Cat. No.: HY-116217

5-Fluoro-2'-deoxycytidine

(Synonyms: FdCyd; NSC-48006)

3 Cited Publications

Customer Review

Based on 3 publication(s) in Google Scholar

5-Fluoro-2'-deoxycytidine (FdCyd), a fluoropyrimidine nucleoside analogue, is a DNA methyltransferase (DNMT) inhibitor. 5-Fluoro-2'-deoxycytidine is a tumor-selective proagent of thymidylate synthase inhibitor 5-fluoro-2′-dUMP. 5-Fluoro-2'-deoxycytidine can induce cell cycle arrest in tumor cells through the DNA damage response, and it has anti-tumor activity.

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

Purity: 99.66%
CAS No.: 10356-76-0
Formula: C₉H₁₂FN₃O₄
Molecular Weight:245.21

Storage:

4°C, protect from light

* In solvent : -80°C, 6 months; -20°C, 1 month (protect from light)

5-Fluoro-2'-deoxycytidine Chemical Structure

CAS No.: 10356-76-0

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Fluorescent Dye

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

Biological Activity
- Description
- IC₅₀ & Target
- Cellular Effect
- In Vitro
- In Vivo
- Clinical Trial
Chemical Information
Publications (3)
Solvent & Solubility
- In Vitro
- In Vivo
Purity & Documentation
References
Help & FAQs
Classifications
Bioz

Biological Activity

Description

IC₅₀ & Target

DNA methyltransferase (DNMT)^[2]

All DNA Methyltransferase Isoforms :

Cellular Effect

Cell Line	Type	Value	Description	References
CCRF-CEM	IC₅₀	>4 μM Compound: 2	Inhibition of dCK in human CCRF-CEM assessed as inhibition of Ara-C phosphorylation Inhibition of dCK in human CCRF-CEM assessed as inhibition of Ara-C phosphorylation	[PMID: 19836229]
COLO 205	IC₅₀	0.02 μM Compound: 9; FUDR	Cytotoxicity against human COLO 205 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay Cytotoxicity against human COLO 205 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay	[PMID: 38547648]
HepG2	IC₅₀	53.9 μM Compound: 9; FUDR	Cytotoxicity against human HepG2 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay Cytotoxicity against human HepG2 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay	[PMID: 38547648]
HT-29	IC₅₀	0.13 μM Compound: 9; FUDR	Cytotoxicity against human HT-29 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay Cytotoxicity against human HT-29 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay	[PMID: 38547648]
MIA PaCa-2	IC₅₀	0.3 μM Compound: 9; FUDR	Cytotoxicity against human MIA PaCa-2 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay Cytotoxicity against human MIA PaCa-2 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay	[PMID: 38547648]
NCI-H1975	IC₅₀	91 μM Compound: 9; FUDR	Cytotoxicity against human NCI-H1975 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay Cytotoxicity against human NCI-H1975 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay	[PMID: 38547648]
OVCAR-3	IC₅₀	0.74 μM Compound: 9; FUDR	Cytotoxicity against human OVCAR-3 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay Cytotoxicity against human OVCAR-3 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay	[PMID: 38547648]
RPMI-8226	IC₅₀	11.77 μM Compound: 9; FUDR	Cytotoxicity against human RPMI-8226 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay Cytotoxicity against human RPMI-8226 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay	[PMID: 38547648]
SK-MES-1	IC₅₀	0.09 μM Compound: 9; FUDR	Cytotoxicity against human SK-MES-1 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay Cytotoxicity against human SK-MES-1 cells assessed as inhibition of cell viability incubated for 72 hrs by MTS assay	[PMID: 38547648]

In Vitro

5-Fluoro-2'-deoxycytidine (0-1 μM; 8-72 h) induces G2/M phase arrest in HCT116 cells by activating the DNA damage response pathway^[1].

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

Western Blot Analysis^[1]

Cell Line:

HCT116 cells
Concentration:

0.05 and 0.5 μM
Incubation Time:

48 h
Result:

Increased the expression level of CyclinB1, which accumulates at G2/M phase.

Western Blot Analysis^[1]

Cell Line:

HCT116 cells
Concentration:

0.5 μM
Incubation Time:

8 h
Result:

Induced phosphorylation of H2AX, ATM and CHK1, but not SAHA.

In Vivo

5-Fluoro-2'-deoxycytidine (25 mg/kg; oral administration/intravenous injection; single dose) is rapidly and sequentially converted to 5-fluoro-2'-deoxyuridine, 5-fluorouracil and 5-fluorouridine in vivo. It has low oral bioavailability, but its exposure can be increased and prolonged when combined with 3,4,5,6-tetrahydrouridine^[2].
Pharmacokinetic Analysis in male CD₂F₁ mice^[2]

Route	Dose (mg/kg)	C_max (μmol/L)	T_max (min)	AUC_inf (μmol/L·h)	Half-life (min)	Distribution volume (mL)	Clearance (mL/min)	% Dose in urine (0-16 h mice)	% Dose in urine (0-24 h mice)
i.v.	25	61.8	5	18.5	10.4	30.6	2.05	1.61	1.94
p.o.	25	0.68	30	0.79	45.1	/	/	/	/

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

Clinical Trial

NCT Number	Sponsor	Condition	Start Date	Phase A549
NCT01329991	Plexxikon\|		2011-05	PHASE1

Chemical Information

CAS No. 10356-76-0
Appearance Solid
Molecular Weight 245.21
Formula C₉H₁₂FN₃O₄
Color White to off-white
SMILES

O[C@H]1C[C@H](N2C(N=C(N)C(F)=C2)=O)O[C@@H]1CO
Synonyms

FdCyd; NSC-48006
Shipping

Room temperature in continental US; may vary elsewhere.
Storage

4°C, protect from light

* In solvent : -80°C, 6 months; -20°C, 1 month (protect from light)

Publications (3)

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Sci Data

High-throughput drug screening identifies novel therapeutics for Low Grade Serous Ovarian Carcinoma. [Abstract]

2024 Sep 19;11(1):1024. PMID: 39300112
ACS Pharmacol Transl Sci

Epigenetic Targeting of Heparan Sulfate 3- O- and 6- O-Sulfation in Breast Cancer Cells: Prospects for Attenuating Prothrombotic Tumor Cell Activities. [Abstract]

2024 Jul 30;7(8):2484-2495. PMID: 39144559
Pathol Res Pract

YY1-VDR axis-mediated autophagy slows the progression of intervertebral disc degeneration. [Abstract]

2025 Sep 3:275:156185. PMID: 40939355

Solvent & Solubility

In Vitro:

DMSO : 50 mg/mL (203.91 mM; Need ultrasonic; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)

H₂O : 16.67 mg/mL (67.98 mM; Need ultrasonic)

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

4.0781 mL

20.3907 mL

40.7814 mL

5 mM

0.8156 mL

4.0781 mL

8.1563 mL

10 mM

0.4078 mL

2.0391 mL

4.0781 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 (protect from light). When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.

* Note: If you choose water as the stock solution, please dilute it to the working solution, then filter and sterilize it with a 0.22 μm filter before use.

Molarity Calculator

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

Mass Mass

Concentration Concentration

Volume Volume

Molecular Weight Molecular Weight

Dilution Calculator

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

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In Vivo:

Select the appropriate dissolution method based on your experimental animal and administration route.

Stock Solution Working Solution

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 (10.20 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.

Protocol 2

Add each solvent one by one: 10% DMSO 90% (20% SBE-β-CD in Saline)

Solubility: ≥ 2.5 mg/mL (10.20 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 900 μL 20% SBE-β-CD in Saline, and mix evenly.

Protocol 3

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

Solubility: ≥ 2.5 mg/mL (10.20 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 Dosage
mg/kg
Animal Weight (Per Animal) Animal Weight (Per Animal)
g
Dosing Volume (Per Animal) Dosing Volume (Per Animal)
μL
Number of Animals Number of Animals

Recommended: Prepare an additional quantity of animals to account for potential losses during experiments.

