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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:52 UTC

Update Date

2022-03-07 02:51:58 UTC

HMDB ID

HMDB0015391

Secondary Accession Numbers

HMDB15391

Metabolite Identification

Common Name

Decitabine

Description

Decitabine, 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

1262
  Mrv0541 02231215212D          

 16 17  0  0  1  0            999 V2000
    3.7464   -1.1305    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1816   -2.5826    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7969   -2.4964    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.1794    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790    0.1794    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    1.4169    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    1.4169    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790    2.6545    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6665   -1.9152    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4115   -1.1305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4915   -1.9152    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0790   -0.6456    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9764   -2.5826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.5919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    0.5919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790    1.8294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  9  2  1  1  0  0  0
  3 13  1  0  0  0  0
  4 14  2  0  0  0  0
 12  5  1  6  0  0  0
  5 14  1  0  0  0  0
  5 15  1  0  0  0  0
  6 14  1  0  0  0  0
  6 16  2  0  0  0  0
  7 15  2  0  0  0  0
  7 16  1  0  0  0  0
  8 16  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0015391

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC(=O)N(C=N1)[C@H]1C[C@H](O)[C@@H](CO)O1

> <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_KEY>
XAUDJQYHKZQPEU-KVQBGUIXSA-N

> <FORMULA>
C8H12N4O4

> <MOLECULAR_WEIGHT>
228.2053

> <EXACT_MASS>
228.085854892

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
21.152792212911397

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydro-1,3,5-triazin-2-one

> <ALOGPS_LOGP>
-1.96

> <JCHEM_LOGP>
-2.1646948889999997

> <ALOGPS_LOGS>
-1.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.787531711736769

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.894836659905877

> <JCHEM_PKA_STRONGEST_BASIC>
-0.24650109584685487

> <JCHEM_POLAR_SURFACE_AREA>
120.73999999999998

> <JCHEM_REFRACTIVITY>
50.6825

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.50e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
decitabine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 1262                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       6.993  -2.110   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       4.072  -4.821   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       8.954  -4.660   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       3.080   0.335   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       5.747   0.335   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       4.414   2.645   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       7.081   2.645   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       5.747   4.955   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       4.977  -3.575   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.501  -2.110   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.517  -3.575   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.747  -1.205   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.423  -4.821   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.414   1.105   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.081   1.105   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.747   3.415   0.000  0.00  0.00           C+0
CONECT    1   11   12                                                       
CONECT    2    9                                                            
CONECT    3   13                                                            
CONECT    4   14                                                            
CONECT    5   12   14   15                                                  
CONECT    6   14   16                                                       
CONECT    7   15   16                                                       
CONECT    8   16                                                            
CONECT    9    2   10   11                                                  
CONECT   10    9   12                                                       
CONECT   11    1    9   13                                                  
CONECT   12    1    5   10                                                  
CONECT   13    3   11                                                       
CONECT   14    4    5    6                                                  
CONECT   15    5    7                                                       
CONECT   16    6    7    8                                                  
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

COMPND    HMDB0015391
HETATM    1  N1  UNL     1       5.216   0.638  -0.251  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.825   0.302  -0.113  1.00  0.00           C  
HETATM    3  N2  UNL     1       2.986   1.203   0.411  1.00  0.00           N  
HETATM    4  C2  UNL     1       1.689   0.879   0.535  1.00  0.00           C  
HETATM    5  N3  UNL     1       1.194  -0.312   0.156  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.172  -0.686   0.274  1.00  0.00           C  
HETATM    7  C4  UNL     1      -0.949   0.101   1.307  1.00  0.00           C  
HETATM    8  C5  UNL     1      -2.346  -0.410   0.988  1.00  0.00           C  
HETATM    9  O1  UNL     1      -2.491  -1.690   1.492  1.00  0.00           O  
HETATM   10  C6  UNL     1      -2.249  -0.473  -0.522  1.00  0.00           C  
HETATM   11  C7  UNL     1      -2.952   0.741  -1.094  1.00  0.00           C  
HETATM   12  O2  UNL     1      -2.384   1.897  -0.619  1.00  0.00           O  
HETATM   13  O3  UNL     1      -0.927  -0.466  -0.869  1.00  0.00           O  
HETATM   14  C8  UNL     1       2.069  -1.194  -0.367  1.00  0.00           C  
HETATM   15  O4  UNL     1       1.687  -2.337  -0.749  1.00  0.00           O  
HETATM   16  N4  UNL     1       3.383  -0.901  -0.507  1.00  0.00           N  
HETATM   17  H1  UNL     1       5.516   1.613  -0.415  1.00  0.00           H  
HETATM   18  H2  UNL     1       5.904  -0.160  -0.175  1.00  0.00           H  
HETATM   19  H3  UNL     1       1.039   1.620   0.958  1.00  0.00           H  
HETATM   20  H4  UNL     1      -0.323  -1.770   0.541  1.00  0.00           H  
HETATM   21  H5  UNL     1      -0.646  -0.138   2.339  1.00  0.00           H  
HETATM   22  H6  UNL     1      -0.945   1.170   1.072  1.00  0.00           H  
HETATM   23  H7  UNL     1      -3.129   0.293   1.327  1.00  0.00           H  
HETATM   24  H8  UNL     1      -2.351  -2.397   0.812  1.00  0.00           H  
HETATM   25  H9  UNL     1      -2.696  -1.417  -0.914  1.00  0.00           H  
HETATM   26  H10 UNL     1      -2.920   0.744  -2.195  1.00  0.00           H  
HETATM   27  H11 UNL     1      -4.022   0.684  -0.800  1.00  0.00           H  
HETATM   28  H12 UNL     1      -3.006   2.465  -0.101  1.00  0.00           H  
CONECT    1    2   17   18
CONECT    2    3   16   16
CONECT    3    4    4
CONECT    4    5   19
CONECT    5    6   14
CONECT    6    7   13   20
CONECT    7    8   21   22
CONECT    8    9   10   23
CONECT    9   24
CONECT   10   11   13   25
CONECT   11   12   26   27
CONECT   12   28
CONECT   14   15   15   16
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
4-Amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-S-triazin-2(1H)-one	ChEBI
5-Azadeoxycytidine	ChEBI
Dacogen	Kegg
4-Amino-1-(2-deoxy-b-D-erythro-pentofuranosyl)-S-triazin-2(1H)-one	Generator
4-Amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-S-triazin-2(1H)-one	Generator
5-Aza-2'-deoxycytidine	HMDB
Azadc	HMDB
Dezocitidine	HMDB
5-Deoxyazacytidine	HMDB
Decitabine mesylate	HMDB
2'-Deoxy-5-azacytidine	HMDB
AzadC compound	HMDB
2' Deoxy 5 azacytidine	HMDB
5 Aza 2' deoxycytidine	HMDB
5 Azadeoxycytidine	HMDB
5 Deoxyazacytidine	HMDB
5-AzadC	HMDB
5AzadC	HMDB
Compound, azadc	HMDB
Mesylate, decitabine	HMDB
Decitabine	ChEBI

Chemical Formula

C₈H₁₂N₄O₄

Average Molecular Weight

228.2053

Monoisotopic Molecular Weight

228.085854892

IUPAC Name

4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydro-1,3,5-triazin-2-one

Traditional Name

decitabine

CAS Registry Number

2353-33-5

SMILES

NC1=NC(=O)N(C=N1)[C@H]1C[C@H](O)[C@@H](CO)O1

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 Key

XAUDJQYHKZQPEU-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.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Triazines

Sub Class

Triazinones

Direct Parent

Triazinones

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 Framework

Aromatic heteromonocyclic compounds

External Descriptors

2'-deoxyribonucleoside (CHEBI:50131 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Cytoplasm (HMDB: HMDB0015391)

Source

Exogenous

Exogenous (HMDB: HMDB0015391)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	5.5 g/L	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	5.5 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.2	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	-0.25	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	120.74 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	50.68 m³·mol⁻¹	ChemAxon
Polarizability	21.15 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	149.153	31661259
DarkChem	[M-H]-	148.356	31661259
DeepCCS	[M+H]+	149.495	30932474
DeepCCS	[M-H]-	147.099	30932474
DeepCCS	[M-2H]-	180.662	30932474
DeepCCS	[M+Na]+	155.839	30932474
AllCCS	[M+H]+	150.9	32859911
AllCCS	[M+H-H2O]+	147.0	32859911
AllCCS	[M+NH4]+	154.6	32859911
AllCCS	[M+Na]+	155.6	32859911
AllCCS	[M-H]-	149.3	32859911
AllCCS	[M+Na-2H]-	149.2	32859911
AllCCS	[M+HCOO]-	149.3	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	1.76 minutes	32390414
Predicted by Siyang on May 30, 2022	9.143 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.99 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	123.9 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	566.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	252.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	62.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	163.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	57.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	289.8 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	258.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	655.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	585.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	67.6 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	834.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	176.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	189.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	601.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	366.9 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	229.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Decitabine	NC1=NC(=O)N(C=N1)[C@H]1C[C@H](O)[C@@H](CO)O1	3468.3	Standard polar	33892256
Decitabine	NC1=NC(=O)N(C=N1)[C@H]1C[C@H](O)[C@@H](CO)O1	2199.0	Standard non polar	33892256
Decitabine	NC1=NC(=O)N(C=N1)[C@H]1C[C@H](O)[C@@H](CO)O1	2503.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Decitabine,1TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](N2C=NC(N)=NC2=O)O[C@@H]1CO	2308.7	Semi standard non polar	33892256
Decitabine,1TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N)=NC2=O)C[C@@H]1O	2294.9	Semi standard non polar	33892256
Decitabine,1TMS,isomer #3	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=N1	2365.9	Semi standard non polar	33892256
Decitabine,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N)=NC2=O)C[C@@H]1O[Si](C)(C)C	2231.9	Semi standard non polar	33892256
Decitabine,2TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO)O2)C=N1	2321.5	Semi standard non polar	33892256
Decitabine,2TMS,isomer #3	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO[Si](C)(C)C)O2)C=N1	2303.3	Semi standard non polar	33892256
Decitabine,2TMS,isomer #4	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	2323.1	Semi standard non polar	33892256
Decitabine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C=N1	2291.2	Semi standard non polar	33892256
Decitabine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C=N1	2440.9	Standard non polar	33892256
Decitabine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O2)C=N1	3383.8	Standard polar	33892256
Decitabine,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O[C@@H]1CO	2306.2	Semi standard non polar	33892256
Decitabine,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O[C@@H]1CO	2464.2	Standard non polar	33892256
Decitabine,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](N2C=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)O[C@@H]1CO	3115.0	Standard polar	33892256
Decitabine,3TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O	2324.5	Semi standard non polar	33892256
Decitabine,3TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O	2492.6	Standard non polar	33892256
Decitabine,3TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O	3137.0	Standard polar	33892256
Decitabine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C	2336.5	Semi standard non polar	33892256
Decitabine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C	2499.8	Standard non polar	33892256
Decitabine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C	2890.6	Standard polar	33892256
