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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Bile acid receptor
A, C
233Homo sapiensMutation(s): 2 
Gene Names: NR1H4HCG_20893
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
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide of Nuclear receptor coactivator 1
B, D
14N/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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / 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
Binding Affinity Annotations 
IDSourceBinding Affinity
OKI BindingDB:  3OKI IC50: 70 (nM) from 1 assay(s)
PDBBind:  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

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
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations