SY-5609
Based on 7 publication(s) in Google Scholar
SY-5609 (CDK7-IN-3) is an orally active, highly selective, noncovalent CDK7 inhibitor with a KD of 0.065 nM. SY-5609 shows poor inhibition on CDK2 (Ki=2600 nM), CDK9 (Ki=960 nM), CDK12 (Ki=870 nM). SY-5609 induces apoptosis in tumor cells and has antitumor activity.
For research use only. We do not sell to patients.
- Purity: 99.93%
- CAS No.: 2417302-07-7
- Formula: C23H26F3N6OP
- Molecular Weight:490.46
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Storage:
4°C, stored under nitrogen
* In solvent : -80°C, 2 years; -20°C, 1 year (stored under nitrogen)
To place orders, for customer services and technical support, please contact: MedChemExpress USA
Tel: 609-228-6898 E-mail: [email protected] [email protected]
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Biological Activity
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Chemical Information
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Solvent & Solubility
- Purity & Documentation
- References
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Help & FAQs
Publications Citing Use of MedChemExpress (MCE) SY-5609
More
Customer Validation & Images
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In Vivo Efficacy Study
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Cell Proliferation/Viability Assay
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Bio/Physico-chemical Assay
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IF
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In Vivo Efficacy Study
Biological Activity
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CDK7 0.065 nM (Kd) |
CDK2 2600 nM (Ki) |
CDK9 960 nM (Ki) |
CDK12 870 nM (Ki) |
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Cell Line
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Type | Value | Description | References |
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| HCC70 | EC50 |
1 nM
Compound: SY-5609
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Antiproliferative activity against human HCC70 cells incubated for 72 hrs by Celltiter-glo assay
Antiproliferative activity against human HCC70 cells incubated for 72 hrs by Celltiter-glo assay
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[PMID: 34726887] |
SY-5609 (0.01-10000 nM; 72 hours) demonstrates strong antiproliferative effects in triple negative breast cancer (TNBC) and ovarian (OVA) cancer cells[1].
SY-5609 (100-500 nM; 48, 72 hours) induces apoptosis[1].
SY-5609 (100-500 nM; 48 hours) induces G2/M cell cycle arrest in HCC70 cells[1].
SY-5609 (25-500 nM; 6-48 hours) results in inhibition of the phosphorylation of CDK2 at Thr160 via loss of CAK function for 24 and 48 h[1].
SY-5609 (compound 101; 126.4 pM-4 μM; 72 hours) has an EC50 of 5.6 nM in HCC70 cell line[2].
MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.
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Cell Line:HCC70, MDA-MB453, COV504, A2780, OVCAR3, CAOV3 cells
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Concentration:0.01-10000 nM
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Incubation Time:72 hours
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Result:Demonstrated strong antiproliferative effects with IC50 of 1-6 nM.
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Cell Line:HCC70, MDA-MB-468, CAOV3 and OVCAR3 cells
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Concentration:100, 250, 500 nM
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Incubation Time:48 and 72 hours
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Result:Induced apoptosis.
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Cell Line:HCC70 cells
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Concentration:100, 250, 500 nM
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Incubation Time:48 hours
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Result:Induced G2/M cell cycle arrest.
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Cell Line:HCC70 cells
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Concentration:25, 50, 100, 250, 500 nM
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Incubation Time:6, 24, 48 hours
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Result:Resulted in inhibition of the phosphorylation of CDK2 at Thr160 via loss of CAK function for 24 and 48 h.
Daily oral dosing of 2 mg/kg SY-5609 in mice provided a plasma exposure of 261.28 ng h/mL with a Cmax of 50.67 ng/mL (103 nM) and an elimination half-life of 3.33 h[1].
MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.
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Animal Model:Six-to-eight-week-old Balb/c nude female mice with HCC70 cell line[1]
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Dosage:2 mg/kg
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Administration:Orally; daily; for 21 days
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Result:Induced tumor regression over the 21-day dosing period and was well tolerated. No regrowth of tumor was observed out to day 28.
| NCT Number | Sponsor | Condition | Start Date |
Phase
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|---|---|---|---|---|
| NCT01329991 | Plexxikon| | 2011-05 | PHASE1 |
Chemical Information
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CAS No. 2417302-07-7
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Appearance Solid
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Molecular Weight 490.46
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Formula C23H26F3N6OP
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Color White to light yellow
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SMILES
N#CC1=C(P(C)(C)=O)C2=C(C=C1)C(C3=NC(N[C@@H]4CNC(C)(C)CC4)=NC=C3C(F)(F)F)=CN2
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Synonyms
CDK7-IN-3
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Shipping
Room temperature in continental US; may vary elsewhere.
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Storage
4°C, stored under nitrogen
* In solvent : -80°C, 2 years; -20°C, 1 year (stored under nitrogen)
Publications (7)
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Journal Impact Factor
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Most Recent
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J Clin Invest
Dual targeting CDK4/6 and CDK7 augments tumor response and anti-tumor immunity in breast cancer models. [Abstract]2025 Aug 12:e188839. PMID: 40794455
SY-5609 purchased from MedChemExpress. Usage Cited in: J Clin Invest. 2025 Aug 12:e188839. [Abstract]
SY-5609 (CDK7i) (2-25 mg/kg; i.g.; once daily) induced a dose-dependent antitumor response of AT3OVA-bearing C57BL/6J mice.
SY-5609 purchased from MedChemExpress. Usage Cited in: J Clin Invest. 2025 Aug 12:e188839. [Abstract]
IC50 of SY-5609 (CDK7i) (0.5-1.5μM; 48 h) on mRNA transcription rates, CDK2 and CDK4/6 activities, and the percentage of S phase cells in MDA-MB-231 and MCF-7 cells.
SY-5609 purchased from MedChemExpress. Usage Cited in: J Clin Invest. 2025 Aug 12:e188839. [Abstract]
Violin plots of EU incorporation in MDA-MB-231 cells treated with SY-5609 (50 nM).
SY-5609 purchased from MedChemExpress. Usage Cited in: J Clin Invest. 2025 Aug 12:e188839. [Abstract]
SY-5609 (CDK7i) (2 mg/kg; i.g.; once daily) reversed a T cell exclusion phenotype and promoted CD8+ T cell infiltration into the core of AT3OVA tumors.
SY-5609 purchased from MedChemExpress. Usage Cited in: J Clin Invest. 2025 Aug 12:e188839. [Abstract]
Individual and final tumor volumes of AT3OVA-bearing C57BL/6J mice treated with SY-5609 (CDK7i) (10 mg/kg; i.g.; once daily).
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Int J Biol Macromol
CDK2-based CDK7 mimic as a tool for structural analysis: Biochemical validation and crystal structure with SY5609. [Abstract]2024 Dec 27:139117. PMID: 39733900 -
EMBO J
Resistance to CDK7 inhibitors directed by acquired mutation of a conserved residue in cancer cells. [Abstract]2025 Sep 8. PMID: 40921851 -
mBio
Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans. [Abstract]2025 Dec 10;16(12):e0289825. PMID: 41171060 -
iScience
2025 Nov 4;28(12):113925. PMID: 41321622 -
bioRxiv
2025 Nov 3:2025.11.02.685764. PMID: 41279360 -
Solvent & Solubility
DMSO : 40 mg/mL (81.56 mM; Need ultrasonic; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 2 years; -20°C, 1 year (stored under nitrogen). When stored at -80°C, please use it within 2 years. When stored at -20°C, please use it within 1 year.
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 2 years; -20°C, 1 year (stored under nitrogen). When stored at -80°C, please use it within 2 years. When stored at -20°C, please use it within 1 year.
Concentration (start) × Volume (start) = Concentration (final) × Volume (final)
Select the appropriate dissolution method based on your experimental animal and administration route.
- For the following dissolution methods, please ensure to first prepare a clear stock solution using an In Vitro approach and then sequentially add co-solvents:
- To ensure reliable experimental results, the clarified stock solution can be appropriately stored based on storage conditions. As for the working solution for In Vivo experiments, it is recommended to prepare freshly and use it on the same day.
- The percentages shown for the solvents indicate their volumetric ratio in the final prepared solution. If precipitation or phase separation occurs during preparation, heat and/or sonication can be used to aid dissolution.
Add each solvent one by one: 10% DMSO 40% PEG300 5% Tween-80 45% Saline
Solubility: ≥ 2.5 mg/mL (5.10 mM); Clear solution
This protocol yields a clear solution of ≥ 2.5 mg/mL (saturation unknown).
Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (25.0 mg/mL) to 400 μL PEG300, and mix evenly; then add 50 μL Tween-80 and mix evenly; then add 450 μL Saline to adjust the volume to 1 mL.
Preparation of Saline: Dissolve 0.9 g sodium chloride in ddH₂O and dilute to 100 mL to obtain a clear Saline solution.
Please enter the basic information of animal experiments:
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Recommended: Prepare an additional quantity of animals to account for potential losses during experiments.
Please enter your animal formula composition:
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%DMSO +
Recommended: Keep the proportion of DMSO in working solution below 2% if your animal is weak.
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%+
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+%Tween-80 + +
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%Saline +
The co-solvents required include: DMSO, . All of co-solvents are available by MedChemExpress (MCE). , Tween 80. All of co-solvents are available by MedChemExpress (MCE).
Working solution concentration: 0.22 mg/mL
Method for preparing stock solution: mg drug dissolved in μL DMSO. Stock solution concentration: mg/mL. * In solvent : -80°C, 2 years; -20°C, 1 year (stored under nitrogen)
1. Take μL DMSO stock solution;
2. Add μL .
μL , mix evenly;
3. Then add μL Tween 80, mix evenly;
4. Then add μL
Please ensure that the stock solution in the first step is dissolved to a clear state, and add co-solvents in sequence. You can use ultrasonic heating (ultrasonic cleaner, recommended frequency 20-40 kHz), vortexing, etc. to assist dissolution.
Purity & Documentation
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Data Sheet (288 KB)
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SDS (394 KB)
- English - EN (394 KB)
- Français - FR (394 KB)
- Deutsch - DE (394 KB)
- Norwegian - NO (394 KB)
- Español - ES (394 KB)
- Swedish - SV (394 KB)
- Italian - IT (394 KB)
- Korean - KR (394 KB)
- Portuguese - PT (394 KB)
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Handling Instructions (2659 KB)
References
Complete Stock Solution Preparation Table
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 2 years; -20°C, 1 year (stored under nitrogen). When stored at -80°C, please use it within 2 years. When stored at -20°C, please use it within 1 year.
| Optional Solvent | Concentration Solvent Mass | 1 mg | 5 mg | 10 mg | 25 mg |
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| DMSO | 1 mM | 2.0389 mL | 10.1945 mL | 20.3890 mL | 50.9726 mL |
| 5 mM | 0.4078 mL | 2.0389 mL | 4.0778 mL | 10.1945 mL | |
| 10 mM | 0.2039 mL | 1.0195 mL | 2.0389 mL | 5.0973 mL | |
| 15 mM | 0.1359 mL | 0.6796 mL | 1.3593 mL | 3.3982 mL | |
| 20 mM | 0.1019 mL | 0.5097 mL | 1.0195 mL | 2.5486 mL | |
| 25 mM | 0.0816 mL | 0.4078 mL | 0.8156 mL | 2.0389 mL | |
| 30 mM | 0.0680 mL | 0.3398 mL | 0.6796 mL | 1.6991 mL | |
| 40 mM | 0.0510 mL | 0.2549 mL | 0.5097 mL | 1.2743 mL | |
| 50 mM | 0.0408 mL | 0.2039 mL | 0.4078 mL | 1.0195 mL | |
| 60 mM | 0.0340 mL | 0.1699 mL | 0.3398 mL | 0.8495 mL | |
| 80 mM | 0.0255 mL | 0.1274 mL | 0.2549 mL | 0.6372 mL |
SY-5609 Related Classifications
HY-138293 Related Classifications
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