3RVF

FXR with SRC1 and GSK2034


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 034Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.bmcl.2011.08.034
  • Primary Citation of 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bile acid receptor232Homo sapiensMutation(s): 0 
Gene Names: BARFXRHRR1NR1H4RIP14
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens)
Explore Q96RI1 
Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1
GTEx:  ENSG00000012504 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RI1
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 121Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
034
Query on 034

Download Ideal Coordinates CCD File 
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
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
034 BindingDB:  3RVF EC50: min: 88, max: 110 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.227 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.331α = 90
b = 158.331β = 90
c = 158.331γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 034Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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