| Size | Price | Stock | Qty |
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| 5mg |
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| 10mg |
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| 25mg |
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| 50mg |
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| Other Sizes |
| Targets |
KDM5-C49 hydrochloride targets KDM5A, KDM5B, and KDM5C with IC50 values of 40 nM, 160 nM, and 100 nM respectively. It binds to the active site of these JmjC-domain demethylases, chelating the Fe(II) ion and competing with the 2-oxoglutarate cofactor, thereby inhibiting demethylase activity. It shows selectivity over other JmjC family demethylases, including KDM6A/UTX and KDM4C. The compound has low cell permeability, but it is a valuable tool for in vitro biochemical studies.
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| ln Vitro |
KDM5-C49 hydrochloride has a low permeability. A cell-permeable prodrug (KDM5-C70) was created by converting the carboxyl group of KDM5-C49 into an ethyl ester.
In cell-free assays, KDM5-C49 hydrochloride inhibits recombinant KDM5A, KDM5B, and KDM5C with high potency (IC50 values: 40 nM for KDM5A, 160 nM for KDM5B, 100 nM for KDM5C). The selectivity is demonstrated by testing against other KDM family members. The compound is a competitive inhibitor of the 2-oxoglutarate cofactor. KDM5-C49 has low cellular permeability, which limits its use in cell-based assays. A cell-permeable prodrug (KDM5-C70) has been developed to overcome this limitation. |
| ln Vivo |
Due to its low cell permeability, KDM5-C49 hydrochloride is primarily used in cell-free assays. However, its cell-permeable prodrug, KDM5-C70 (generated by converting the carboxyl group to an ethyl ester), is used in cell-based studies. In cancer cells treated with the prodrug, increased H3K4me3 levels (the product of KDM5 inhibition) are observed by Western blot. The compound may inhibit cancer cell proliferation in KDM5-dependent cancer types; for example, in multiple myeloma and MLL-rearranged leukemia.
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| Enzyme Assay |
The enzymatic activity of KDM5A is measured using a cell-free demethylase assay. Recombinant KDM5A enzyme is incubated with a biotinylated H3K4me3 peptide substrate (0.5 uM) in assay buffer containing Tris-HCl (50 mM, pH 7.5), NaCl (50 mM), 2-oxoglutarate (10 uM), ascorbate (2 mM), FeSO4 (2 uM), and DTT (1 mM). Varying concentrations (0.1-1000 nM) of KDM5-C49 hydrochloride are added. After 60 minutes at 30degC, the reaction is stopped with EDTA. The amount of remaining H3K4me3 is quantified by ELISA using an anti-H3K4me3 antibody and HRP-conjugated secondary antibody. IC50 values are calculated from dose-response curves.
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| Cell Assay |
KDM5-C49 hydrochloride is primarily used in cell-free assays; its low permeability makes it unsuitable for most cellular experiments without derivatization. For cell-based studies, the prodrug KDM5-C70 is used. However, KDM5-C49 hydrochloride can be used as a reference standard in LC-MS/MS assays to quantify KDM5 inhibitor levels in biochemical samples. A typical assay would involve incubating the compound with recombinant KDM5 enzymes in a cell-free system as described above.
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| Animal Protocol |
KDM5-C49 hydrochloride is generally evaluated in mouse xenograft models using its prodrug form. For example, mice bearing KDM5-dependent tumor xenografts (e.g., multiple myeloma) are treated with KDM5-C70 (the ethyl ester prodrug) at doses of 10-50 mg/kg, administered intraperitoneally daily for 2-3 weeks. Tumor growth is measured by caliper, and tumor tissues are harvested for analysis of H3K4me3 levels (Western blot or immunohistochemistry), proliferation markers (Ki67), and apoptosis (cleaved caspase-3).
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| ADME/Pharmacokinetics |
KDM5-C49 hydrochloride is not directly used in in vivo studies due to its low cell permeability. A cell-permeable prodrug (KDM5-C70) is created by converting the carboxyl group of KDM5-C49 into an ethyl ester. This prodrug can cross cell membranes and is converted back to the active compound intracellularly. The prodrug is typically formulated in a solution containing DMSO, PEG300, Tween 80, and saline for intraperitoneal or oral administration. The half-life is likely 2-6 hours in mice.
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| Toxicity/Toxicokinetics |
KDM5-C49 hydrochloride is a research compound; comprehensive toxicity data are not publicly available. Based on its chemical class (JmjC demethylase inhibitor), it is expected to be well-tolerated at low micromolar concentrations in vitro. The compound is not known to be genotoxic or acutely toxic. Standard laboratory safety precautions (gloves, lab coat, safety glasses, fume hood for powder handling) should be followed. The compound is for research use only and not for human therapeutic use.
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| References | |
| Additional Infomation |
KDM5-C49 hydrochloride is a research compound not approved for clinical use. The KDM5 family (also known as JARID1) is overexpressed in certain cancers, including drug-resistant cancers. KDM5 inhibitors like KDM5-C49 are being investigated as potential anti-cancer agents that can reverse drug resistance (e.g., to tyrosine kinase inhibitors). The compound is also known as KDOAM-20. CAS number: 3026728-26-4. The hydrochloride salt is the preferred form for stability and handling.
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| Molecular Formula |
C15H25CLN4O3
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|---|---|
| Molecular Weight |
344.84
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| Exact Mass |
344.162
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| CAS # |
3026728-26-4
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| Related CAS # |
KDM5-C49;1596348-16-1
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| PubChem CID |
169553387
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| Appearance |
Colorless to light yellow solid-liquid Mixture
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| Hydrogen Bond Donor Count |
3
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| Hydrogen Bond Acceptor Count |
6
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| Rotatable Bond Count |
9
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| Heavy Atom Count |
23
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| Complexity |
363
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| Defined Atom Stereocenter Count |
0
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| SMILES |
CCN(CCN(C)C)C(=O)CNCC1=NC=CC(=C1)C(=O)O.Cl
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| HS Tariff Code |
2934.99.9001
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| Storage |
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month Note: Please store this product in a sealed and protected environment, avoid exposure to moisture. |
| Shipping Condition |
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
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| Solubility (In Vitro) |
DMSO :~125 mg/mL (~362.49 mM)
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|---|---|
| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.08 mg/mL (6.03 mM) (saturation unknown) in 10% DMSO + 40% PEG300 + 5% Tween80 + 45% Saline (add these co-solvents sequentially from left to right, and one by one), clear solution.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 20.8 mg/mL clear DMSO stock solution to 400 μL PEG300 and mix evenly; then add 50 μL Tween-80 to the above solution and mix evenly; then add 450 μL normal saline to adjust the volume to 1 mL. Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH₂ O to obtain a clear solution. Solubility in Formulation 2: ≥ 2.08 mg/mL (6.03 mM) (saturation unknown) in 10% DMSO + 90% (20% SBE-β-CD in Saline) (add these co-solvents sequentially from left to right, and one by one), clear solution. For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 20.8 mg/mL clear DMSO stock solution to 900 μL of 20% SBE-β-CD physiological saline solution and mix evenly. Preparation of 20% SBE-β-CD in Saline (4°C，1 week): Dissolve 2 g SBE-β-CD in 10 mL saline to obtain a clear solution. (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 2.8999 mL | 14.4995 mL | 28.9990 mL | |
| 5 mM | 0.5800 mL | 2.8999 mL | 5.7998 mL | |
| 10 mM | 0.2900 mL | 1.4499 mL | 2.8999 mL |
*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.
Calculation results
Working concentration： mg/mL；
Method for preparing DMSO stock solution： mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.
Method for preparing in vivo formulation:：Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O，mix and clarify.
(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
(2) Be sure to add the solvent(s) in order.
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