5KYA

Brain penetrant liver X receptor (LXR) modulators based on a 2,4,5,6-tetrahydropyrrolo[3,4-c]pyrazole core

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Brain penetrant liver X receptor (LXR) modulators based on a 2,4,5,6-tetrahydropyrrolo[3,4-c]pyrazole core.

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

(2016) Bioorg Med Chem Lett 26: 5044-5050

  • DOI: https://doi.org/10.1016/j.bmcl.2016.08.089
  • Primary Citation of Related Structures:  
    5KYA, 5KYJ

  • PubMed Abstract: 

    Liver X receptor (LXR) agonists have been reported to lower brain amyloid beta (Aβ) and thus to have potential for the treatment of Alzheimer's disease. Structure and property based design led to the discovery of a series of orally bioavailable, brain penetrant LXR agonists. Oral administration of compound 18 to rats resulted in significant upregulation of the expression of the LXR target gene ABCA1 in brain tissue, but no significant effect on Aβ levels was detected.

    • Organizational Affiliation: 

    Vitae Pharmaceuticals, 502 West Office Center Drive, Fort Washington, PA 19034, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxysterols receptor LXR-betaA,
C [auth E]		287Homo sapiensMutation(s): 6 
Gene Names: NR1H2, LXRB, NER, UNR
UniProt & NIH Common Fund Data Resources
Find proteins for P55055 (Homo sapiens)
Go to UniProtKB:  P55055
PHAROS:  P55055
GTEx:  ENSG00000131408 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-betaB,
D [auth F]		256Homo sapiensMutation(s): 1 
Gene Names: RXRB, NR2B2
UniProt & NIH Common Fund Data Resources
Find proteins for P28702 (Homo sapiens)
Go to UniProtKB:  P28702
PHAROS:  P28702
GTEx:  ENSG00000204231 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6Y4
Query on 6Y4
Download Ideal Coordinates CCD File 
E [auth A],
F [auth E]		[2-[(6~{R})-2-(3-methylsulfonylphenyl)-6-propan-2-yl-4,6-dihydropyrrolo[3,4-c]pyrazol-5-yl]-4-(trifluoromethyl)pyrimidin-5-yl]methanol
C21 H22 F3 N5 O3 S
NCZXBZJVJRJUSC-GOSISDBHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6Y4 BindingDB:  5KYA Ki: 6 (nM) from 1 assay(s)
EC50: 46 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.439α = 90
b = 101.089β = 90
c = 143.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Refinement description