Cat. No.: HY-168593

PROTAC KDM3 degrader-1

Customer Review

Based on 1 Customer Validation

PROTAC KDM3 degrader-1 is a KDM3A/KDM3B PROTAC degrader with DC₅₀ values of 13.73 nM and 172.6 nM in SW480 cells, respectively. PROTAC KDM3 degrader-1 induces cereblon-dependent proteasomal degradation of KDM3A and KDM3B. PROTAC KDM3 degrader-1 inhibits the oncogenic Wnt/β-catenin signaling pathway. PROTAC KDM3 degrader-1 eliminates colorectal cancer stem cells, suppresses their self-renewal, and blocks colony formation of colorectal cancer cells. PROTAC KDM3 degrader-1 inhibits tumor growth in a colorectal cancer xenograft mouse model. PROTAC KDM3 degrader-1 can be used for the research of colorectal cancer.
(Pink: KDM3A and KDM3B ligand (HY-12304); Blue: Cereblon ligand (HY-41547); Black: linker (HY-22335)).

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

Purity: 99.07%
CAS No.: 3119090-33-1
Formula: C₃₃H₃₇N₅O₁₀
Molecular Weight:663.67

Storage:

Powder -20°C, 3 years , 4°C, 2 years ; In solvent -80°C, 6 months , -20°C, 1 month

PROTAC KDM3 degrader-1 Chemical Structure

CAS No.: 3119090-33-1

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Top Publications Citing

Use of MCE Products

Fluorescent Dye

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

Biological Activity
- Description
- IC₅₀ & Target
- In Vitro
- In Vivo
Chemical Information
Solvent & Solubility
- In Vitro
Purity & Documentation
References
Help & FAQs
Classifications
Bioz

Biological Activity

Description

PROTAC KDM3 degrader-1 is a KDM3A/KDM3B PROTAC degrader with DC₅₀ values of 13.73 nM and 172.6 nM in SW480 cells, respectively. PROTAC KDM3 degrader-1 induces cereblon-dependent proteasomal degradation of KDM3A and KDM3B. PROTAC KDM3 degrader-1 inhibits the oncogenic Wnt/β-catenin signaling pathway. PROTAC KDM3 degrader-1 eliminates colorectal cancer stem cells, suppresses their self-renewal, and blocks colony formation of colorectal cancer cells. PROTAC KDM3 degrader-1 inhibits tumor growth in a colorectal cancer xenograft mouse model. PROTAC KDM3 degrader-1 can be used for the research of colorectal cancer^[1]. (Pink: KDM3A and KDM3B ligand (HY-12304); Blue: Cereblon ligand (HY-41547); Black: linker (HY-22335)).

IC₅₀ & Target^[1]

KDM3A

KDM3B

All PROTACs Isoforms :

All Histone Demethylase Isoforms :

All Wnt Isoforms :

In Vitro

PROTAC KDM3 degrader-1 (Compound 4) (16 h) potently inhibits the Wnt/β-catenin signaling pathway in 293T-TCF-Luc cells, with an IC₅₀ of 8.9 μM^[1].
PROTAC KDM3 degrader-1 (48 h) exhibits low basal toxicity in normal human colonic epithelial CRL-1790 cells, with a TD₅₀ of 285.4 μM^[1].
PROTAC KDM3 degrader-1 (0-30 μM) exhibits low hERG inhibitory activity, with an IC₅₀ > 30 μM^[1].
PROTAC KDM3 degrader-1 (0.001-100 μM; 16 h) selectively degrades KDM3A and KDM3B in SW480 and HCP-1 colon cancer cells via a CRBN-dependent proteasomal pathway, with no effect on KDM4 family proteins or the novel substrate GSPT1, and its DC₅₀ values are 13.73 nM and 172.6 nM, respectively^[1].
PROTAC KDM3 degrader-1 (50 μM; 16 h) potently inhibits the expression of Wnt target genes and colorectal cancer CSC signature genes in SW480 and HCP-1 cells^[1].
PROTAC KDM3 degrader-1 (2 weeks) potently inhibits the self-renewal of ALDH_High colorectal cancer stem cells, with an ED₅₀ value of 0.95 μM in SW480 cells and 0.28 μM in HCP-1 cells^[1].

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

Western Blot Analysis^[1]

Cell Line:

SW480 cells, HCP-1 cells
Concentration:

0.001, 0.01, 0.1, 1, 10, 100 μM
Incubation Time:

16 h
Result:

Degraded KDM3A and KDM3B in a dose-dependent manner, with DC₅₀ values of 13.73 nM for KDM3A and 172.6 nM for KDM3B; Dₘₐₓ values were 65.34% for KDM3A and 88.55% for KDM3B.
Observed a "hook effect" for KDM3A degradation at higher doses.
Did not dramatically affect KDM4 family proteins (KDM4A, KDM4B, KDM4C).
Reversed degradation of KDM3A and KDM3B by pre-treatment with 1 μM MLN4924, 100 μM pomalidomide, or IOX1, confirming proteasomal degradation dependent on CRBN binding and target protein interaction.
Degraded KDM3A and KDM3B in freshly isolated human CRC HCP-1 cells.
Did not induce degradation of the known neo-substrate GSPT1 in SW480 cells.

Real Time qPCR^[1]

Cell Line:

human colorectal cancer SW480 and HCP-1 cells
Concentration:

50 μM
Incubation Time:

16 h
Result:

Profoundly suppressed expression of Wnt target genes (AXIN2, DKK1, CCND1) and colorectal CSC signature genes (ASCL2, RNF43, ZNRF3, LGR5) by 50% or more in both SW480 and HCP-1 cells.
Showed a more dramatic inhibitory effect than the parent compound IOX1.

In Vivo

PROTAC KDM3 degrader-1 (3-35 mg/kg, i.p.; daily administration; for 16 consecutive days) significantly inhibits the growth of tumors derived from colorectal cancer stem cells in NSG mice^[1].

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

Animal Model:

NSG mice^[1]
Dosage:

3 mg/kg; 10 mg/kg; 35 mg/kg
Administration:

i.p.; daily; 16 days
Result:

Significantly inhibited tumor growth compared to the control group.
Reduced tumor volume and weight at 10 mg/kg and 35 mg/kg doses.
Confirmed degradation of KDM3A and KDM3B in tumor tissues, along with downregulated expression of the Wnt target gene CCND1.
Slightly upregulated KDM3A (but not KDM3B) in tumors from mice treated with the 35 mg/kg dose, consistent with an in vitro "hook effect," though tumor growth remained drastically reduced.
Had no significant impact on mouse body weight, indicating good tolerability.

Chemical Information

CAS No. 3119090-33-1
Appearance Solid
Molecular Weight 663.67
Formula C₃₃H₃₇N₅O₁₀
Color Light yellow to green yellow
SMILES

O=C(C1=C2C=CC=NC2=C(O)C=C1)NCCOCCOCCOCCOCCNC3=CC=CC(C(N4C(CC5)C(NC5=O)=O)=O)=C3C4=O
Shipping

Room temperature in continental US; may vary elsewhere.

Storage

Powder	-20°C	3 years
	4°C	2 years
In solvent	-80°C	6 months
	-20°C	1 month

Solvent & Solubility

In Vitro:

DMSO : 100 mg/mL (150.68 mM; Need ultrasonic; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)

View the Complete Stock Solution Preparation Table

Preparing Stock Solutions

View the Complete Stock Solution Preparation Table

Concentration Solvent Mass

1 mg

5 mg

10 mg

Concentration

Solvent

Mass

1 mM

1.5068 mL

7.5339 mL

15.0677 mL

5 mM

0.3014 mL

1.5068 mL

3.0135 mL

10 mM

0.1507 mL

0.7534 mL

1.5068 mL

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, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.

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Purity & Documentation

Select Batch:

Purity: 99.98%

Assay: 99.98%

ee.: 99.98%

Data Sheet (276 KB)
SDS (254 KB)
- English - EN (254 KB)
- Français - FR (254 KB)
- Deutsch - DE (254 KB)
- Norwegian - NO (254 KB)
- Español - ES (254 KB)
- Swedish - SV (254 KB)
- Italian - IT (254 KB)
- Korean - KR (254 KB)
- Portuguese - PT (254 KB)
COA (2659 KB)
Elemental Analysis Report (2659 KB)
HNMR (2659 KB)
CNMR (2659 KB)
RP-HPLC (2659 KB)
NP-HPLC (2659 KB)
MS (2659 KB)
LCMS (2659 KB)
IR (2659 KB)
GC (2659 KB)
OR (2659 KB)
SDS-PAGE (2659 KB)
SEC-HPLC (2659 KB)
Other Report (2659 KB)
Handling Instructions (2659 KB)

References

[1]. Zaman SU, et al. Novel PROTAC probes targeting KDM3 degradation to eliminate colorectal cancer stem cells through inhibition of Wnt/β-catenin signaling. RSC medicinal chemistry. 2024 Sep 13;15(11):3746-58. [Content Brief]

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.

Complete Stock Solution Preparation Table

Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.

Optional Solvent	Concentration Solvent Mass	1 mg	5 mg	10 mg	25 mg
DMSO	1 mM	1.5068 mL	7.5339 mL	15.0677 mL	37.6693 mL
	5 mM	0.3014 mL	1.5068 mL	3.0135 mL	7.5339 mL
	10 mM	0.1507 mL	0.7534 mL	1.5068 mL	3.7669 mL
	15 mM	0.1005 mL	0.5023 mL	1.0045 mL	2.5113 mL
	20 mM	0.0753 mL	0.3767 mL	0.7534 mL	1.8835 mL
	25 mM	0.0603 mL	0.3014 mL	0.6027 mL	1.5068 mL
	30 mM	0.0502 mL	0.2511 mL	0.5023 mL	1.2556 mL
	40 mM	0.0377 mL	0.1883 mL	0.3767 mL	0.9417 mL
	50 mM	0.0301 mL	0.1507 mL	0.3014 mL	0.7534 mL
	60 mM	0.0251 mL	0.1256 mL	0.2511 mL	0.6278 mL
	80 mM	0.0188 mL	0.0942 mL	0.1883 mL	0.4709 mL
	100 mM	0.0151 mL	0.0753 mL	0.1507 mL	0.3767 mL

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PROTAC KDM3 degrader-1

Bioactive Compound Library Max

Bioactive Compound Library

Epigenetics Compound Library

Stem Cell Signaling Compound Library

Wnt/Hedgehog/Notch Compound Library

Histone Modification Research Compound Library

Anti-Cancer Compound Library

Anti-Aging Compound Library

Differentiation Inducing Compound Library

Cytoskeleton Compound Library

Neuroprotective Compound Library

Anti-Breast Cancer Compound Library

Anti-Cancer Metabolism Compound Library

Transcription Factor-Targeted Library

Anti-Liver Cancer Compound Library

Anti-Colorectal Cancer Compound Library

Anti-Prostate Cancer Compound Library

Anti-Pulmonary Fibrosis Compound Library

Cancer Stem Cells Compound Library

Antihypertensive Compound Library

PROTAC Library

Extracellular Vesicles (EVs) Compound Library

Anti-Ovarian Cancer Compound Library

Multi-Target Compound Library

MCE Bioactive Compound Library

Anti-Gastric Cancer Compound Library

Anti-Fibrosis Compound Library

Cell Proliferation Compound Library

Methylation Compound Library

High-Throughput Bioactive Compound Library

Anti-Rheumatic Arthritis Compound Library

All PROTACs Isoforms

All Histone Demethylase Isoforms

All Wnt Isoforms

Biological Activity

Chemical Information

Solvent & Solubility

Purity & Documentation

References

Help & FAQs

Complete Stock Solution Preparation Table

PROTAC KDM3 degrader-1 Related Classifications

HY-168593 Related Classifications