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5-Aza-2'-deoxycytidine

HCID 451668
NotesReactions
Basic informationOverviewNames & identifiersPropertiesSafety & regulationChemistry & industryRelated reactionsCompound notes
Substructure searchFind similar structures

Basic information

CAS
2353-33-5
Standard SMILES
Nc1ncn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)n1
InChIKey
XAUDJQYHKZQPEU-KVQBGUIXSA-N
Molecular formula
C8H12N4O4
Average molar mass
228.21 g/mol
Monoisotopic mass
228.08585486

Overview

5-aza-2'-deoxycytidine is a fine white crystalline powder. Used as a drug.

Names & identifiers

Preferred name
5-Aza-2'-deoxycytidine
IUPAC
4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,3,5-triazin-2-one
English name
5-Aza-2'-deoxycytidine
Molecular formula
C8H12N4O4
Molecular weight
228.21

Names & synonyms

Decitabine5-Aza-2'-deoxycytidine2353-33-55-Azadeoxycytidine2'-Deoxy-5-azacytidine5-Aza-deoxycytidine2-Desoxy-5-azacytidineDecitabina5-AZAdCNSC 127716NSC-127716DTXSID7030432
Show more names
Dacogen5-AZA-CDR5-AZA-DCCS-1979DecitabinMCE DecitabineAza deoxycytidine
4-Amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-s-triazin-2(1H)-one4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,3,5-triazin-2-one776B62CQ27DTXCID5010432CHEBI:50131INQOVI COMPONENT DECITABINE4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydro-1,3,5-triazin-2-one1,3,5-Triazin-2(1H)-one, 4-amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-

Database identifiers

CAS
2353-33-5
PubChem CID
451668
DTXSID
DTXSID7030432
ChEMBL
CHEMBL1201129
ChEBI
CHEBI:50131

Properties

Computed structural properties

XLogP
-1.2
Topological polar surface area
121 Ų
Hydrogen bond donors
3
Hydrogen bond acceptors
4
Rotatable bonds
2
Heavy atoms
16
Formal charge
0
Complexity
356

Experimental & physicochemical properties

DrugsPharmaceuticals -> Listed in ZINC15
Solubility5.50e+00 g/L
Human Drugs · 4 items

Breast Feeding; Lactation; Milk, Human; Antimetabolites; Antineoplastic Agents; Enzyme Inhibitors

FDA approved drugs -> Active ingredient

EMA approved medicines: Human medicine

FDA approved drugs -> Active ingredient

Melting Point193-196
Physical Description · 2 items

5-aza-2'-deoxycytidine is a fine white crystalline powder. Used as a drug.

Solid

Physicochemical properties

Melting point
200 °C · ~200 °C (dec.)
alpha
22 · D22 +68.5° (30 min) +57.8° (6 hr) (c = 0.5 in water)
Boiling point
370.01 °C · 370.01°C (rough estimate)
Density
1.3771 · 1.3771 (rough estimate)

Safety & regulation

Safety information is for reference only and does not replace the supplier’s Safety Data Sheet (SDS), applicable regulations, or professional assessment.

GHS classification

GHS Classification · 4 items

Danger

H302 (91.5%): Harmful if swallowed [Warning Acute toxicity, oral]

P203, P261, P264, P264+P265, P270, P271, P280, P301+P317, P302+P352, P304+P340, P305+P351+P338, P318, P319, P321, P330, P332+P317, P337+P317, P362+P364, P403+P233, P405, and P501 (click each P-code to see the statement)

Aggregated GHS information provided per 47 reports by companies from 8 notifications to the ECHA C&L Inventory. Each notification may be associated with multiple companies.

Hazard information

Fire HazardsFlash point data for this chemical are not available. It is probably combustible. (NTP, 1992)
Reactive GroupAlcohols and Polyols
Reactivity Profile · 1 item

5-AZA-2'-DEOXYCYTIDINE is an organic compound with both amine and alcohol substituents. Amines are chemical bases. They neutralize acids to form salts plus water. These acid-base reactions are exothermic. The amount of heat that is evolved per mole of amine in a neutralization is largely independent of the strength of the amine as a base. Amines may be incompatible with isocyanates, halogenated organics, peroxides, phenols (acidic), epoxides, anhydrides, and acid halides. Flammable gaseous hydrogen is generated by amines in combination with strong reducing agents, such as hydrides.

Air and Water Reactions · 1 item

Probably light and air sensitive. Water soluble. Decomposes in aqueous solution at a rate that depends on pH: at pH 7 the drug is more stable than at pH 9, but is less stable than at pH 6. At pH 7 and 99 °F, approximately 7% conversion occurs in 1 hour (NTP, 1992).

Hazard Classes and CategoriesAcute Tox. 4 (91.5%)

Chemistry & industry

Pharmacology

ATC Code · 3 items

L01BC08

L - Antineoplastic and immunomodulating agents

QL - Antineoplastic and immunomodulating agents

Protein BindingDecitabine exhibits negligible (< 1%) plasma protein binding.
Pharmacodynamics · 1 item

Decitabine is a prodrug analogue of the natural nucleotide 2’-deoxycytidine, which, upon being phosphorylated intracellularly, is incorporated into DNA and exerts numerous effects on gene expression. The use of decitabine is associated with neutropenia and thrombocytopenia. In addition, decitabine can cause fetal harm in pregnant women; effective contraception and avoidance of pregnancy are recommended during treatment with decitabine.

Mechanism of Action · 1 item

Myelodysplastic syndromes (MDS) are a group of hematopoietic neoplasms that manifest in peripheral cytopenias and may eventually progress to secondary acute myeloid leukemia (sAML). Included in the over 45 genes commonly mutated in MDS patients are those involved in DNA methylation and histone modification, and it is well-established that alteration of the epigenetic landscape is a feature of myeloid leukemias. Decitabine is considered a prodrug, as it requires transport into cells and subsequent phosphorylation by distinct kinases to generate the active molecule 5-aza-2'-deoxycytidine-triphosphate, which is incorporated by DNA polymerase during DNA replication. Once incorporated into DNA, decitabine is recognized as a substrate by DNA methyltransferase enzymes (DNMTs), specifically DNMT1, but due to the presence of an N5 rather than C5 atom, traps the DNMT through the irreversible formation of a covalent bond. At low concentrations, this mode of action depletes DNMTs and results in global DNA hypomethylation while at high concentrations, it additionally results in double-strand breaks and cell death. The general hypothesis regarding decitabine's therapeutic efficacy is that the global hypomethylation it induces results in the expression of previously silent tumour suppressor genes. However, there are other putative mechanisms also related to this change in DNA methylation, including indirect alteration of transcription through effects on transcription factors, indirectly altering histone modifications and chromatin structure, and activating pathways involved in DNA damage response. The overall effect of decitabine is a decrease in neoplastic cell proliferation and an increase in the expression of tumour suppressor genes.

Related reactions

5 records
New reaction record
HRID 500343 reaction equation
HRID 500343As reactantuspto-grants-2010_08
HRID 1510806 reaction equation
HRID 1510806As productuspto-grants-2012_07
HRID 1777284 reaction equation
HRID 1777284As productuspto-grants-2016_02
HRID 1988570 reaction equation
HRID 1988570As reactantuspto-grants-2010_01
HRID 2043793 reaction equation
HRID 2043793As productuspto-grants-2013_11

