| Size | Price | Stock | Qty |
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| 5mg |
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| 10mg |
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| Other Sizes |
| Targets |
CDK7 53.5 nM (IC50) CDK7/Mat1/CycH 9.7 nM (IC50) CDK2 1300 nM (IC50) CDK9 3020 nM (IC50)
YKL-5-124 TFA specifically targets Cyclin-Dependent Kinase 7 (CDK7). It is a covalent inhibitor that binds irreversibly to a cysteine residue in the active site of CDK7. It inhibits CDK7 alone with an IC50 of 53.5 nM and the CDK7/Mat1/CycH complex with an IC50 of 9.7 nM. The compound is >100-fold more selective for CDK7 over CDK9 and CDK2, and it is inactive against CDK12 and CDK13, demonstrating exceptional selectivity. |
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| ln Vitro |
G1- and G2/M-phase cell numbers rise while S-phase cell numbers decrease in a dose-dependent manner in response to YKL-5-124 (0-2000 nM; 72 hours; HAP1 cells) treatment[1]. ?In a concentration-dependent manner, YKL-5-124 (0-2000 nM; 24 hours; HAP1 WT cells) treatment suppresses the phosphorylation of CDK1 T-loop and, to a lesser extent, CDK2 T-loop[1]. ?The pull-down of CDK7-cyclin H is blocked when cells treated with YKL -5-124 as a competitor at a concentration of roughly 30 nM, but it has no effect on the pull-down of cyclin K-CDK12/13 in HAP1 cells. CDK7-cyclin H binding to bioTHZ1 is reduced by >50% after 30 minutes of treatment with 100 nM YKL-5 -124[1].
In vitro, YKL-5-124 TFA potently inhibits its target. By inhibiting CDK7, it induces a strong cell-cycle arrest and inhibits E2F-driven gene expression, demonstrating its role in cell cycle control. Importantly, it exhibits little effect on the phosphorylation status of RNA Polymerase II, which is a primary function of CDK9. This highlights its unique cellular mechanism and distinguishes it from CDK9 inhibitors. |
| ln Vivo |
In vivo data for YKL-5-124 TFA is not extensively detailed in the provided literature. As a research tool, its primary use is for in vitro mechanistic studies to understand the role of CDK7. However, as an irreversible covalent inhibitor with high target selectivity, it is also suitable for in vivo pharmacokinetic (PK) and efficacy studies in xenograft mouse models to evaluate its potential for treating cancers that are dependent on CDK7 for proliferation and survival.
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| Enzyme Assay |
A cell-free assay is performed using purified CDK7, Mat1, and CycH proteins (the CDK7 complex). A peptide substrate (e.g., a fragment of CDK9 or RNA Polymerase II) and ATP (with gamma-33P-ATP for detection) are added to the reaction. The compound is pre-incubated with the enzyme to allow for covalent bond formation. The reaction is initiated by adding the substrate and ATP. The incorporation of radioactive phosphate is measured to determine the IC50.
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| Cell Assay |
Cell Cycle Analysis[1]
Cell Types: HAP1 cells Tested Concentrations: 0 nM, 0.2 nM, 0.7 nM, 2 nM, 6.3 nM, 20 nM, 60 nM, 200 nM, 633.3 nM, 2000 nM Incubation Duration: 72 hrs (hours) Experimental Results: Caused a dose-dependent increase in G1- and G2/M-phase cells and a corresponding loss of S-phase cells. Western Blot Analysis[1] Cell Types: HAP1 WT cells Tested Concentrations: 0 nM, 125 nM, 250 nM, 500 nM, 1000 nM, 2000 nM Incubation Duration: 24 hrs (hours) Experimental Results: Inhibited CDK1 T-loop phosphorylation, and to a lesser extent CDK2 T-loop phosphorylation in a concentration-dependent fashion. For cellular studies, cancer cell lines (e.g., HeLa or HCC1806) are seeded in 96-well plates and treated with serial dilutions of YKL-5-124 TFA. Cell viability is measured after 72-96 hours using the CellTiter-Glo luminescent assay. Mechanistically, cells are lysed and analyzed by Western blot. Target engagement can be assessed using a "kinase-inactivation" antibody that detects the covalent binding, or by measuring downstream effects such as cell-cycle markers (e.g., cyclins) and E2F-target gene expression. |
| Animal Protocol |
A standard protocol for a CDK7 inhibitor would involve a xenograft mouse model. Immunocompromised mice are subcutaneously implanted with human cancer cells (e.g., triple-negative breast cancer cells). Once tumors reach a target size (e.g., 150 mm3), mice are randomized and treated with YKL-5-124 TFA. The compound can be formulated in a vehicle (e.g., 10% DMSO, 40% PEG300, 5% Tween-80, 45% saline) and administered by intraperitoneal (IP) injection. Tumor volume is measured with calipers to assess anti-tumor activity.
