3OKI

Crystal structure of human FXR in complex with (2S)-2-[2-(4-chlorophenyl)-1H-benzimidazol-1-yl]-N,2-dicyclohexylethanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of novel and orally active FXR agonists for the potential treatment of dyslipidemia & diabetes

Richter, H.G.F.Benson, G.M.Blum, D.Chaput, E.Feng, S.Gardes, C.Grether, U.Hartman, P.Kuhn, B.Martin, R.E.Plancher, J.-M.Rudolph, M.G.Schuler, F.Taylor, S.Bleicher, K.H.

(2010) Bioorg Med Chem Lett 21: 191-194

  • DOI: 10.1016/j.bmcl.2010.11.039
  • Primary Citation of Related Structures:  
    3OKH, 3OKI

  • PubMed Abstract: 
  • Herein we describe the synthesis and structure activity relationship of a new class of FXR agonists identified from a high-throughput screening campaign. Further optimization of the original hits led to molecules that were highly active in an LDL-receptor KO model for dyslipidemia ...

    Herein we describe the synthesis and structure activity relationship of a new class of FXR agonists identified from a high-throughput screening campaign. Further optimization of the original hits led to molecules that were highly active in an LDL-receptor KO model for dyslipidemia. The most promising candidate is discussed in more detail.


    Organizational Affiliation

    F Hoffmann-La Roche AG, Grenzacherstrasse, CH-4070 Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bile acid receptorA, C233Homo sapiensMutation(s): 2 
Gene Names: NR1H4HCG_20893BARFXRHRR1RIP14
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
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
peptide of Nuclear receptor coactivator 1B, D14N/AMutation(s): 0 
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OKI
Query on OKI

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
(2S)-2-[2-(4-chlorophenyl)-1H-benzimidazol-1-yl]-N,2-dicyclohexylethanamide
C27 H32 Cl N3 O
DZGNRZLPMHOISU-VWLOTQADSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
OKI PDBBind:  3OKI IC50: 70 (nM) from 1 assay(s)
BindingDB:  3OKI IC50: 70 (nM) from 1 assay(s)
Binding MOAD:  3OKI IC50: 70 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.215α = 90
b = 84.528β = 90
c = 190.24γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
SADABSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2010-08-25 
  • Released Date: 2010-12-29 
  • Deposition Author(s): Rudolph, M.G.

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance