3GD2 | pdb_00003gd2

isoxazole ligand bound to farnesoid X receptor (FXR)

• PDB DOI: https://doi.org/10.2210/pdb3GD2/pdb

• Classification: TRANSCRIPTION/TRANSCRIPTION ACTIVATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-02-23 Released: 2009-07-07 
• Deposition Author(s): Madauss, K.P., Williams, S.P., Deaton, D.N., Wisely, G.B., Mcfadyen, R.B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.297 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Literature

Substituted isoxazole analogs of farnesoid X receptor (FXR) agonist GW4064.

Bass, J.Y., Caldwell, R.D., Caravella, J.A., Chen, L., Creech, K.L., Deaton, D.N., Madauss, K.P., Marr, H.B., McFadyen, R.B., Miller, A.B., Parks, D.J., Todd, D., Williams, S.P., Wisely, G.B.

(2009) Bioorg Med Chem Lett 19: 2969-2973

• PubMed: 19410460 
• DOI: https://doi.org/10.1016/j.bmcl.2009.04.047
• Primary Citation of Related Structures:  
  3GD2


• PubMed Abstract: 
  

  Starting from the known FXR agonist GW 4064 1a, a series of alternately 3,5-substituted isoxazoles was prepared. Several of these analogs were potent full FXR agonists. A subset of this series, with a tether between the isoxazole ring and the 3-position aryl substituent, were equipotent FXR agonists to GW 4064 1a, with the 2,6-dimethyl phenol analog 1t having greater FRET FXR potency than GW 4064 1a.

---

Organizational Affiliation: 

Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.68 kDa 
• Atom Count: 1,901 
• Modelled Residue Count: 238 
• Deposited Residue Count: 240 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bile acid receptor	A	229	Homo sapiens	Mutation(s): 2  Gene Names: NR1H4, BAR, FXR, HRR1, RIP14
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens) Explore Q96RI1  Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1 GTEx:  ENSG00000012504

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
activator peptide	B	11	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
708	C [auth A]	3-[(E)-2-(2-chloro-4-{[3-{[(R)-(2,6-dichlorophenyl)(hydroxy)-lambda~4~-sulfanyl]methyl}-5-(1-methylethyl)isoxazol-4-yl]methoxy}phenyl)ethenyl]benzoic acid C29 H26 Cl3 N O5 S MUAOISKUROHRCK-MDZDMXLPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.297 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.749	α = 90
b = 158.749	β = 90
c = 158.749	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Madauss, K.P., Williams, S.P., Deaton, D.N., Wisely, G.B., Mcfadyen, R.B.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-21
  Changes: Data collection