3KDU

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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: 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor alpha AB277Homo sapiensMutation(s): 0 
Gene Names: PPARANR1C1PPAR
Find proteins for Q07869 (Homo sapiens)
Explore Q07869 
Go to UniProtKB:  Q07869
NIH Common Fund Data Resources
PHAROS:  Q07869
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NKS
Query on NKS

Download Ideal Coordinates CCD File 
A, B
N-(3-{[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy}benzyl)-N-[(4-methylphenoxy)carbonyl]glycine
C28 H25 Cl N2 O6
HUZRXZVIBUNCKL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NKSIC50 :  347   nM  PDBBind
NKSIC50:  347   nM  Binding MOAD
NKSEC50:  8   nM  BindingDB
NKSIC50:  347   nM  BindingDB
NKSEC50:  8.800000190734863   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-10-23 
  • Released Date: 2010-04-28 
  • Deposition Author(s): Muckelbauer, J.K.

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