bursulaya, B., Kreusch, A., Tuntland, T., Gerken, A., Iskandar, M., Saez, E., Seidel, H.M., Tian, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

3,4,5-Trisubstituted Isoxazoles as Novel Ppardelta Agonists. Part 2

Epple, R., Azimioara, M., Russo, R., Xie, Y., Wang, X., Cow, C., Wityak, J., Karanewsky, D., Bursulaya, B., Kreusch, A., Tuntland, T., Gerken, A., Iskandar, M., Saez, E., Seidel, H.M., Tian, S.S.

(2006) Bioorg Med Chem Lett 16: 5488

• PubMed: 16931011 
• DOI: https://doi.org/10.1016/j.bmcl.2006.08.052
• Primary Citation of Related Structures:  
  2J14


• PubMed Abstract: 
  

  A series of PPARdelta-selective agonists was investigated and optimized for a favorable in vivo pharmacokinetic profile. Isoxazole LCI765 (17d) was found to be a potent and selective PPARdelta agonist with good in vivo PK properties in mouse (C(max)=5.1 microM, t(1/2)=3.1 h). LCI765 regulated expression of genes involved in energy homeostasis in relevant tissues when dosed orally in C57BL6 mice. A co-crystal structure of compound LCI765 and the LBD of PPARdelta is discussed.

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Organizational Affiliation: 

Department of Medicinal Chemistry, The Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 66.38 kDa 
• Atom Count: 4,273 
• Modelled Residue Count: 506 
• Deposited Residue Count: 570 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA	A, B	285	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens) Explore Q03181  Go to UniProtKB:  Q03181
PHAROS:  Q03181 GTEx:  ENSG00000112033

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNI	C [auth A], D [auth B]	(3-{4-[2-(2,4-DICHLORO-PHENOXY)-ETHYLCARBAMOYL]-5-PHENYL-ISOXAZOL-3-YL}-PHENYL)-ACETIC ACID C26 H20 Cl2 N2 O5 HINPKGVWVQYESB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GNI	BindingDB:  2J14	EC50: 70 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.376	α = 90
b = 93.39	β = 90
c = 92.258	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-06 
Deposition Author(s): Epple, R., Azimioara, M., Russo, R., Xie, Y., Wang, X., Cow, C., Wityak, J., Karanewsky, D., Bursulaya, B., Kreusch, A., Tuntland, T., Gerken, A., Iskandar, M., Saez, E., Seidel, H.M., Tian, S.S.

Revision History  

• Version 1.0: 2006-09-06
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Refinement description