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: 2.7 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.253 

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:  

  • 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 h ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor alpha
A, B
277Homo sapiensMutation(s): 0 
Gene Names: PPARA (NR1C1, PPAR)
Find proteins for Q07869 (Homo sapiens)
Go to Gene View: PPARA
Go to UniProtKB:  Q07869
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7HA
Query on 7HA

Download SDF File 
Download CCD File 
A, 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7HAEC50: 317 - 488 nM (92) BINDINGDB
7HAIC50: 260 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.253 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 64.754α = 90.00
b = 64.754β = 90.00
c = 123.664γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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