5I4V

Discovery of novel, orally efficacious Liver X Receptor (LXR) beta agonists

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Discovery of a Novel, Orally Efficacious Liver X Receptor (LXR) beta Agonist.

Zheng, Y., Zhuang, L., Fan, K.Y., Tice, C.M., Zhao, W., Dong, C., Lotesta, S.D., Leftheris, K., Lindblom, P.R., Liu, Z., Shimada, J., Noto, P.B., Meng, S., Hardy, A., Howard, L., Krosky, P., Guo, J., Lipinski, K., Kandpal, G., Bukhtiyarov, Y., Zhao, Y., Lala, D., Van Orden, R., Zhou, J., Chen, G., Wu, Z., McKeever, B.M., McGeehan, G.M., Gregg, R.E., Claremon, D.A., Singh, S.B.

(2016) J.Med.Chem. 59: 3264-3271

  • DOI: 10.1021/acs.jmedchem.5b02029

  • PubMed Abstract: 

    • This article describes the application of Contour to the design and discovery of a novel, potent, orally efficacious liver X receptor β (LXRβ) agonist (17). Contour technology is a structure-based drug design platform that generates molecules using a ...

    This article describes the application of Contour to the design and discovery of a novel, potent, orally efficacious liver X receptor β (LXRβ) agonist (17). Contour technology is a structure-based drug design platform that generates molecules using a context perceptive growth algorithm guided by a contact sensitive scoring function. The growth engine uses binding site perception and programmable growth capability to create drug-like molecules by assembling fragments that naturally complement hydrophilic and hydrophobic features of the protein binding site. Starting with a crystal structure of LXRβ and a docked 2-(methylsulfonyl)benzyl alcohol fragment (6), Contour was used to design agonists containing a piperazine core. Compound 17 binds to LXRβ with high affinity and to LXRα to a lesser extent, and induces the expression of LXR target genes in vitro and in vivo. This molecule served as a starting point for further optimization and generation of a candidate which is currently in human clinical trials for treating atopic dermatitis.

    Organizational Affiliation: 

    Vitae Pharmaceuticals, Inc. , 502 W. Office Center Drive, Fort Washington, Pennsylvania 19034, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxysterols receptor LXR-beta,Nuclear receptor coactivator 2
A, E
270Homo sapiensMutation(s): 6 
Gene Names: NR1H2 (LXRB, NER, UNR), NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for P55055 (Homo sapiens)
Go to Gene View: NR1H2
Go to UniProtKB:  P55055
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-beta,Nuclear receptor coactivator 2
B, F
255Homo sapiensMutation(s): 1 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2), RXRB (NR2B2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Find proteins for P28702 (Homo sapiens)
Go to Gene View: RXRB
Go to UniProtKB:  P28702
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
67S
Query on 67S
Download SDF File 
Download CCD File 
A, E
{2-[(2R)-4-[4-(hydroxymethyl)-3-(methylsulfonyl)phenyl]-2-(propan-2-yl)piperazin-1-yl]-4-(trifluoromethyl)pyrimidin-5-yl}methanol
C21 H27 F3 N4 O4 S
FPVIRRAMNBCEDK-KRWDZBQOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
67SEC50: 4 - 21 nM (97) BINDINGDB
67SKi: 3 nM (97) BINDINGDB
67SIC50: >10000 nM (88) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.637α = 90.00
b = 101.221β = 90.00
c = 143.274γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release