3L1B | pdb_00003l1b

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 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/jm901650u
  • Primary Citation 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-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

Macromolecule Content 

  • Total Structure Weight: 27.71 kDa 
  • Atom Count: 1,833 
  • Modeled Residue Count: 216 
  • Deposited Residue Count: 233 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Farnesoid X receptor233Homo sapiensMutation(s): 0 
Gene Names: NR1H4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens)
Explore Q96RI1 
Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1
GTEx:  ENSG00000012504 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RI1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
635

Query on 635



Download:Ideal Coordinates CCD File
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
635 BindingDB:  3L1B EC50: min: 52, max: 88 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.271 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description