3OOK | pdb_00003ook

Crystal structure of human FXR in complex with 4-({(2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-2-cyclohexylacetyl}amino)-3,5-difluorobenzoic acid

• PDB DOI: https://doi.org/10.2210/pdb3OOK/pdb

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


• Deposited: 2010-08-31 Released: 2011-01-19 
• Deposition Author(s): Rudolph, M.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.271 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: other

Literature

Optimization of a novel class of benzimidazole-based farnesoid X receptor (FXR) agonists to improve physicochemical and ADME properties

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

(2011) Bioorg Med Chem Lett 21: 1134-1140

• PubMed: 21269824 
• DOI: https://doi.org/10.1016/j.bmcl.2010.12.123
• Primary Citation Related Structures: 
  3OLF, 3OMK, 3OMM, 3OOF, 3OOK


• PubMed Abstract: 
  

  Structure-guided lead optimization of recently described benzimidazolyl acetamides addressed the key liabilities of the previous lead compound 1. These efforts culminated in the discovery of 4-{(S)-2-[2-(4-chloro-phenyl)-5,6-difluoro-benzoimidazol-1-yl]-2-cyclohexyl-acetylamino}-3-fluoro-benzoic acid 7g, a highly potent and selective FXR agonist with excellent physicochemical and ADME properties and potent lipid lowering activity after oral administration to LDL receptor deficient mice.

---

Organizational Affiliation: 
• F. Hoffmann-La Roche Ltd, Pharmaceutical Research, Grenzacherstrasse, CH-4070 Basel, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.9 kDa 
• Atom Count: 4,212 
• Modeled Residue Count: 483 
• Deposited Residue Count: 494 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bile acid receptor	A, C	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, D	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
OOK	E [auth A], F [auth C]	4-({(2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-2-cyclohexylacetyl}amino)-3,5-difluorobenzoic acid C28 H22 Cl F4 N3 O3 MRVUTCGFXDGVGC-VWLOTQADSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.271 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.477	α = 90
b = 83.288	β = 90
c = 190.007	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Rudolph, M.G.

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-02-26
  Changes: Database references
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description