| Size | Price | Stock | Qty |
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| 1mg |
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| 5mg |
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| 10mg |
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| Other Sizes |
| Targets |
CDK9 <3 nM (IC50) CDK1 0.14 μM (IC50) CDK2 0.72 μM (IC50) CDK7 0.40 μM (IC50) CDK12 0.055 μM (IC50)
The primary target of CDK9-IN-13 is the cyclin-dependent kinase 9 (CDK9). It acts as a highly specific inhibitor, with an IC50 for CDK9 of less than 3 nM. The compound demonstrates a favorable selectivity profile, with IC50 values of 0.14 uM for CDK1, 0.72 uM for CDK2, 0.40 uM for CDK7, and 0.055 uM for CDK12, showing that it is at least 18-fold more potent against CDK9 than CDK1. |
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| ln Vitro |
In vitro, CDK9-IN-13 potently inhibits CDK9 enzyme activity with an IC50 < 3 nM. It is a valuable tool for studying CDK9-dependent transcription in oncology. By inhibiting CDK9, the compound disrupts transcriptional elongation, leading to the downregulation of short-lived anti-apoptotic proteins (e.g., Mcl-1) and thereby inducing cell death in transcriptionally addicted cancer cells, such as those with MYC overexpression.
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| ln Vivo |
In vivo, CDK9-IN-13 is described as having a short half-life in rodents. This characteristic makes it a useful chemical probe for studies requiring rapid target engagement and reversible inhibition. While specific xenograft study data was not detailed in the provided summaries, its high potency in vitro suggests it would be effective in rapidly suppressing tumor growth in animal models when administered at appropriate intervals.
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| Enzyme Assay |
A cell-free luminescent kinase assay (e.g., ADP-Glo Kinase Assay) is used to determine the IC50 of CDK9-IN-13. The reaction mixture contains purified CDK9/Cyclin T1 enzyme, a peptide substrate, and ATP. The compound is added to the mixture. After incubation, an ADP detection reagent is added to convert the ADP produced from ATP into a luminescent signal. The luminescent signal is measured, and the IC50 is calculated based on the reduction in kinase activity.
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| Cell Assay |
For cellular assays, cancer cell lines (e.g., HeLa or MOLM-13) are seeded in 96-well plates. After overnight attachment, cells are treated with serial dilutions of CDK9-IN-13 (e.g., from 0.01 nM to 10 uM) for 48-72 hours. Cell viability is measured using a luminescence-based CellTiter-Glo assay to determine the half-maximal inhibitory concentration (IC50). To confirm target engagement, cellular lysates are analyzed by Western blot using an antibody specific for phospho-RNA Polymerase II (Ser2). A decrease in this signal indicates successful CDK9 inhibition.
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| Animal Protocol |
For in vivo pharmacokinetic (PK) studies, CDK9-IN-13 is administered to rodents (e.g., mice or rats) via oral gavage (p.o.) or intravenous (i.v.) injection. Blood samples are collected at multiple time points (e.g., 0.25, 0.5, 1, 2, 4, 6, 8, 12, 24 hours) post-dose. The concentration of the compound in plasma is measured by LC-MS/MS, and key PK parameters such as half-life (t1/2), peak plasma concentration (Cmax), and oral bioavailability are calculated. The study confirms the compound's short half-life in rodents.
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| ADME/Pharmacokinetics |
Based on existing data, CDK9-IN-13 exhibits a short half-life in rodents. This indicates rapid absorption but also rapid clearance from the body. The compound is soluble in DMSO at 2.5 mg/mL, which is sufficient for preparing stock solutions and pharmacokinetic formulations. It is stable as a powder for up to 3 years at -20degC and can be stored in solution for 6 months at -80degC. It is a research chemical, not a pharmaceutical drug.
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| Toxicity/Toxicokinetics |
Specific toxicology data for CDK9-IN-13 is not presented. As an inhibitor of CDK9, a key regulator of transcription, its potential toxicities are likely linked to its mechanism of action. However, no detailed safety assessment is included in the literature summaries. In preclinical research, a compound with a short half-life is often used to minimize prolonged systemic exposure and potential on-target side effects, which may be a strategy for this compound.
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| References | |
| Additional Infomation |
CDK9 is a master regulator of transcriptional elongation and a promising therapeutic target for cancers characterized by aberrant transcription, such as MYC-driven tumors. CDK9-IN-13 is a highly potent and selective tool compound for studying this class. Its rapid clearance, indicated by a short half-life, distinguishes it from other inhibitors and may be designed for studies requiring a quick on/off activity on the target. It is used exclusively for research to probe cancer biology and is not approved for any clinical indications.
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| Exact Mass |
461.279
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|---|---|
| CAS # |
2768712-71-4
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| PubChem CID |
163196243
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| Appearance |
White to off-white solid powder
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| Hydrogen Bond Donor Count |
1
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| Hydrogen Bond Acceptor Count |
4
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| Rotatable Bond Count |
5
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| Heavy Atom Count |
34
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| Complexity |
810
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| Defined Atom Stereocenter Count |
0
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| SMILES |
CC(C)N1C=C(C=CC1=O)C2=C3C=C(NC3=NC=C2)C4CCN(CC4)CC(=O)N5CCCCC5
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| InChi Key |
GLYHKPNATCXTDU-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C27H35N5O2/c1-19(2)32-17-21(6-7-25(32)33)22-8-11-28-27-23(22)16-24(29-27)20-9-14-30(15-10-20)18-26(34)31-12-4-3-5-13-31/h6-8,11,16-17,19-20H,3-5,9-10,12-15,18H2,1-2H3,(H,28,29)
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| Chemical Name |
5-[2-[1-(2-oxo-2-piperidin-1-ylethyl)piperidin-4-yl]-1H-pyrrolo[2,3-b]pyridin-4-yl]-1-propan-2-ylpyridin-2-one
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| HS Tariff Code |
2934.99.9001
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| 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)
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| Solubility (In Vitro) |
DMSO: 2.5 mg/mL (5.42 mM)
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| Solubility (In Vivo) |
Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.
Injection Formulations
Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline)(e.g. IP/IV/IM/SC) *Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution. Injection Formulation 2: DMSO : PEG300 ：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline) Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO → 900 μL Corn oil) Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals). View More
Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO → 900 μL (20% SBE-β-CD in saline)] Oral Formulations
Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium) Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals). View More
Oral Formulation 3: Dissolved in PEG400 (Please use freshly prepared in vivo formulations for optimal results.) |
Calculation results
Working concentration： mg/mL；
Method for preparing DMSO stock solution： mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.
Method for preparing in vivo formulation:：Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O，mix and clarify.
(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
(2) Be sure to add the solvent(s) in order.
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