3L1B

Complex Structure of FXR Ligand-binding domain with a tetrahydroazepinoindole compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Improvement of Physiochemical Properties of the Tetrahydroazepinoindole Series of Farnesoid X Receptor (FXR) Agonists: Beneficial Modulation of Lipids in Primates.

Lundquist, J.T.Harnish, D.C.Kim, C.Y.Mehlmann, J.F.Unwalla, R.J.Phipps, K.M.Crawley, M.L.Commons, T.Green, D.M.Xu, W.Hum, W.T.Eta, J.E.Feingold, I.Patel, V.Evans, M.J.Lai, K.Borges-Marcucci, L.Mahaney, P.E.Wrobel, J.E.

(2010) J Med Chem 53: 1774-1787

  • DOI: 10.1021/jm901650u
  • Primary Citation of Related Structures:  
    3L1B

  • PubMed Abstract: 
  • In an effort to develop orally active farnesoid X receptor (FXR) agonists, a series of tetrahydroazepinoindoles with appended solubilizing amine functionalities were synthesized. The crystal structure of the previously disclosed FXR agonist, 1 (FXR-4 ...

    In an effort to develop orally active farnesoid X receptor (FXR) agonists, a series of tetrahydroazepinoindoles with appended solubilizing amine functionalities were synthesized. The crystal structure of the previously disclosed FXR agonist, 1 (FXR-450), aided in the design of compounds with tethered solubilizing functionalities designed to reach the solvent cavity around the hFXR receptor. These compounds were soluble in 0.5% methylcellulose/2% Tween-80 in water (MC/T) for oral administration. In vitro and in vivo optimization led to the identification of 14dd and 14cc, which in a dose-dependent fashion regulated low density lipoprotein cholesterol (LDLc) in low density lipoprotein receptor knockout (LDLR(-/-)) mice. Compound 14cc was dosed in female rhesus monkeys for 4 weeks at 60 mg/kg daily in MC/T vehicle. After 7 days, triglyceride (TG) levels and very low density lipoprotein cholesterol (VLDLc) levels were significantly decreased and LDLc was decreased 63%. These data are the first to demonstrate the dramatic lowering of serum LDLc levels by a FXR agonist in primates and supports the potential utility of 14cc in treating dyslipidemia in humans beyond just TG lowering.


    Organizational Affiliation

    Department of Chemical Sciences, Wyeth Research, 500 Arcola Road, Collegeville, Pennsylvania 19426, USA. lundquj@wyeth.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Farnesoid X receptorA233Homo sapiensMutation(s): 0 
Gene Names: NR1H4BARFXRHRR1RIP14
Find proteins for Q96RI1 (Homo sapiens)
Explore Q96RI1 
Go to UniProtKB:  Q96RI1
NIH Common Fund Data Resources
PHAROS  Q96RI1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
635
Query on 635

Download CCD File 
A
1-methylethyl 8-fluoro-1,1-dimethyl-3-{[4-(3-morpholin-4-ylpropoxy)phenyl]carbonyl}-1,2,3,6-tetrahydroazepino[4,5-b]indole-5-carboxylate
C32 H38 F N3 O5
PIVQVFFIZHFKHL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
635EC50:  52   nM  BindingDB
635EC50:  88   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.845α = 90
b = 55.365β = 90
c = 118.569γ = 90
Software Package:
Software NamePurpose
AMoREphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance