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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:52 UTC
Update Date2021-09-14 15:48:16 UTC
HMDB IDHMDB0015391
Secondary Accession Numbers
  • HMDB15391
Metabolite Identification
Common NameDecitabine
DescriptionDecitabine, also known as azadc or dacogen, belongs to the class of organic compounds known as triazinones. Triazinones are compounds containing a triazine ring which bears a ketone group a carbon atom. Decitabine is a drug which is used for treatment of patients with myelodysplastic syndromes (mds) including previously treated and untreated, de novo and secondary mds of all french-american-british subtypes (refractory anemia, refractory anemia with ringed sideroblasts, refractory anemia with excess blasts, refractory anemia with excess blasts in transformation, and chronic myelomonocytic leukemia) and intermediate-1, intermediate-2, and high-risk international prognostic scoring system groups (scores ≥0.5). Decitabine is an extremely weak basic (essentially neutral) compound (based on its pKa). It has been found that use of this DNA methyltranferase inhibitor prevents atherosclerosis lesion formation and reduces the production of inflammatory cytokines by macrophages. It functions in a similar manner to azacitidine, although decitabine can only be incorporated into DNA strands while azacitidine can be incorporated into both DNA and RNA chains. Therefore, the action of decitabine is division-dependent, meaning the cells have to divide in order for the pharmaceutical to act. Methylation of CpG islands upstream of tumor suppressor genes in order to silence them seems to be critical for these type of cancers. It incorporates into DNA strands upon replication, and then when DNA methyltransferases (DNMTs) such as DNMT1, are engaged to bind the DNA and to replicate the methylation to the daughter strand, DNMTs are bound to decitabine irreversibly and cannot disengage. This upregulates DNA methyltransferase expression, which leads to genome-wide DNA methylation alterations and global gene expression changes. Decitabine is used to treat myelodysplastic syndromes (MDS) including previously treated and untreated, de novo and secondary MDS of all French-American-British subtypes (refractory anemia, refractory anemia with ringed sideroblasts, refractory anemia with excess blasts, refractory anemia with excess blasts in transformation, and chronic myelomonocytic leukemia) and Intermediate-1, Intermediate-2, and High-Risk International Prognostic Scoring System groups. In cancer cells, and more specifically in haematological malignancies, it seems that DNA hypermethylation is really critical for their development. It is a drug for the treatment of myelodysplastic syndromes, a class of conditions where certain blood cells are dysfunctional, and for acute myeloid leukemia (AML).
Structure
Data?1582753291
Synonyms
ValueSource
4-Amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-S-triazin-2(1H)-oneChEBI
5-AzadeoxycytidineChEBI
DacogenKegg
4-Amino-1-(2-deoxy-b-D-erythro-pentofuranosyl)-S-triazin-2(1H)-oneGenerator
4-Amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-S-triazin-2(1H)-oneGenerator
5-Aza-2'-deoxycytidineHMDB
AzadcHMDB
DezocitidineHMDB
5-DeoxyazacytidineHMDB
Decitabine mesylateHMDB
2'-Deoxy-5-azacytidineHMDB
AzadC compoundHMDB
2' Deoxy 5 azacytidineHMDB
5 Aza 2' deoxycytidineHMDB
5 AzadeoxycytidineHMDB
5 DeoxyazacytidineHMDB
5-AzadCHMDB
5AzadCHMDB
Compound, azadcHMDB
Mesylate, decitabineHMDB
DecitabineChEBI
Chemical FormulaC8H12N4O4
Average Molecular Weight228.2053
Monoisotopic Molecular Weight228.085854892
IUPAC NameNot Available
Traditional NameNot Available
CAS Registry Number2353-33-5
SMILESNot Available
InChI Identifier
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
InChI KeyXAUDJQYHKZQPEU-KVQBGUIXSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as triazinones. Triazinones are compounds containing a triazine ring which bears a ketone group a carbon atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTriazines
Sub ClassTriazinones
Direct ParentTriazinones
Alternative Parents
Substituents
  • Amino-1,3,5-triazine
  • Aminotriazine
  • Triazinone
  • 1,3,5-triazine
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organic oxide
  • Organopnictogen compound
  • Alcohol
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Amine
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility5.5 g/LNot Available
LogPNot AvailableNot Available
Experimental Spectral PropertiesNot Available
Predicted Molecular PropertiesNot Available
Predicted Spectral Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+149.15331661259
DarkChem[M-H]-148.35631661259

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Decitabine,1TMS,#1C[Si](C)(C)O[C@H]1C[C@H](N2C=NC(N)=NC2=O)O[C@@H]1CO2308.7Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,1TMS,#2C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N)=NC2=O)C[C@@H]1O2294.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,1TMS,#3C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=N12365.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,2TMS,#1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N)=NC2=O)C[C@@H]1O[Si](C)(C)C2231.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,2TMS,#2C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO)O2)C=N12321.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,2TMS,#3C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO[Si](C)(C)C)O2)C=N12303.3Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,2TMS,#4C[Si](C)(C)N(C1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=N1)[Si](C)(C)C2323.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,1TBDMS,#1CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=NC(N)=NC2=O)O[C@@H]1CO2555.0Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,1TBDMS,#2CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N)=NC2=O)C[C@@H]1O2551.4Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,1TBDMS,#3CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=N12578.3Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,2TBDMS,#1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C2706.7Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,2TBDMS,#2CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O2)C=N12738.0Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,2TBDMS,#3CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO[Si](C)(C)C(C)(C)C)O2)C=N12736.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Decitabine,2TBDMS,#4CC(C)(C)[Si](C)(C)N(C1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=N1)[Si](C)(C)C(C)(C)C2737.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Decitabine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9500000000-93e2d9110f2fded5b2922017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Decitabine GC-MS (2 TMS) - 70eV, Positivesplash10-0gi0-6792000000-f27b73769db73752ebde2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Decitabine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 10V, Positive-QTOFsplash10-03di-0900000000-7976ff1b54184471f7f12016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 20V, Positive-QTOFsplash10-03di-5900000000-30985d6b34f33fc971bd2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 40V, Positive-QTOFsplash10-03dl-9600000000-7eb826f89c6a9e79fd1a2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 10V, Negative-QTOFsplash10-003r-4920000000-1d57eb49c2bfcee4a0852016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 20V, Negative-QTOFsplash10-0006-9610000000-41445cf04cf3061ec5472016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 40V, Negative-QTOFsplash10-014l-9200000000-49c5c1822d5d6ef31f042016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 10V, Positive-QTOFsplash10-03di-0900000000-ad27e26e064f360f30062021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 20V, Positive-QTOFsplash10-03di-4900000000-8baaf44cbb1e8b1eec0e2021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 40V, Positive-QTOFsplash10-03di-7900000000-c1581650f477cf91f3692021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 10V, Negative-QTOFsplash10-01ri-1940000000-983ffb62a26d8077f3b02021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 20V, Negative-QTOFsplash10-000x-8900000000-db8318379b860e59d0872021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Decitabine 40V, Negative-QTOFsplash10-0006-9300000000-8f2a29e2dd6708ebd1ed2021-10-11Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01262 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01262 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01262
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID397844
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDecitabine
METLIN IDNot Available
PubChem Compound451668
PDB IDNot Available
ChEBI ID50131
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Daskalakis M, Blagitko-Dorfs N, Hackanson B: Decitabine. Recent Results Cancer Res. 2010;184:131-57. doi: 10.1007/978-3-642-01222-8_10. [PubMed:20072836 ]
  2. Saba HI, Wijermans PW: Decitabine in myelodysplastic syndromes. Semin Hematol. 2005 Jul;42(3 Suppl 2):S23-31. [PubMed:16015501 ]
  3. Jabbour E, Issa JP, Garcia-Manero G, Kantarjian H: Evolution of decitabine development: accomplishments, ongoing investigations, and future strategies. Cancer. 2008 Jun;112(11):2341-51. doi: 10.1002/cncr.23463. [PubMed:18398832 ]
  4. Stresemann C, Lyko F: Modes of action of the DNA methyltransferase inhibitors azacytidine and decitabine. Int J Cancer. 2008 Jul 1;123(1):8-13. doi: 10.1002/ijc.23607. [PubMed:18425818 ]
  5. Oki Y, Aoki E, Issa JP: Decitabine--bedside to bench. Crit Rev Oncol Hematol. 2007 Feb;61(2):140-52. Epub 2006 Oct 4. [PubMed:17023173 ]
  6. Wijermans PW, Ruter B, Baer MR, Slack JL, Saba HI, Lubbert M: Efficacy of decitabine in the treatment of patients with chronic myelomonocytic leukemia (CMML). Leuk Res. 2008 Apr;32(4):587-91. Epub 2007 Sep 18. [PubMed:17881052 ]
  7. Appleton K, Mackay HJ, Judson I, Plumb JA, McCormick C, Strathdee G, Lee C, Barrett S, Reade S, Jadayel D, Tang A, Bellenger K, Mackay L, Setanoians A, Schatzlein A, Twelves C, Kaye SB, Brown R: Phase I and pharmacodynamic trial of the DNA methyltransferase inhibitor decitabine and carboplatin in solid tumors. J Clin Oncol. 2007 Oct 10;25(29):4603-9. [PubMed:17925555 ]

Enzymes

General function:
Involved in ATP binding
Specific function:
Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.
