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 

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

  • 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 wi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NR1H4 protein
A
233Homo sapiensMutation(s): 2 
Gene Names: NR1H4 (BAR, FXR, HRR1, RIP14)
Find proteins for Q96RI1 (Homo sapiens)
Go to Gene View: NR1H4
Go to UniProtKB:  Q96RI1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
12-meric peptide from Nuclear receptor coactivator 1
B
13Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
643
Query on 643

Download SDF File 
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-carboxylic acid
6-{4-[3-(3,5-Dichloro-pyridin-4-yl)-5-isopropyl-isoxazol-4-ylmethoxy]-2-methyl-phenyl}-1-methyl-1H-indole-3-carboxylic acid
C29 H25 Cl2 N3 O4
JTRRVYQZHXAOGI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
643IC50: 94 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 94.796α = 90.00
b = 94.796β = 90.00
c = 48.274γ = 120.00
Software Package:
Software NamePurpose
COMOphasing
HKL-2000data reduction
BUSTER-TNTrefinement
SADABSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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