3DCT | pdb_00003dct

FXR with SRC1 and GW4064

• PDB DOI: https://doi.org/10.2210/pdb3DCT/pdb

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


• Deposited: 2008-06-04 Released: 2008-08-12 
• Deposition Author(s): Williams, S.P., Madauss, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.240 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Conformationally constrained farnesoid X receptor (FXR) agonists: Naphthoic acid-based analogs of GW 4064.

Akwabi-Ameyaw, A., Bass, J.Y., Caldwell, R.D., Caravella, J.A., Chen, L., Creech, K.L., Deaton, D.N., Jones, S.A., Kaldor, I., Liu, Y., Madauss, K.P., Marr, H.B., McFadyen, R.B., Miller, A.B., III, F.N., Parks, D.J., Spearing, P.K., Todd, D., Williams, S.P., Wisely, G.B.

(2008) Bioorg Med Chem Lett 18: 4339-4343

• PubMed: 18621523 
• DOI: https://doi.org/10.1016/j.bmcl.2008.06.073
• Primary Citation of Related Structures:  
  3DCT, 3DCU


• PubMed Abstract: 
  

  Starting from the known FXR agonist GW 4064 1a, a series of stilbene replacements were prepared. The 6-substituted 1-naphthoic acid 1b was an equipotent FXR agonist with improved developability parameters relative to 1a. Analog 1b also reduced the severity of cholestasis in the ANIT acute cholestatic rat model.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, GlaxoSmithKline, 5 Moore Drive, PO Box 13398, 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: 30.7 kDa 
• Atom Count: 1,920 
• Modeled Residue Count: 240 
• Deposited Residue Count: 256 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bile acid receptor	A	235	Homo sapiens	Mutation(s): 0  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
Nuclear receptor coactivator 1	B	21	N/A	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
064	C [auth A]	3-[(E)-2-(2-chloro-4-{[3-(2,6-dichlorophenyl)-5-(1-methylethyl)isoxazol-4-yl]methoxy}phenyl)ethenyl]benzoic acid C28 H22 Cl3 N O4 BYTNEISLBIENSA-MDZDMXLPSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
064	BindingDB:  3DCT	IC50: min: 20, max: 2600 (nM) from 4 assay(s)
		EC50: min: 12, max: 1.50e+4 (nM) from 32 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.240 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.180 (DCC) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.449	α = 90
b = 159.449	β = 90
c = 159.449	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Williams, S.P., Madauss, K.P.

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description