SKI II   Click here for help

GtoPdb Ligand ID: 6041

Synonyms: SKI 2 | SKI-II
PDB Ligand
Compound class: Synthetic organic
Comment: The discovery of this selective sphingosine kinase inhibitor is described in [3], where it is called compound II.
The above article cites [8] for the creation of the human sphingosine kinase protein used in their kinase assay. BLAST searches using the accession numbers in this article indicate the kinase assay was performed using the SPHK1 isozyme. SKI II exhibits some selectivity toward SK2 as a kinase inhibitor (Ki for SK2 = 7.9 μM vs. SK1 = 16 μM) [3]. It is a more powerful promoter of SK1-degradation than of SK2-degradation [7].
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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species

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2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 2
Hydrogen bond donors 2
Rotatable bonds 3
Topological polar surface area 73.39
Molecular weight 302.03
XLogP 4.29
No. Lipinski's rules broken 0

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES Oc1ccc(cc1)Nc1scc(n1)c1ccc(cc1)Cl
Isomeric SMILES Oc1ccc(cc1)Nc1scc(n1)c1ccc(cc1)Cl
InChI InChI=1S/C15H11ClN2OS/c16-11-3-1-10(2-4-11)14-9-20-15(18-14)17-12-5-7-13(19)8-6-12/h1-9,19H,(H,17,18)
InChI Key ZFGXZJKLOFCECI-UHFFFAOYSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
References
1. Anastassiadis T, Deacon SW, Devarajan K, Ma H, Peterson JR. (2011)
Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity.
Nat Biotechnol, 29 (11): 1039-45. [PMID:22037377]
2. Cingolani F, Casasampere M, Sanllehí P, Casas J, Bujons J, Fabrias G. (2014)
Inhibition of dihydroceramide desaturase activity by the sphingosine kinase inhibitor SKI II.
J Lipid Res, 55 (8): 1711-20. [PMID:24875537]
3. French KJ, Schrecengost RS, Lee BD, Zhuang Y, Smith SN, Eberly JL, Yun JK, Smith CD. (2003)
Discovery and evaluation of inhibitors of human sphingosine kinase.
Cancer Res, 63 (18): 5962-9. [PMID:14522923]
4. French KJ, Zhuang Y, Maines LW, Gao P, Wang W, Beljanski V, Upson JJ, Green CL, Keller SN, Smith CD. (2010)
Pharmacology and antitumor activity of ABC294640, a selective inhibitor of sphingosine kinase-2.
J Pharmacol Exp Ther, 333 (1): 129-39. [PMID:20061445]
5. Gao P, Peterson YK, Smith RA, Smith CD. (2012)
Characterization of isoenzyme-selective inhibitors of human sphingosine kinases.
PLoS ONE, 7 (9): e44543. [PMID:22970244]
6. Gao Y, Davies SP, Augustin M, Woodward A, Patel UA, Kovelman R, Harvey KJ. (2013)
A broad activity screen in support of a chemogenomic map for kinase signalling research and drug discovery.
Biochem J, 451 (2): 313-28. [PMID:23398362]
7. Loveridge C, Tonelli F, Leclercq T, Lim KG, Long JS, Berdyshev E, Tate RJ, Natarajan V, Pitson SM, Pyne NJ et al.. (2010)
The sphingosine kinase 1 inhibitor 2-(p-hydroxyanilino)-4-(p-chlorophenyl)thiazole induces proteasomal degradation of sphingosine kinase 1 in mammalian cells.
J Biol Chem, 285 (50): 38841-52. [PMID:20926375]
8. Pitson SM, D'andrea RJ, Vandeleur L, Moretti PA, Xia P, Gamble JR, Vadas MA, Wattenberg BW. (2000)
Human sphingosine kinase: purification, molecular cloning and characterization of the native and recombinant enzymes.
Biochem J, 350 Pt 2: 429-41. [PMID:10947957]