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.

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SY-5609 Chemical Structure

SY-5609 Chemical Structure

CAS No. : 2417302-07-7

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Based on 1 publication(s) in Google Scholar

SY-5609 Related Antibodies

Top Publications Citing Use of Products

1 Publications Citing Use of MCE SY-5609

View All CDK Isoform Specific Products:

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CDK1 CDK2 CDK3 CDK4 CDK5 CDK6 CDK7 CDK8 CDK9 CDK11 CDK12 CDK13 CDK14 CDK16 CDK19 CDC CLK Pho85

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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)

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.

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  • Dilution Calculator

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

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

This equation is commonly abbreviated as: C1V1 = C2V2

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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    90% (20% SBE-β-CD in Saline)

    Solubility: 4 mg/mL (8.16 mM); Suspended solution; Need ultrasonic

    This protocol yields a suspended solution of 4 mg/mL. Suspended solution can be used for oral and intraperitoneal injection.

    Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (40.0 mg/mL) to 900 μL 20% SBE-β-CD in Saline, and mix evenly.

    Preparation of 20% SBE-β-CD in Saline (4°C, storage for one week): 2 g SBE-β-CD powder is dissolved in 10 mL Saline, completely dissolve until clear.
  • Protocol 2

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

    Solubility: ≥ 4 mg/mL (8.16 mM); Clear solution

    This protocol yields a clear solution of ≥ 4 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 (40.0 mg/mL) to 900 μL Corn oil, and mix evenly.

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

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mg/kg

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(per animal)

g

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(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 +
% 
+
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%
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: 99.66%

COA (263 KB) HNMR (256 KB) LCMS (110 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
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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

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