Recommended: Prepare an additional quantity of animals to account for potential losses during experiments.

Working solution concentration: 0.22 mg/mL

This product has good water solubility, please refer to the measured solubility data in water/PBS/Saline for details.

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) .

Purity & Documentation

Select Batch:

Purity: 99.98%

Assay: 99.98%

ee.: 99.98%

Data Sheet (280 KB)
SDS (394 KB)
- 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)
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]. Zhao Q, et al. Inhibition of cancer cell proliferation by 5-fluoro-2'-deoxycytidine, a DNA methylation inhibitor, through activation of DNA damage response pathway. Springerplus. 2012 Dec;1(1):65. [Content Brief]

[2]. Beumer JH, et, al. Pharmacokinetics, metabolism, and oral bioavailability of the DNA methyltransferase inhibitor 5-fluoro-2'-deoxycytidine in mice. Clin Cancer Res. 2006 Dec 15;12(24):7483-91. [Content Brief]

[3]. Osterman DG, et, al. 5-Fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase. Biochemistry. 1988 Jul 12;27(14):5204-10. [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

Optional Solvent	Concentration Solvent Mass	1 mg	5 mg	10 mg	25 mg
H₂O / DMSO	1 mM	4.0781 mL	20.3907 mL	40.7814 mL	101.9534 mL
	5 mM	0.8156 mL	4.0781 mL	8.1563 mL	20.3907 mL
	10 mM	0.4078 mL	2.0391 mL	4.0781 mL	10.1953 mL
	15 mM	0.2719 mL	1.3594 mL	2.7188 mL	6.7969 mL
	20 mM	0.2039 mL	1.0195 mL	2.0391 mL	5.0977 mL
	25 mM	0.1631 mL	0.8156 mL	1.6313 mL	4.0781 mL
	30 mM	0.1359 mL	0.6797 mL	1.3594 mL	3.3984 mL
	40 mM	0.1020 mL	0.5098 mL	1.0195 mL	2.5488 mL
	50 mM	0.0816 mL	0.4078 mL	0.8156 mL	2.0391 mL
	60 mM	0.0680 mL	0.3398 mL	0.6797 mL	1.6992 mL
DMSO	80 mM	0.0510 mL	0.2549 mL	0.5098 mL	1.2744 mL
DMSO	100 mM	0.0408 mL	0.2039 mL	0.4078 mL	1.0195 mL

* Note: If you choose water as the stock solution, please dilute it to the working solution, then filter and sterilize it with a 0.22 μm filter before use.

Keywords

5-Fluoro-2'-deoxycytidine

3 Cited Publications

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5-Fluoro-2'-deoxycytidine

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Publications Citing Use of MedChemExpress (MCE) 5-Fluoro-2'-deoxycytidine

All DNA Methyltransferase Isoforms

Biological Activity

Chemical Information

Publications (3)

Solvent & Solubility

Purity & Documentation

References

Help & FAQs

Complete Stock Solution Preparation Table

5-Fluoro-2'-deoxycytidine

Bioactive Compound Library Max

Bioactive Compound Library

3D Diverse Fragment Library

Epigenetics Compound Library

Anti-Cancer Compound Library

Clinical Compound Library

Drug Repurposing Compound Library

Nucleotide Compound Library

Anti-Blood Cancer Compound Library

Transcription Factor-Targeted Library

Human Metabolite Library

Anti-Hematopathy Compound Library

MCE Bioactive Compound Library

Drug Repurposing Compound Library Plus

Clinical Compound Library Plus

Methylation Compound Library

High-Throughput Bioactive Compound Library

Mass Spectrometry Human Metabolite Library

Posttranslational Modification Library

Publications Citing Use of MedChemExpress (MCE) 5-Fluoro-2'-deoxycytidine

All DNA Methyltransferase Isoforms

Biological Activity

Chemical Information

Publications (3)

Solvent & Solubility

Purity & Documentation

References

Help & FAQs

Complete Stock Solution Preparation Table

5-Fluoro-2'-deoxycytidine Related Classifications

HY-116217 Related Classifications