3FXV

Identification of an N-oxide pyridine GW4064 analogue as a potent FXR agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification of an N-oxide pyridine GW4064 analog as a potent FXR agonist

Feng, S.Yang, M.Zhang, Z.Wang, Z.Hong, D.Richter, H.Benson, G.M.Bleicher, K.Grether, U.Martin, R.E.Plancher, J.-M.Kuhn, B.Rudolph, M.G.Chen, L.

(2009) Bioorg Med Chem Lett 19: 2595-2598

  • DOI: 10.1016/j.bmcl.2009.03.008
  • Primary Citation of Related Structures:  
    3FXV

  • PubMed Abstract: 
  • According to the docking studies and the analysis of a co-crystal structure of GW4064 with FXR, a series of 3-aryl heterocyclic isoxazole analogs were designed and synthesized. N-Oxide pyridine analog (7b) was identified as a promising FXR agonist with potent binding affinity and good efficacy, supporting our hypothesis that through an additional hydrogen bond interaction between the pyridine substituent of isoxazole analogs and Tyr373 and Ser336 of FXR, binding affinity and functional activity could be improved ...

    According to the docking studies and the analysis of a co-crystal structure of GW4064 with FXR, a series of 3-aryl heterocyclic isoxazole analogs were designed and synthesized. N-Oxide pyridine analog (7b) was identified as a promising FXR agonist with potent binding affinity and good efficacy, supporting our hypothesis that through an additional hydrogen bond interaction between the pyridine substituent of isoxazole analogs and Tyr373 and Ser336 of FXR, binding affinity and functional activity could be improved.


    Organizational Affiliation

    Roche R&D Center(China) Ltd, 720 Cai Lun Road, Building 5, Pudong, Shanghai 201203, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NR1H4 proteinA233Homo sapiensMutation(s): 2 
Gene Names: NR1H4hCG_20893BARFXRHRR1RIP14
Find proteins for Q96RI1 (Homo sapiens)
Explore Q96RI1 
Go to UniProtKB:  Q96RI1
NIH Common Fund Data Resources
PHAROS  Q96RI1
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
12-meric peptide from Nuclear receptor coactivator 1B13N/AMutation(s): 0 
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS  Q15788
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
643
Query on 643

Download CCD File 
A
6-(4-{[3-(3,5-dichloropyridin-4-yl)-5-(1-methylethyl)isoxazol-4-yl]methoxy}-2-methylphenyl)-1-methyl-1H-indole-3-carbox ylic acid
C29 H25 Cl2 N3 O4
JTRRVYQZHXAOGI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
643IC50 :  94   nM  PDBBind
643IC50:  94   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.796α = 90
b = 94.796β = 90
c = 48.274γ = 120
Software Package:
Software NamePurpose
COMOphasing
BUSTER-TNTrefinement
HKL-2000data reduction
SADABSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description