3OKH

Crystal structure of human FXR in complex with 2-(4-chlorophenyl)-1-[(1S)-1-cyclohexyl-2-(cyclohexylamino)-2-oxoethyl]-1H-benzimidazole-6-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb3OKH/pdb

• Classification: HORMONE RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Starting Model: other

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

• PubMed: 21134747 
• 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.

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Organizational Affiliation: 

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

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: 29.88 kDa 
• Atom Count: 2,031 
• Modelled Residue Count: 237 
• Deposited Residue Count: 247 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bile acid receptor	A	233	Homo sapiens	Mutation(s): 2  Gene Names: NR1H4, HCG_20893
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
peptide of Nuclear receptor coactivator 1	B	14	N/A	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OKH	C [auth A], D [auth A]	2-(4-chlorophenyl)-1-[(1S)-1-cyclohexyl-2-(cyclohexylamino)-2-oxoethyl]-1H-benzimidazole-6-carboxylic acid C28 H32 Cl N3 O3 BGTNSFBYQMPTOK-VWLOTQADSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OKH	BindingDB:  3OKH	IC50: 5720 (nM) from 1 assay(s)
	PDBBind:  3OKH	IC50: 5720 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.73	α = 90
b = 153.68	β = 90
c = 115.32	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
BUSTER	refinement
XDS	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.3: 2024-04-03
  Changes: Refinement description