Experimental Data Snapshot
Starting Model:experimental
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(2016) J Med Chem 59: 3264-3271
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.
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (67S)
Biological assembly 1 assigned by authors and generated by PISA (software)
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (67S)
Biological assembly 2 assigned by authors and generated by PISA (software)
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Oxysterols receptor LXR-beta,Nuclear receptor coactivator 2 | A, C [auth E] | 270 | Homo sapiens | Mutation(s): 6  Gene Names: NR1H2, LXRB, NER, UNR, NCOA2, BHLHE75, SRC2, TIF2 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P55055 (Homo sapiens) Explore P55055  Go to UniProtKB:  P55055 | |||||
PHAROS:  P55055 GTEx:  ENSG00000131408  | |||||
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596 | |||||
PHAROS:  Q15596 GTEx:  ENSG00000140396  | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Groups | Q15596P55055 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Retinoic acid receptor RXR-beta,Nuclear receptor coactivator 2 | B, D [auth F] | 255 | Homo sapiens | Mutation(s): 1  Gene Names: RXRB, NR2B2, NCOA2, BHLHE75, SRC2, TIF2 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P28702 (Homo sapiens) Explore P28702  Go to UniProtKB:  P28702 | |||||
PHAROS:  P28702 GTEx:  ENSG00000204231  | |||||
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596 | |||||
PHAROS:  Q15596 GTEx:  ENSG00000140396  | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Groups | Q15596P28702 | ||||
Sequence AnnotationsExpand | |||||
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| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 67S Query on 67S Download Ideal Coordinates CCD File  | E [auth A], F [auth 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 | |||
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 68.637 | α = 90 |
| b = 101.221 | β = 90 |
| c = 143.274 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.