Compound notes

Loading…

On this pageBasic informationOverviewNames & identifiersPropertiesSafety & regulationChemistry & industryRelated reactionsCompound notes
UNII
776B62CQ27
EC Number
219-089-4
Nikkaji
J91.053H
refractive index
1.659 · 1.6590 (estimate)
storage temp.
-20 °C · Keep in dark place,Inert atmosphere,Store in freezer, under -20°C
solubility
acetic acid/water (1:1): 50 mg/mL
form
Powder
pka
14.02 · 14.02±0.60(Predicted)
color
White to Off-white
Merck
14 · 14,2853
BRN
617982 · 617982
Stability
Stable. May be light or air sensitive. Incompatible with strong oxidizing agents.
InChI
1S/C8H12N4O4/c9-7-10-3-12(8(15)11-7)6-1-4(14)5(2-13)16-6/h3-6,13-14H,1-2H2,(H2,9,11,15)/t4-,5+,6+/m0/s1
InChIKey
XAUDJQYHKZQPEU-KVQBGUIXSA-N
SMILES
NC1=NC(=O)N(C=N1)[C@H]2C[C@H](O)[C@@H](CO)O2
CAS DataBase Reference
2353 · 2353-33-5(CAS DataBase Reference)
NCI Dictionary of Cancer Terms
Dacogen; decitabine
FDA UNII
776 B62CQ27 · 776B62CQ27
NCI Drug Dictionary
Dacogen
ATC code
1 BC08 · L01BC08
EPA Substance Registry System
5 · 5-Aza-2'-deoxycytidine (2353-33-5)
UNSPSC Code
41116107 · 41116107
NACRES
77 · NA.77
Protein binding
1 % · <1%
Excreted unchanged in urine
4 % · Approx 4%
Volume of distribution
69.1 Litres1 · 69.1 Litres1(L/kg)
Biological half-life
30 · 30-35 minutes / -
Symbol(GHS)
7 · GHS07,GHS08
Signal word
Danger
Hazard statements
302 · H302-H315-H319-H335-H341-H360
Precautionary statements
201 · P201-P202-P301+P312-P302+P352-P305+P351+P338-P308+P313
target organs
Respiratory system
PPE
95 · dust mask type N95 (US), Eyeshields, Gloves
Hazard Codes
Xn,Xi,T
Risk Statements
22 · 22-36/37/38-68-61
Safety Statements
26 · 26-36-36/37
WGK Germany
3 · 3
RTECS
3012000 · XZ3012000
F
10 · 10-34
HS Code
29349990 · 29349990
Storage Class
6.1 C · 6.1C - Combustible acute toxic Cat.3toxic compounds or compounds which causing chronic effects
Hazard Classifications
4 OralEye · Acute Tox. 4 OralEye Irrit. 2Muta. 2Repr. 1BSkin Irrit. 2STOT SE 3
Toxicity
50 in · LD50 in mice (mg/kg): 190 i.p. (Momparler, 1985)

Safety & protection

Fire FightingFires involving this material can be controlled with a dry chemical, carbon dioxide or Halon extinguisher. (NTP, 1992)
First Aid · 1 item

EYES: First check the victim for contact lenses and remove if present. Flush victim's eyes with water or normal saline solution for 20 to 30 minutes while simultaneously calling a hospital or poison control center. Do not put any ointments, oils, or medication in the victim's eyes without specific instructions from a physician. IMMEDIATELY transport the victim after flushing eyes to a hospital even if no symptoms (such as redness or irritation) develop.

Nonfire Spill Response · 1 item

SMALL SPILLS AND LEAKAGE: If you spill this chemical, you should dampen the solid spill material with water, then transfer the dampened material to a suitable container. Use absorbent paper dampened with water to pick up any remaining material. Seal your contaminated clothing and the absorbent paper in a vapor-tight plastic bag for eventual disposal. Wash all contaminated surfaces with a soap and water solution. Do not reenter the contaminated area until the Safety Officer (or other responsible person) has verified that the area has been properly cleaned.

Personal Protective Equipment (PPE) · 1 item

RECOMMENDED RESPIRATOR: Where the neat test chemical is weighed and diluted, wear a NIOSH-approved half face respirator equipped with a combination filter cartridge, i.e. organic vapor/acid gas/HEPA (specific for organic vapors, HCl, acid gas, SO2 and a high efficiency particulate filter). (NTP, 1992)

Toxicology

Hepatotoxicity · 1 item

In early clinical trials using high doses of decitabine, serum enzyme elevations occurred in up to 16% of patients with underlying liver disease or liver metastases, but rarely in persons without hepatic illness. In subsequent studies, serum ALT elevations were reported in 5% to 15% of treated patients, but all were self-limited and no clinically apparent liver injury was reported. Recent studies have reported elevations in serum bilirubin levels in 7% to 12% of treated patients, but the elevations resolved rapidly and were not associated with other clinical or laboratory evidence of liver injury. Monitoring of serum enzyme levels during treatment is recommended only in patients with concurrent liver disease.

Drug Induced Liver Injury · 6 items

Drug Induced Liver Injury Rank (DILIrank 2.0)

Decitabine

Ambiguous-DILI-concern

4

Adverse reactions

DOI:10.1016/j.drudis.2016.02.015

Effects During Pregnancy and Lactation◉ Summary of Use during Lactation

Safety data

F
10-34
PPE
dust mask type N95 (US), Eyeshields, Gloves
wgk
3
rtecs
XZ3012000
hs_code
29349990
Toxicity
LD50 in mice (mg/kg): 190 i.p. (Momparler, 1985)
risk_code
22-36/37/38-68-61
Signal word
Danger
Symbol(GHS)
GHS07,GHS08
hazard_code
Xn,Xi,T
safety_code
26-36-36/37
Storage Class
6.1C - Combustible acute toxic Cat.3toxic compounds or compounds which causing chronic effects
target organs
Respiratory system
Hazard statements
H302-H315-H319-H335-H341-H360
Hazard Classifications
Acute Tox. 4 OralEye Irrit. 2Muta. 2Repr. 1BSkin Irrit. 2STOT SE 3
Precautionary statements
P201-P202-P301+P312-P302+P352-P305+P351+P338-P308+P313
Biological Half-Life · 1 item

Decitabine has a half-life of 0.62 hours (49% CV) when administered intravenously at 15 mg/m<sup>2</sup> for three hours every eight hours over three days, and a half-life of 0.54 hours (43% CV) at 20 mg/m<sup>2</sup> for one hour once daily over five days.

Metabolism/Metabolites · 1 item

Decitabine is phosphorylated inside cells by the sequential action of deoxycytidine kinase, nucleotide monophosphate kinase, and nucleotide diphosphate kinase, prior to being incorporated into newly synthesized DNA by DNA polymerase. Decitabine not incorporated into cellular DNA undergoes deamination by cytidine deaminase followed by additional degradation prior to excretion.

FDA Pharmacological Classification · 6 items

776B62CQ27

DECITABINE

Mechanisms of Action [MoA] - Nucleic Acid Synthesis Inhibitors

Established Pharmacologic Class [EPC] - Nucleoside Metabolic Inhibitor

Decitabine is a Nucleoside Metabolic Inhibitor. The mechanism of action of decitabine is as a Nucleic Acid Synthesis Inhibitor.

DECITABINE

MeSH Pharmacological Classification · 2 items

Antimetabolites that are useful in cancer chemotherapy.

Compounds or agents that combine with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.

Absorption, Distribution and Excretion · 4 items

Decitabine administered intravenously at 15 mg/m2 for three hours every eight hours over three days resulted in a Cmax of 73.8 ng/mL (66% coefficient of variation, CV), an AUC0-∞ of 163 ng\*h/mL (62% CV), and a cumulative AUC of 1332 ng\*h/mL (95% CI of 1010-1730). Similarly, decitabine at 20 mg/m2 for one hour once daily over five days resulted in a Cmax of 147 ng/mL (49% CV), an AUC0-∞ of 115 ng\*h/mL (43% CV), and a cumulative AUC of 570 ng\*h/mL (95% CI of 470-700).

Less than 1% of administered decitabine is excreted in the urine.

Decitabine as an apparent volume of distribution of 4.59 ± 1.42 L/kg.

Decitabine has a clearance of 125 L/hr/m<sup>2</sup> (53% CV) when administered intravenously at 15 mg/m<sup>2</sup> for three hours every eight hours over three days, and a clearance of 210 L/hr/m<sup>2</sup> (47% CV) at 20 mg/m<sup>2</sup> for one hour once daily over five days.

Cellular LocationsCytoplasm
Applications · 5 items

DescriptionDecitabine, 5-aza-2’-deoxycytidine, has been launched for the treatment of myelodysplastic syndromes (MDS). MDS are a set of hematologic disorders affecting the bone marrow that result in ineffective formation and development of blood cells. Furthermore, patients with MDS have a high risk of progressing to acute myeloid leukemia (AML). Traditional treatments include blood transfusions, hematopoietic growth factors, and prophylactic antibiotics, but these measures merely improve the quality of life with questionable effects on disease modification. While stem-cell transplantation is an aggressive, potentially curative approach, the advanced age or the other complicating health issues of most patients preclude them from considering this option. Recent advances in the underlying etiology of MDS, however, have led to the development of a new class of compounds known as ‘‘demethylating agents’’. Decitabine follows the successful introduction of the first DNA methyltransferase inhibitor azacitidine.

UsesUsed as cancer treatment, in particular to inhibit the growth of pancreatic endocrine tumor cell lines.

UsesDecitabine is a potent inhibitor of DNA methylation with IC50 of 438 nM and 4.38 nM in HL-60 and KG1a cells, respectively

Uses5-Aza-2′-deoxycytidine has been used as a demethylating agent in breast cancer cell line, chromatin, DNA and promoter region of p16 gene.

General DescriptionFine white crystalline powder. Used as a drug.

