2NPA

the crystal structure of the human PPARaplpha ligand binding domain in complex with a a-hydroxyimino phenylpropanoic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.220 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Design and synthesis of oxime ethers of alpha-acyl-beta-phenylpropanoic acids as PPAR dual agonists

Han, H.O., Kim, S.H., Kim, K.H., Hur, G.C., Yim, H.J., Chung, H.K., Woo, S.H., Koo, K.D., Lee, C.S., Koh, J.S., Kim, G.T.

(2007) Bioorg Med Chem Lett 17: 937-941

  • DOI: https://doi.org/10.1016/j.bmcl.2006.11.050
  • Primary Citation of Related Structures:  
    2NPA

  • PubMed Abstract: 

    Oxime ethers of alpha-acyl-beta-phenylpropanoic acids were prepared to apply as PPARalpha and gamma dual agonists. Among them, compound 11l proved to exhibit potent in vitro activities with EC(50) of 19 and 13nM in PPARalpha and gamma, respectively. It showed better glucose lowering effects than rosiglitazone 1 and ameliorated the lipid profile like plasma triglyceride in db/db mice model.

    • Organizational Affiliation: 

    Research and Development, LG Life Sciences, 104-1 Munji-dong, Yuseong-gu, Daejon 305-380, Republic of Korea.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor alpha
A, C
270Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07869 (Homo sapiens)
Explore Q07869 
Go to UniProtKB:  Q07869
PHAROS:  Q07869
GTEx:  ENSG00000186951 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07869
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SRC- peptide from Nuclear receptor coactivator 1
B, D
15N/AMutation(s): 0 
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MMB
Query on MMB
Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]		(2R,3E)-2-{4-[(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)METHOXY]BENZYL}-3-(PROPOXYIMINO)BUTANOIC ACID
C25 H28 N2 O5
YAWURVGPVQWWHE-UJUJBVAOSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MMB BindingDB:  2NPA EC50: 19 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.909α = 90
b = 100.074β = 100.14
c = 61.311γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing

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: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description