3HC5 | pdb_00003hc5

FXR with SRC1 and GSK826

• PDB DOI: https://doi.org/10.2210/pdb3HC5/pdb

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


• Deposited: 2009-05-05 Released: 2009-07-21 
• Deposition Author(s): Williams, S.P., Madauss, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.269 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

FXR agonist activity of conformationally constrained analogs of GW 4064.

Akwabi-Ameyaw, A., 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., Navas, F., Parks, D.J., Spearing, P.K., Todd, D., Williams, S.P., Bruce Wisely, G.

(2009) Bioorg Med Chem Lett 19: 4733-4739

• PubMed: 19586769 
• DOI: https://doi.org/10.1016/j.bmcl.2009.06.062
• Primary Citation of Related Structures:  
  3HC5, 3HC6


• PubMed Abstract: 
  

  Two series of conformationally constrained analogs of the FXR agonist GW 4064 1 were prepared. Replacement of the metabolically labile stilbene with either benzothiophene or naphthalene rings led to the identification of potent full agonists 2a and 2g.

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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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.43 kDa 
• Atom Count: 1,952 
• Modelled Residue Count: 240 
• Deposited Residue Count: 253 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bile acid receptor	A	232	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	B	21	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
82X	C [auth A]	3-(6-{[3-(2,6-dichlorophenyl)-5-(1-methylethyl)isoxazol-4-yl]methoxy}-1-benzothiophen-2-yl)benzoic acid C28 H21 Cl2 N O4 S WPHVYHBQJIXGIJ-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
82X	BindingDB:  3HC5	EC50: min: 63, max: 140 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.269 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.893	α = 90
b = 159.893	β = 90
c = 159.893	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Williams, S.P., Madauss, K.P.

Revision History  

• Version 1.0: 2009-07-21
  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: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description