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-((4-methylphenoxy)carbonyl)glycine

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

Starting Model: experimental
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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. 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor alpha
A, B
277Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07869 (Homo sapiens)
Explore Q07869 
Go to UniProtKB:  Q07869
GTEx:  ENSG00000186951 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07869
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NKS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C28 H25 Cl N2 O6
Binding Affinity Annotations 
IDSourceBinding Affinity
NKS PDBBind:  3KDU IC50: 347 (nM) from 1 assay(s)
BindingDB:  3KDU IC50: 347 (nM) from 1 assay(s)
EC50: min: 8, max: 8.8 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.93α = 90
b = 63.93β = 90
c = 126.771γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

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
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description