3FLI

Discovery of XL335, a Highly Potent, Selective and Orally-Active Agonist of the Farnesoid X Receptor (FXR)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of XL335 (WAY-362450), a highly potent, selective, and orally active agonist of the farnesoid X receptor (FXR).

Flatt, B.Martin, R.Wang, T.L.Mahaney, P.Murphy, B.Gu, X.H.Foster, P.Li, J.Pircher, P.Petrowski, M.Schulman, I.Westin, S.Wrobel, J.Yan, G.Bischoff, E.Daige, C.Mohan, R.

(2009) J Med Chem 52: 904-907

  • DOI: https://doi.org/10.1021/jm8014124
  • Primary Citation of Related Structures:  
    3FLI

  • PubMed Abstract: 

    Azepino[4,5-b]indoles have been identified as potent agonists of the farnesoid X receptor (FXR). In vitro and in vivo optimization has led to the discovery of 6m (XL335, WAY-362450) as a potent, selective, and orally bioavailable FXR agonist (EC(50) = 4 nM, Eff = 149%). Oral administration of 6m to LDLR(-/-) mice results in lowering of cholesterol and triglycerides. Chronic administration in an atherosclerosis model results in significant reduction in aortic arch lesions.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Exelixis Inc., 4757 Nexus Centre Drive, San Diego, California 92121, USA. bflatt@exelixis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bile acid receptor231Homo sapiensMutation(s): 0 
Gene Names: BARFXRHRR1NR1H4RIP14
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
33Y
Query on 33Y

Download Ideal Coordinates CCD File 
B [auth A]1-methylethyl 3-[(3,4-difluorophenyl)carbonyl]-1,1-dimethyl-1,2,3,6-tetrahydroazepino[4,5-b]indole-5-carboxylate
C25 H24 F2 N2 O3
INASOKQDNHHMRE-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
33Y BindingDB:  3FLI EC50: min: 4, max: 152 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.519α = 90
b = 66.519β = 90
c = 125.434γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    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