3KDT

Crystal structure of peroxisome proliferator-activatedeceptor alpha (PPARalpha) complex with N-3-((2-(4-Chlorophenyl)-5-methyl-1,3-oxazol-4-yl)methoxy)benzyl)-N-(methoxycarbonyl)glycine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 

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Literature

Discovery of an oxybenzylglycine based peroxisome proliferator activated receptor alpha selective agonist 2-((3-((2-(4-chlorophenyl)-5-methyloxazol-4-yl)methoxy)benzyl)(methoxycarbonyl)amino)acetic acid (BMS-687453).

Li, J., Kennedy, L.J., Shi, Y., Tao, S., Ye, X.Y., Chen, S.Y., Wang, Y., Hernandez, A.S., Wang, W., Devasthale, P.V., Chen, S., Lai, Z., Zhang, H., Wu, S., Smirk, R.A., Bolton, S.A., Ryono, D.E., Zhang, H., Lim, N.K., Chen, B.C., Locke, K.T., O'Malley, K.M., Zhang, L., Srivastava, R.A., Miao, B., Meyers, D.S., Monshizadegan, H., Search, D., Grimm, D., Zhang, R., Harrity, T., Kunselman, L.K., Cap, M., Kadiyala, P., Hosagrahara, V., Zhang, L., Xu, C., Li, Y.X., Muckelbauer, J.K., Chang, C., An, Y., Krystek, S.R., Blanar, M.A., Zahler, R., Mukherjee, R., Cheng, P.T., Tino, J.A.

(2010) J Med Chem 53: 2854-2864

  • DOI: https://doi.org/10.1021/jm9016812
  • Primary Citation of Related Structures:  
    3KDT, 3KDU

  • PubMed Abstract: 

    • An 1,3-oxybenzylglycine based compound 2 (BMS-687453) was discovered to be a potent and selective peroxisome proliferator activated receptor (PPAR) alpha agonist, with an EC(50) of 10 nM for human PPARalpha and approximately 410-fold selectivity vs human PPARgamma in PPAR-GAL4 transactivation assays ...

    An 1,3-oxybenzylglycine based compound 2 (BMS-687453) was discovered to be a potent and selective peroxisome proliferator activated receptor (PPAR) alpha agonist, with an EC(50) of 10 nM for human PPARalpha and approximately 410-fold selectivity vs human PPARgamma in PPAR-GAL4 transactivation assays. Similar potencies and selectivity were also observed in the full length receptor co-transfection assays. Compound 2 has negligible cross-reactivity against a panel of human nuclear hormone receptors including PPARdelta. Compound 2 demonstrated an excellent pharmacological and safety profile in preclinical studies and thus was chosen as a development candidate for the treatment of atherosclerosis and dyslipidemia. The X-ray cocrystal structures of the early lead compound 12 and compound 2 in complex with PPARalpha ligand binding domain (LBD) were determined. The role of the crystal structure of compound 12 with PPARalpha in the development of the SAR that ultimately resulted in the discovery of compound 2 is discussed.

    Related Citations: 
    • Synthesis and Structure-Activity Relationships of 2-Aryl-4-oxazolylmethoxy Benzylglycines and 2-Aryl-4-thiazolylmethoxy Benzylglycines as Novel, Potent PPARalpha Selective Activators-PPARalpha and PPARgamma Selective Modulation
      Ye, X.-Y., Chen, S., Zhang, H., Locke, K.T., O'Malley, K., Zhang, L., Srivastava, R., Miao, B., Meyers, D., Monshizadegan, H., Search, D., Grimm, D., Zhang, R., Lippy, J., Twamley, C., Muckelbauer, J.K., Chang, C., An, Y., Hosagrahara, V., Zhang, L., Yang, T.-J., Mukherjee, R., Cheng, P.T.W., Tino, J.A.
      () To be published --: --
    Organizational Affiliation: 

    Metabolic Diseases Chemistry, Bristol-Myers Squibb, Building 13, P.O. Box 5400, Princeton, New Jersey 08543-5400, USA. jun.li@bms.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor alpha
A, B
277Homo sapiensMutation(s): 0 
Gene Names: PPARA, NR1C1, PPAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q07869 (Homo sapiens)
Explore Q07869 
Go to UniProtKB:  Q07869
PHAROS:  Q07869
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07869
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7HA
Query on 7HA
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		N-(3-{[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy}benzyl)-N-(methoxycarbonyl)glycine
C22 H21 Cl N2 O6
UJIBXDMNCMEJAY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
7HA PDBBind:  3KDT IC50: 260 (nM) from 1 assay(s)
BindingDB:  3KDT IC50: 260 (nM) from 1 assay(s)
EC50: min: 9.6, max: 488 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.754α = 90
b = 64.754β = 90
c = 123.664γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance