CLK-IN-T3 is a novel, potent and highly selective CLK (CDC-like kinase) inhibitor with high specificity to CLK1-3 protein isoforms and with IC50s of 0.67 nM, 15 nM, and 110 nM for CLK1, CLK2, and CLK3 protein kinases, respectively. CLK-IN-T3 has anti-cancer activity.
Physicochemical Properties
| Molecular Formula | C28H30N6O2 |
| Molecular Weight | 482.576805591583 |
| Exact Mass | 482.243 |
| Elemental Analysis | C, 64.79; H, 6.02; Cl, 6.83; N, 16.19; O, 6.16 |
| CAS # | 2109805-56-1 |
| Related CAS # | 2109805-56-1; |
| PubChem CID | 132585205 |
| Appearance | Off-white to light yellow solid powder |
| Density | 1.3±0.1 g/cm3 |
| Index of Refraction | 1.659 |
| LogP | 2.36 |
| Hydrogen Bond Donor Count | 1 |
| Hydrogen Bond Acceptor Count | 5 |
| Rotatable Bond Count | 5 |
| Heavy Atom Count | 36 |
| Complexity | 768 |
| Defined Atom Stereocenter Count | 0 |
| SMILES | O=C(C(C)(C)C1C=CC(C(NC2=CN3C=C(C4C=CN=CC=4)C=CC3=N2)=O)=CC=1)N1CCN(C)CC1 |
| InChi Key | IEFFSHLHNYVSEF-UHFFFAOYSA-N |
| InChi Code | InChI=1S/C28H30N6O2/c1-28(2,27(36)33-16-14-32(3)15-17-33)23-7-4-21(5-8-23)26(35)31-24-19-34-18-22(6-9-25(34)30-24)20-10-12-29-13-11-20/h4-13,18-19H,14-17H2,1-3H3,(H,31,35) |
| Chemical Name | 4-[2-methyl-1-(4-methylpiperazin-1-yl)-1-oxopropan-2-yl]-N-(6-pyridin-4-ylimidazo[1,2-a]pyridin-2-yl)benzamide |
| Synonyms | T3; CLK Inhibitor T3; T3-CLK; MDK 5561; MDK-5561; MDK5561; MDK-5561 hydrochloride; MDK-5561 HCl |
| HS Tariff Code | 2934.99.9001 |
| Storage |
Powder-20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month |
| Shipping Condition | Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs) |
Biological Activity
| Targets | CLK1 (IC50 = 0.67 nM); CLK2 (IC50 = 15 nM); CLK3 (IC50 = 110 nM); DYRK1A (IC50 = 260 nM); DYRK1B (IC50 = 230 nM) |
| ln Vitro |
CLK-IN-T3 suppresses the activity of DYRK1A (IC50=260 nM) and DYRK1B (IC50=230 nM).[1] CLK-IN-T3 (0.1-10.0 µM; 24 hours) results in a long-lasting (24 hours) mild cell cycle arrest at the G2/M boundary[1]. CLK-IN-T3 (0.5-1.0 µM; 6 hours) reduces the phosphorylation of SR proteins that are targeted by CLK, while CLK proteins slightly increase[1]. |
| Cell Assay |
Cell Line: HCT-116 cells Concentration: 0.1, 0.5, 1.0, 5.0, 10.0 µM Incubation Time: 24 hours Result: Resulted in mild cell cycle arrest at the G2/M boundary with long-duration (24 h). |
| References |
[1]. CLK-dependent exon recognition and conjoined gene formation revealed with a novel smallmolecule inhibitor. Nat Commun. 2017 Feb 23;8(1):7. |
Solubility Data
| Solubility (In Vitro) | DMSO: ~4.8 mg/mL (~10.0 mM) |
| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.08 mg/mL (4.31 mM) (saturation unknown) in 10% DMSO + 40% PEG300 + 5% Tween80 + 45% Saline (add these co-solvents sequentially from left to right, and one by one), clear solution. For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 20.8 mg/mL clear DMSO stock solution to 400 μL PEG300 and mix evenly; then add 50 μL Tween-80 to the above solution and mix evenly; then add 450 μL normal saline to adjust the volume to 1 mL. Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH₂ O to obtain a clear solution. Solubility in Formulation 2: ≥ 2.08 mg/mL (4.31 mM) (saturation unknown) in 10% DMSO + 90% (20% SBE-β-CD in Saline) (add these co-solvents sequentially from left to right, and one by one), clear solution. For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 20.8 mg/mL clear DMSO stock solution to 900 μL of 20% SBE-β-CD physiological saline solution and mix evenly. Preparation of 20% SBE-β-CD in Saline (4°C，1 week): Dissolve 2 g SBE-β-CD in 10 mL saline to obtain a clear solution. (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 2.0722 mL | 10.3610 mL | 20.7220 mL | |
| 5 mM | 0.4144 mL | 2.0722 mL | 4.1444 mL | |
| 10 mM | 0.2072 mL | 1.0361 mL | 2.0722 mL |