5KYA | pdb_00005kya

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

• PDB DOI: https://doi.org/10.2210/pdb5KYA/pdb

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


• Deposited: 2016-07-21 Released: 2016-09-21 
• Deposition Author(s): Chen, G., McKeever, B.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.249 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

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

• PubMed: 27599745 
• DOI: https://doi.org/10.1016/j.bmcl.2016.08.089
• Primary Citation 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.

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Organizational Affiliation: 
• Vitae Pharmaceuticals, 502 West Office Center Drive, Fort Washington, PA 19034, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 122.38 kDa 
• Atom Count: 7,550 
• Modeled Residue Count: 928 
• Deposited Residue Count: 1,086 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxysterols receptor LXR-beta	A, C [auth E]	287	Homo sapiens	Mutation(s): 6  Gene Names: NR1H2, LXRB, NER, UNR
UniProt & NIH Common Fund Data Resources
Find proteins for P55055 (Homo sapiens) Explore P55055  Go to UniProtKB:  P55055
PHAROS:  P55055 GTEx:  ENSG00000131408

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-beta	B, D [auth F]	256	Homo sapiens	Mutation(s): 1  Gene Names: RXRB, NR2B2
UniProt & NIH Common Fund Data Resources
Find proteins for P28702 (Homo sapiens) Explore P28702  Go to UniProtKB:  P28702
PHAROS:  P28702 GTEx:  ENSG00000204231

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6Y4	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.249 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.439	α = 90
b = 101.089	β = 90
c = 143.58	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

• Released Date: 2016-09-21 
Deposition Author(s): Chen, G., McKeever, B.M.

Revision History  

• 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