Gene Name:
DCK
Uniprot ID:
P27707
Molecular weight:
30518.315
References
  1. Schwarzenberg J, Radu CG, Benz M, Fueger B, Tran AQ, Phelps ME, Witte ON, Satyamurthy N, Czernin J, Schiepers C: Human biodistribution and radiation dosimetry of novel PET probes targeting the deoxyribonucleoside salvage pathway. Eur J Nucl Med Mol Imaging. 2011 Apr;38(4):711-21. doi: 10.1007/s00259-010-1666-z. Epub 2010 Dec 3. [PubMed:21127859 ]
General function:
Involved in DNA binding
Specific function:
Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9.
Gene Name:
DNMT1
Uniprot ID:
P26358
Molecular weight:
184817.425
References
  1. Ando T, Nishimura M, Oka Y: Decitabine (5-Aza-2'-deoxycytidine) decreased DNA methylation and expression of MDR-1 gene in K562/ADM cells. Leukemia. 2000 Nov;14(11):1915-20. [PubMed:11069027 ]
  2. Karpf AR, Moore BC, Ririe TO, Jones DA: Activation of the p53 DNA damage response pathway after inhibition of DNA methyltransferase by 5-aza-2'-deoxycytidine. Mol Pharmacol. 2001 Apr;59(4):751-7. [PubMed:11259619 ]
  3. Csankovszki G, Nagy A, Jaenisch R: Synergism of Xist RNA, DNA methylation, and histone hypoacetylation in maintaining X chromosome inactivation. J Cell Biol. 2001 May 14;153(4):773-84. [PubMed:11352938 ]
  4. Takebayashi S, Nakao M, Fujita N, Sado T, Tanaka M, Taguchi H, Okumura K: 5-Aza-2'-deoxycytidine induces histone hyperacetylation of mouse centromeric heterochromatin by a mechanism independent of DNA demethylation. Biochem Biophys Res Commun. 2001 Nov 9;288(4):921-6. [PubMed:11688997 ]
  5. Saunthararajah Y, Hillery CA, Lavelle D, Molokie R, Dorn L, Bressler L, Gavazova S, Chen YH, Hoffman R, DeSimone J: Effects of 5-aza-2'-deoxycytidine on fetal hemoglobin levels, red cell adhesion, and hematopoietic differentiation in patients with sickle cell disease. Blood. 2003 Dec 1;102(12):3865-70. Epub 2003 Aug 7. [PubMed:12907443 ]
  6. Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]
  7. Daskalakis M, Blagitko-Dorfs N, Hackanson B: Decitabine. Recent Results Cancer Res. 2010;184:131-57. doi: 10.1007/978-3-642-01222-8_10. [PubMed:20072836 ]
  8. Saba HI, Wijermans PW: Decitabine in myelodysplastic syndromes. Semin Hematol. 2005 Jul;42(3 Suppl 2):S23-31. [PubMed:16015501 ]
  9. Jabbour E, Issa JP, Garcia-Manero G, Kantarjian H: Evolution of decitabine development: accomplishments, ongoing investigations, and future strategies. Cancer. 2008 Jun;112(11):2341-51. doi: 10.1002/cncr.23463. [PubMed:18398832 ]
  10. Stresemann C, Lyko F: Modes of action of the DNA methyltransferase inhibitors azacytidine and decitabine. Int J Cancer. 2008 Jul 1;123(1):8-13. doi: 10.1002/ijc.23607. [PubMed:18425818 ]
  11. Oki Y, Aoki E, Issa JP: Decitabine--bedside to bench. Crit Rev Oncol Hematol. 2007 Feb;61(2):140-52. Epub 2006 Oct 4. [PubMed:17023173 ]