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Cat. No.: HY-13828

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CDK9-IN-53

CDK9-IN-53 is a potent and selective CDK9 inhibitor with a K_i of 7 nM and an IC₅₀ of 14 nM against CDK9/Cyclin T1. CDK9-IN-53 achieves highly selective inhibition by competitively binding to the ATP pocket of CDK9, thereby blocking RNAPII transcription and downregulating the anti-apoptotic protein Mcl-1, ultimately triggering Caspase-dependent apoptosis in cancer cells. CDK9-IN-53 can be used for research on chronic lymphocytic leukemia.

For research use only. We do not sell to patients.

CAS No.: 1421340-50-2
Formula: C₂₁H₂₄N₈S
Molecular Weight:420.54

Storage:

Please store the product under the recommended conditions in the Certificate of Analysis.

CDK9-IN-53 Chemical Structure

CAS No.: 1421340-50-2

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Use of MCE Products

Strong Fluorescence Signal / Multi-Disciplinary Applications / High Fluorescence Specificity

Biological Activity
- Description
- IC₅₀ & Target
- Cellular Effect
- In Vitro
Chemical Information
Purity & Documentation
References
Calculators
Help & FAQs
Classifications
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Biological Activity

Description

IC₅₀ & Target

^[1]

CDK9

7 nM (Ki)

CDK9/cyclinT1

14 nM (IC₅₀)

Caspase-3

Mcl-1

All CDK Isoforms :

All Caspase Isoforms :

All Bcl-2 Family Isoforms :

Cellular Effect

Cell Line	Type	Value	Description	References
HCT-116	GI₅₀	0.420 μM	Antiproliferative activity against human HCT-116 (p53wt, pRb+) cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human HCT-116 (p53wt, pRb+) cells assessed as GI50 by MTT assay after 48 hrs.	23301767
HCT-116	GI₅₀	0.780 μM	Antiproliferative activity against human HCT-116 (p53null) cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human HCT-116 (p53null) cells assessed as GI50 by MTT assay after 48 hrs.	23301767
HCC 2998	GI₅₀	0.385 μM	Antiproliferative activity against human HCC 2998 (p53wt, pRb+) cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human HCC 2998 (p53wt, pRb+) cells assessed as GI50 by MTT assay after 48 hrs.	23301767
MCF7	GI₅₀	0.690 μM	Antiproliferative activity against human MCF-7 (p53wt, pRb+, ER+) cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human MCF-7 (p53wt, pRb+, ER+) cells assessed as GI50 by MTT assay after 48 hrs.	23301767
MDA-MB-468	GI₅₀	0.402 μM	Antiproliferative activity against human MDA-MB468 (p53mut, pRb−, ER−) cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human MDA-MB468 (p53mut, pRb−, ER−) cells assessed as GI50 by MTT assay after 48 hrs.	23301767
A2780	GI₅₀	0.320 μM	Antiproliferative activity against human A2780 cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human A2780 cells assessed as GI50 by MTT assay after 48 hrs.	23301767
HeLa	GI₅₀	0.630 μM	Antiproliferative activity against human HeLa cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human HeLa cells assessed as GI50 by MTT assay after 48 hrs.	23301767
TK-10	GI₅₀	0.747 μM	Antiproliferative activity against human TK 10 cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human TK 10 cells assessed as GI50 by MTT assay after 48 hrs.	23301767
PANC-1	GI₅₀	0.590 μM	Antiproliferative activity against human PANC-1 cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human PANC-1 cells assessed as GI50 by MTT assay after 48 hrs.	23301767
HMEC-1	GI₅₀	3.120 μM	Antiproliferative activity against human HMEC-1 cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human HMEC-1 cells assessed as GI50 by MTT assay after 48 hrs.	23301767
MRC5	GI₅₀	5.960 μM	Antiproliferative activity against human MRC-5 cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human MRC-5 cells assessed as GI50 by MTT assay after 48 hrs.	23301767
WI-38	GI₅₀	5.490 μM	Antiproliferative activity against human WI-38 cells assessed as GI50 by MTT assay after 48 hrs. Antiproliferative activity against human WI-38 cells assessed as GI50 by MTT assay after 48 hrs.	23301767
A2780	GI₅₀	0.493 μM	Antiproliferative activity against human A2780 cells assessed as GI50 by MTT assay after 24 hrs. Antiproliferative activity against human A2780 cells assessed as GI50 by MTT assay after 24 hrs.	23301767
A2780	GI₅₀	0.288 μM	Antiproliferative activity against human A2780 cells assessed as GI50 by MTT assay after 72 hrs. Antiproliferative activity against human A2780 cells assessed as GI50 by MTT assay after 72 hrs.	23301767
MRC5	GI₅₀	6.250 μM	Antiproliferative activity against human MRC-5 cells assessed as GI50 by MTT assay after 24 hrs. Antiproliferative activity against human MRC-5 cells assessed as GI50 by MTT assay after 24 hrs.	23301767
MRC5	GI₅₀	5.670 μM	Antiproliferative activity against human MRC-5 cells assessed as GI50 by MTT assay after 72 hrs. Antiproliferative activity against human MRC-5 cells assessed as GI50 by MTT assay after 72 hrs.	23301767
HMEC-1	GI₅₀	7.500 μM	Antiproliferative activity against human HMEC-1 cells assessed as GI50 by MTT assay after 24 hrs. Antiproliferative activity against human HMEC-1 cells assessed as GI50 by MTT assay after 24 hrs.	23301767
HMEC-1	GI50	4.500 μM	Antiproliferative activity against human HMEC-1 cells assessed as GI50 by MTT assay after 72 hrs. Antiproliferative activity against human HMEC-1 cells assessed as GI50 by MTT assay after 72 hrs.	23301767

In Vitro

Anti-cancerApoptosisCell Cycle RegulationOthers

Anti-cancer

CDK9-IN-53 (compound 12u) (48 h) inhibited the proliferation of HCT-116, A2780, MCF-7, and other tumor cell lines with GI₅₀ values of 0.320-0.780 μM, whereas non-transformed HMEC-1, MRC-5, and WI-38 cells were less sensitive with GI₅₀ values of 3.120-5.960 μM^[1].

Anti-cancer

Apoptosis

Cell Cycle Regulation

CDK9-IN-53 (GI₅₀-10 x GI₅₀; 24-48 h) significantly activates Caspase-3 activity, induces apoptosis in a dose-dependent manner, causes G2/M phase cell cycle arrest, inhibits RNAPII Ser-2 phosphorylation, downregulates Mcl-1 and HDM2 expression levels, and induces PARP cleavage in A2780 ovarian cancer cells^[1].

Anti-cancer

Apoptosis

CDK9-IN-53 (1.0-10 μM; 8-48 h) strongly induced Caspase-3 activity and apoptosis in primary chronic lymphocytic leukemia (CLL) cells (LD₅₀ = 2.6 μM) and significantly downregulated the expression level of the anti-apoptotic protein Mcl-1^[1].

Others

CDK9-IN-53 inhibits CDK9/cyclin T1 with IC₅₀ = 14 nM in in vitro kinase biochemical inhibition assays, and CDK9 K_i = 7 nM has been reported, showing >80-fold selectivity over CDK2^[1].

MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.

Apoptosis Analysis^[1]

Cell Line:

A2780 ovarian carcinoma cells
Concentration:

GI₅₀, 5 x GI₅₀
Incubation Time:

48 h
Result:

Induced caspase-dependent apoptosis in a dose-dependent manner (38% at GI₅₀ and 50% at 5 x GI₅₀).

Cell Cycle Analysis^[1]

Cell Line:

A2780 ovarian carcinoma cells
Concentration:

GI₅₀, 5 x GI₅₀
Incubation Time:

24 h
Result:

Caused accumulation of cells in the G2/M phase at the 5 x GI₅₀ concentration.

Western Blot Analysis^[1]

Cell Line:

A2780 ovarian carcinoma cells
Concentration:

GI₅₀, 5 x GI₅₀
Incubation Time:

24 h
Result:

Inhibited the phosphorylation of Ser-2 of RNAPII CTD, down-regulated the expression of Mcl-1 and HDM2, and induced PARP cleavage, confirming cellular CDK9 inhibition and apoptosis induction.

Related Protocols :

Chemical Information

CAS No. 1421340-50-2
Molecular Weight 420.54
Formula C₂₁H₂₄N₈S
SMILES

N#CC=1C=NC(=NC1C=2SC(=NC2C)NC)NC3=CC=CC(=C3)N4CCNCCC4
Shipping

Room temperature in continental US; may vary elsewhere.
Storage

Please store the product under the recommended conditions in the Certificate of Analysis.

Purity & Documentation

Handling Instructions (2659 KB)

References

[1]. Shao H, et al. Substituted 4-(thiazol-5-yl)-2-(phenylamino)pyrimidines are highly active CDK9 inhibitors: synthesis, X-ray crystal structures, structure-activity relationship, and anticancer activities. Journal of medicinal chemistry. 2013 Feb 14;56(3):640-59. [Content Brief]

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Help & FAQs

How should lyophilized recombinant proteins be reconstituted and stored?

1. Before opening the cap, centrifuge the vial at 13000 rpm for 20-30 seconds. This step will ensure that any lyophilized powder that may have adhered to the cap or walls is collected at the bottom of the vial, minimizing the risk of product loss.

Bioz

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100 mg

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Biological Activity
- Description
- IC₅₀ & Target
- In Vitro
Chemical Information
Purity & Documentation
References

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CDK9-IN-53

All CDK Isoforms

All Caspase Isoforms

All Bcl-2 Family Isoforms