3FLI

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

• PDB DOI: https://doi.org/10.2210/pdb3FLI/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-18 Released: 2009-12-22 
• Deposition Author(s): Foster, P.G., Stout, T.J.

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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 

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

• PubMed: 19159286 
• 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.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Exelixis Inc., 4757 Nexus Centre Drive, San Diego, California 92121, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.39 kDa 
• Atom Count: 2,052 
• Modelled Residue Count: 221 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bile acid receptor	A	231	Homo sapiens	Mutation(s): 0  Gene Names: BAR, FXR, HRR1, NR1H4, RIP14
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens) Explore Q96RI1  Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1 GTEx:  ENSG00000012504

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
33Y	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
ID	Source	Binding 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 = 66.519	α = 90
b = 66.519	β = 90
c = 125.434	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Foster, P.G., Stout, T.J.

Revision History  

• 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