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| ADME/Pharmacokinetics |
Specific ADME (Absorption, Distribution, Metabolism, and Excretion) data for YKL-5-124 TFA is not provided in the summaries. The compound is highly soluble in DMSO (≥ 100 mg/mL) and water (50 mg/mL). For in vivo administration, a standard formulation (10% DMSO, 40% PEG300, 5% Tween-80, 45% saline) has been developed, producing a clear solution. This formulation is suitable for intraperitoneal (IP) injection, which is a common route for preclinical in vivo studies of this compound.
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| Toxicity/Toxicokinetics |
No specific toxicology data for YKL-5-124 TFA is provided. As a research tool, its toxicological profile is likely being characterized. The compound's high selectivity for CDK7 over other CDKs suggests it may have a reduced risk of off-target toxicities compared to other CDK inhibitors. However, on-target CDK7 inhibition is known to have antiproliferative effects, which would be the primary mechanism for both its efficacy and potential dose-limiting toxicity. It is a research-grade compound only.
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| References | |
| Additional Infomation |
YKL-5-124 TFA is a highly selective and irreversible covalent inhibitor. It is a valuable chemical probe for deconvoluting the specific functions of CDK7 in transcription and cell cycle regulation. Unlike many other CDK7 inhibitors that also inhibit CDK9, YKL-5-124 TFA is >100-fold selective, allowing researchers to distinguish between the two. This makes it a crucial tool for understanding the mechanism of CDK7 in driving cancer cell proliferation. It is not approved for any clinical use and remains in the preclinical research stage.
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| Molecular Formula |
C30H34F3N7O5
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|---|---|
| Molecular Weight |
629.630076885223
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| Exact Mass |
629.257
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| CAS # |
2748220-93-9
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| Related CAS # |
YKL-5-124;1957203-01-8
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| PubChem CID |
146025947
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| Appearance |
White to off-white solid powder
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| Hydrogen Bond Donor Count |
5
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| Hydrogen Bond Acceptor Count |
10
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| Rotatable Bond Count |
8
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| Heavy Atom Count |
45
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| Complexity |
948
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| Defined Atom Stereocenter Count |
1
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| SMILES |
C(F)(F)(F)C(=O)O.N(C1=NNC2C(C)(C)N(C(=O)N[C@@H](C3C=CC=CC=3)CN(C)C)CC1=2)C(C1C=CC(NC(=O)C=C)=CC=1)=O
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| InChi Key |
CPYGDECNKKKQGE-VZYDHVRKSA-N
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| InChi Code |
InChI=1S/C28H33N7O3.C2HF3O2/c1-6-23(36)29-20-14-12-19(13-15-20)26(37)31-25-21-16-35(28(2,3)24(21)32-33-25)27(38)30-22(17-34(4)5)18-10-8-7-9-11-18;3-2(4,5)1(6)7/h6-15,22H,1,16-17H2,2-5H3,(H,29,36)(H,30,38)(H2,31,32,33,37);(H,6,7)/t22-;/m1./s1
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| Chemical Name |
N-[(1S)-2-(dimethylamino)-1-phenylethyl]-6,6-dimethyl-3-[[4-(prop-2-enoylamino)benzoyl]amino]-1,4-dihydropyrrolo[3,4-c]pyrazole-5-carboxamide;2,2,2-trifluoroacetic acid
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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 Note: Please store this product in a sealed and protected environment, avoid exposure to moisture. |
| 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: ≥ 100 mg/mL (158.82 mM)
H2O: 50 mg/mL (79.41 mM) |
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| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.5 mg/mL (3.97 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 25.0 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: ≥ 2.5 mg/mL (3.97 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 25.0 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. View More
Solubility in Formulation 3: ≥ 2.5 mg/mL (3.97 mM) (saturation unknown) in 10% DMSO + 90% Corn Oil (add these co-solvents sequentially from left to right, and one by one), clear solution. Solubility in Formulation 4: 50 mg/mL (79.41 mM) in PBS (add these co-solvents sequentially from left to right, and one by one), clear solution; with ultrasonication. |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 1.5882 mL | 7.9412 mL | 15.8823 mL | |
| 5 mM | 0.3176 mL | 1.5882 mL | 3.1765 mL | |
| 10 mM | 0.1588 mL | 0.7941 mL | 1.5882 mL |
*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.
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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