3RVF | pdb_00003rvf

FXR with SRC1 and GSK2034

• PDB DOI: https://doi.org/10.2210/pdb3RVF/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-06 Released: 2011-09-21 
• Deposition Author(s): Williams, S.P., Madauss, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.290 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Conformationally constrained farnesoid X receptor (FXR) agonists: Alternative replacements of the stilbene.

Akwabi-Ameyaw, A., Caravella, J.A., Chen, L., Creech, K.L., Deaton, D.N., Madauss, K.P., Marr, H.B., Miller, A.B., Navas, F., Parks, D.J., Spearing, P.K., Todd, D., Williams, S.P., Wisely, G.B.

(2011) Bioorg Med Chem Lett 21: 6154-6160

• PubMed: 21890356 
• DOI: https://doi.org/10.1016/j.bmcl.2011.08.034
• Primary Citation Related Structures: 
  3RUT, 3RUU, 3RVF


• PubMed Abstract: 
  

  To further explore the optimum placement of the acid moiety in conformationally constrained analogs of GW 4064 1a, a series of stilbene replacements were prepared. The benzothiophene 1f and the indole 1g display the optimal orientation of the carboxylate for enhanced FXR agonist potency.

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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: 30.32 kDa 
• Atom Count: 1,889 
• Modeled Residue Count: 239 
• 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  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
034	D [auth A]	5-(4-{[3-(2,6-dichlorophenyl)-5-(propan-2-yl)-1,2-oxazol-4-yl]methoxy}phenyl)-1H-indole-2-carboxylic acid C28 H22 Cl2 N2 O4 RYEIPXVNZXWZFN-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.290 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.331	α = 90
b = 158.331	β = 90
c = 158.331	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Williams, S.P., Madauss, K.P.

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2011-10-05
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations