2. Cell Cycle/DNA Damage Apoptosis
  3. CDK Apoptosis
  4. SY-5609

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.

CAS No. : 2417302-07-7

Size Price Stock Quantity
Solid + Solvent (Highly Recommended)
10 mM * 1 mL in DMSO
ready for reconstitution
 In-stock
Solution
10 mM * 1 mL in DMSO In-stock
Solid
1 mg In-stock
5 mg In-stock
10 mg In-stock
25 mg In-stock
50 mg In-stock
100 mg In-stock
200 mg   Get quote  
500 mg   Get quote  

* Please select Quantity before adding items.

This product is a controlled substance and not for sale in your territory.

Customer Review

Based on 7 publication(s) in Google Scholar

SY-5609 Related Antibodies

Top Publications Citing Use of Products

    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).

    View All CDK Isoform Specific Products:

    View All Isoforms
    CDK1 CDK2 CDK3 CDK4 CDK5 CDK6 CDK7 CDK8 CDK9 CDK11 CDK12 CDK13 CDK14 CDK16 CDK19 CDC CLK Pho85 CDK10 CDK15 CDK17 CDK18 CDK20 PITSLRE

    • Biological Activity

    • Purity & Documentation

    • References

    • Customer Review

    Description

    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[1][2].

    IC50 & Target[1]

    CDK7

    0.065 nM (Kd)

    CDK2

    2600 nM (Ki)

    CDK9

    960 nM (Ki)

    CDK12

    870 nM (Ki)

    Cellular Effect
    Cell Line Type Value Description References
    HCC70 EC50
    1 nM
    Compound: SY-5609
    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
    		[PMID: 34726887]
    In Vitro

    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.

    SY-5609 Related Antibodies

    Cell Proliferation Assay[1]

    Cell Line: HCC70, MDA-MB453, COV504, A2780, OVCAR3, CAOV3 cells
    Concentration: 0.01-10000 nM
    Incubation Time: 72 hours
    Result: Demonstrated strong antiproliferative effects with IC50 of 1-6 nM.

    Apoptosis Analysis[1]

    Cell Line: HCC70, MDA-MB-468, CAOV3 and OVCAR3 cells
    Concentration: 100, 250, 500 nM
    Incubation Time: 48 and 72 hours
    Result: Induced apoptosis.

    Cell Cycle Analysis[1]

    Cell Line: HCC70 cells
    Concentration: 100, 250, 500 nM
    Incubation Time: 48 hours
    Result: Induced G2/M cell cycle arrest.

    Western Blot Analysis[1]

    Cell Line: HCC70 cells
    Concentration: 25, 50, 100, 250, 500 nM
    Incubation Time: 6, 24, 48 hours
    Result: Resulted in inhibition of the phosphorylation of CDK2 at Thr160 via loss of CAK function for 24 and 48 h.
    In Vivo

    SY-5609 (2 mg/kg/day; orally; for 21 days) induces tumor regression over the 21-day dosing period[1].
    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.

    Animal Model: Six-to-eight-week-old Balb/c nude female mice with HCC70 cell line[1]
    Dosage: 2 mg/kg
    Administration: Orally; daily; for 21 days
    Result: Induced tumor regression over the 21-day dosing period and was well tolerated. No regrowth of tumor was observed out to day 28.
    Clinical Trial
    Molecular Weight

    490.46

    Formula

    C23H26F3N6OP
    CAS No.
    Appearance

    Solid

    Color

    White to light yellow

    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
    Shipping

    Room temperature in continental US; may vary elsewhere.
    Storage

    4°C, stored under nitrogen

    *In solvent : -80°C, 2 years; -20°C, 1 year (stored under nitrogen)

    Solvent & Solubility
    In Vitro: 

    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)

    Preparing
    Stock Solutions
    Concentration Solvent Mass 1 mg 5 mg 10 mg
    1 mM 2.0389 mL 10.1945 mL 20.3890 mL
    5 mM 0.4078 mL 2.0389 mL 4.0778 mL
    View the 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.

    • Molarity Calculator

    • Dilution Calculator

    Mass (g) = Concentration (mol/L) × Volume (L) × Molecular Weight (g/mol)

    Mass
    =
    Concentration
    ×
    Volume
    ×
    Molecular Weight *

    Concentration (start) × Volume (start) = Concentration (final) × Volume (final)

    This equation is commonly abbreviated as: C1V1 = C2V2

    Concentration (start)

    C1

    ×
    Volume (start)

    V1

    =
    Concentration (final)

    C2

    ×
    Volume (final)

    V2

    In Vivo:

    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.

    • Protocol 1

      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.
    • Protocol 2

      Add each solvent one by one:  10% DMSO    90% Corn Oil

      Solubility: ≥ 2.5 mg/mL (5.10 mM); Clear solution

      This protocol yields a clear solution of ≥ 2.5 mg/mL (saturation unknown). If the continuous dosing period exceeds half a month, please choose this protocol carefully.

      Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (25.0 mg/mL) to 900 μL Corn oil, and mix evenly.

    In Vivo Dissolution Calculator
    Please enter the basic information of animal experiments:

    Dosage

    mg/kg

    Animal weight
    (per animal)

    g

    Dosing volume
    (per animal)

    μL

    Number of animals

    Recommended: Prepare an additional quantity of animals to account for potential losses during experiments.
    Please enter your animal formula composition:
    %
    DMSO +
    % 
    +
    %
    Tween-80 +
    %
    Saline
    Recommended: Keep the proportion of DMSO in working solution below 2% if your animal is weak.
    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).
    Calculation results:
    Working solution concentration: 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)

    The concentration of the stock solution you require exceeds the measured solubility. The following solution is for reference only. If necessary, please contact MedChemExpress (MCE).
    Method for preparing in vivo working solution for animal experiments: Take μL DMSO stock solution, add μL . μL , mix evenly, next add μL Tween 80, mix evenly, then add μL Saline.
     If the continuous dosing period exceeds half a month, please choose this protocol carefully.
    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

    Purity: 99.93%

    SDS (394 KB)

    COA (263 KB) HNMR (140 KB) RP-HPLC (163 KB) NP-HPLC (125 KB) LCMS (105 KB)

    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
    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
    • No file chosen (Maximum size is: 1024 Kb)
    • If you have published this work, please enter the PubMed ID.
    • Your name will appear on the site.

    SY-5609 Related Classifications

    Help & FAQs
    • Do most proteins show cross-species activity?

      Species cross-reactivity must be investigated individually for each product. Many human cytokines will produce a nice response in mouse cell lines, and many mouse proteins will show activity on human cells. Other proteins may have a lower specific activity when used in the opposite species.

    Keywords:

    SY-56092417302-07-7CDK7-IN-3SY5609SY 5609CDKApoptosisCyclin dependent kinaseHCC70MDA-MB453COV504A2780OVCAR3CAOV3triplenegativebreastovarianG2/MCDK2Thr160Inhibitorinhibitorinhibit

    Your Recently Viewed Products:

    Inquiry Online

    Your information is safe with us. * Required Fields.

    Product Name

    		  

    Requested Quantity *

    Applicant Name *

    		 

    Salutation

    Email Address *

    		 

    Phone Number *

    Department

    		 

    Organization Name *

    City

    State

    Country or Region *

    		      

    Remarks

    Bulk Inquiry

    Inquiry Information

    Product Name:
    SY-5609
    Cat. No.:
    HY-138293
    Quantity:
    MCE Japan Authorized Agent:

    Customer Review

    Thank You for Your Feedback!

    Request for HNMR Report

    Please fill out this form to request the QC report. We will send it to your Email address shortly.

    Your information is safe with us. * Required Fields.

    Product Name

    		  

    Lot #

    Applicant Name *

    		 

    Email Address *

    Phone Number

    		 

    Department *

    Organization Name *

    		 

    Country or Region *

    Remarks

    SAFETY DATA SHEET (SDS)

    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)

    Request for HNMR Report

    We have received your request and will respond to you as soon as possible.