Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 118.34 kDa 
• Atom Count: 7643 
• Modelled Residue Count: 938 
• Deposited Residue Count: 1050 
• Unique protein chains: 2

5I4V

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

• DOI: 10.2210/pdb5I4V/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-02-12 Released: 2016-06-29 
• Deposition Author(s): Chen, G., McKeever, B.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.248 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

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

• PubMed: 26990539 
• DOI: 10.1021/acs.jmedchem.5b02029
• Primary Citation of Related Structures:  
  5I4V


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxysterols receptor LXR-beta,Nuclear receptor coactivator 2	A, E	270	Homo sapiens	Mutation(s): 6  Gene Names: NR1H2, LXRB, NER, UNR, NCOA2, BHLHE75, SRC2, TIF2
Find proteins for P55055 (Homo sapiens) Explore P55055  Go to UniProtKB:  P55055
NIH Common Fund Data Resources
PHAROS:  P55055 GTEx:  ENSG00000131408
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS:  Q15596 GTEx:  ENSG00000140396

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-beta,Nuclear receptor coactivator 2	B, F	255	Homo sapiens	Mutation(s): 1  Gene Names: RXRB, NR2B2, NCOA2, BHLHE75, SRC2, TIF2
Find proteins for P28702 (Homo sapiens) Explore P28702  Go to UniProtKB:  P28702
NIH Common Fund Data Resources
PHAROS:  P28702 GTEx:  ENSG00000204231
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
67S	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
67S	Ki:  3   nM  BindingDB
67S	EC50:  6   nM  BindingDB
67S	EC50:  21   nM  BindingDB
67S	EC50:  4   nM  BindingDB
67S	IC50:  10000   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.248 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.637	α = 90
b = 101.221	β = 90
c = 143.274	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-02-12 
• Released Date: 2016-06-29 
Deposition Author(s): Chen, G., McKeever, B.M.

Revision History  

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