Upstream & downstream products

Upstream raw materials

N-(Trimethylsilyl)-4-[(trimethylsilyl)oxy]-2-amine-1,3,5-triazin3',5'-di-o-p-chlorobenzoyl-2-deoxy-5-azacytosineD-erythro-Pentofuranosyl chloride, 2-deoxy-1,1'-Bi-2-naphtholTriethylamineN,N-DimethylformamideCobaltous nitrate hexahydrate

Suppliers100 total

北京华美互利生物化工010-56205725 · [email protected]
梯希爱(上海)化成工业发展有限公司021-67121386 · [email protected]
上海阿拉丁生化科技股份有限公司400-6206333 13167063860 · [email protected]
江苏杏林医药有限公司18036652731 · [email protected]
南京云志欣合生物科技有限公司18115209001 · [email protected]
INTATRADE GmbH+49 3493/605464 · [email protected]
T&W GROUP021-61551611 13296011611 · [email protected]
爱斯特(成都)生物制药股份有限公司+86-28-85122536 85324413 · [email protected]
南京百芙利科技有限责任公司25-25-58740604 15951658055 · [email protected]
LGM Pharma1-(800)-881-8210 · [email protected]
Syntechem Co.,Ltd[email protected]
上海迈瑞尔生化科技有限公司4006356688 18621169109 · [email protected]
武汉易泰科技有限公司上海分公司18930552037 · [email protected]
宁波亿诺化学品有限公司86-574-27787657 · [email protected]
大连美仑生物技术有限公司0411-62910999 13889544652 · [email protected]
南京仕浪药业有限公司86-25-87797880,81,82 -809 · [email protected]
安耐吉化学&3A(安徽泽升科技股份有限公司)400-0056266 · [email protected]
广州市亿邦医药科技有限公司+86 (20) 28996708,29078958,28139708,29076128,28133708,28139728,28139738,28133718,021-31663278,021-31663578,021-60538387
连云港加佰力生化科技有限公司+86 (518) 8548-7361 · [email protected]
上海柯维化学技术有限公司021-64609169 18901607656 · [email protected]
China Kouting Group Limited+86 (21) 5811-6473 5811-6475 · [email protected]
上海相辉医药科技有限公司13761987713 · [email protected]
上海景颜化工科技有限公司13817811078 · [email protected]
芜湖华仁科技有限公司5842013 18155347026 · [email protected]
上海泰坦科技股份有限公司4006009262 13023226327 · [email protected]
上海隆盛化工有限公司58099637 13585536065 · [email protected]
MedChemexpress LLC021-58955995 · [email protected]
医恩医疗系统研发(上海)有限公司021-58958002 18930822973 · [email protected]
上海攀鸿化工科技有限公司021-56491756 13512199871 · [email protected]
武汉丰泰威远科技有限公司027-87465837 19945049750 · [email protected]
上海升华医药科技有限公司021-50793966 18917198199 · [email protected]
孝感深远化工有限公司15527621225; 15527621225 · [email protected]
济南精合医药科技有限公司0531-88811783 · [email protected]
武汉百科药物开发有限公司027-84222527, 13774034449 · [email protected]
天津希恩思生化科技有限公司400 638 7771 · [email protected]
河南多贝化工有限公司0370-2785118 17550508557 · [email protected]
上海源叶生物科技有限公司18916372613 · [email protected]
深圳菲斯生物科技有限公司0755-83725681-603
上海思域化工科技有限公司86-21-34053660 · [email protected]
赛默飞世尔科技(中国)有限公司800-810-5118 · [email protected]
南京精瑞久安生物技术有限公司025-58196018 800028039 · [email protected]
AdooQ BioScience, LLC+1 (866) 930-6790 · [email protected]
Wuhan NCE Biomedical Co.,Ltd.4000-027-021 |24 +86-13986109188 | +86-15623472865 | +81-08033611988
上海遐瑞医药科技有限公司+86 21 61551611
TCI AMERICA800-4238616 · [email protected]
TOKYO CHEMICAL INDUSTRY CO., LTD.03-36680489 · [email protected]
TCI Europe320-37350700 · [email protected]
深圳振强药物研发有限公司0755-66853366 13670046396 · [email protected]
深圳康特腾科技有限公司86-0755-86635001 · [email protected]
Shanghai Witofly Chemical Co.,Ltd[email protected]

Additional notes

DefinitionChEBI: 5-aza-2'-deoxycytidine is a 2'-deoxyribonucleoside.