Decitabine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=NC(N)=NC2=O)O[C@@H]1CO	2555.0	Semi standard non polar	33892256
Decitabine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N)=NC2=O)C[C@@H]1O	2551.4	Semi standard non polar	33892256
Decitabine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@H]2C[C@H](O)[C@@H](CO)O2)C=N1	2578.3	Semi standard non polar	33892256
Decitabine,2TBDMS,isomer #1	CC(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)C	2706.7	Semi standard non polar	33892256
Decitabine,2TBDMS,isomer #2	CC(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=N1	2738.0	Semi standard non polar	33892256
Decitabine,2TBDMS,isomer #3	CC(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=N1	2736.9	Semi standard non polar	33892256
Decitabine,2TBDMS,isomer #4	CC(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)C	2737.1	Semi standard non polar	33892256
Decitabine,3TBDMS,isomer #1	CC(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[Si](C)(C)C(C)(C)C)O2)C=N1	2928.5	Semi standard non polar	33892256
Decitabine,3TBDMS,isomer #1	CC(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[Si](C)(C)C(C)(C)C)O2)C=N1	3092.4	Standard non polar	33892256
Decitabine,3TBDMS,isomer #1	CC(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[Si](C)(C)C(C)(C)C)O2)C=N1	3476.1	Standard polar	33892256
Decitabine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O[C@@H]1CO	2934.2	Semi standard non polar	33892256
Decitabine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O[C@@H]1CO	3106.6	Standard non polar	33892256
Decitabine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)O[C@@H]1CO	3237.5	Standard polar	33892256
Decitabine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O	2925.8	Semi standard non polar	33892256
Decitabine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O	3123.2	Standard non polar	33892256
Decitabine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O	3270.7	Standard polar	33892256
Decitabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C	3135.1	Semi standard non polar	33892256
Decitabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C	3325.1	Standard non polar	33892256
Decitabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C	3181.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Decitabine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9500000000-93e2d9110f2fded5b292	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Decitabine GC-MS (2 TMS) - 70eV, Positive	splash10-0gi0-6792000000-f27b73769db73752ebde	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Decitabine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 10V, Positive-QTOF	splash10-03di-0900000000-7976ff1b54184471f7f1	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 20V, Positive-QTOF	splash10-03di-5900000000-30985d6b34f33fc971bd	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 40V, Positive-QTOF	splash10-03dl-9600000000-7eb826f89c6a9e79fd1a	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 10V, Negative-QTOF	splash10-003r-4920000000-1d57eb49c2bfcee4a085	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 20V, Negative-QTOF	splash10-0006-9610000000-41445cf04cf3061ec547	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 40V, Negative-QTOF	splash10-014l-9200000000-49c5c1822d5d6ef31f04	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 10V, Positive-QTOF	splash10-03di-0900000000-ad27e26e064f360f3006	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 20V, Positive-QTOF	splash10-03di-4900000000-8baaf44cbb1e8b1eec0e	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 40V, Positive-QTOF	splash10-03di-7900000000-c1581650f477cf91f369	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 10V, Negative-QTOF	splash10-01ri-1940000000-983ffb62a26d8077f3b0	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 20V, Negative-QTOF	splash10-000x-8900000000-db8318379b860e59d087	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Decitabine 40V, Negative-QTOF	splash10-0006-9300000000-8f2a29e2dd6708ebd1ed	2021-10-11	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB01262	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB01262	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB01262

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

397844

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Decitabine

METLIN ID

Not Available

PubChem Compound

451668

PDB ID

Not Available

ChEBI ID

50131

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]
Saba HI, Wijermans PW: Decitabine in myelodysplastic syndromes. Semin Hematol. 2005 Jul;42(3 Suppl 2):S23-31. [PubMed:16015501 ]
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 ]
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 ]
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 ]
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 ]
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

Enzyme Details

1. Deoxycytidine kinase

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

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 ]

Enzyme Details

2. DNA (cytosine-5)-methyltransferase 1

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

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 ]
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 ]
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 ]
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 ]
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 ]
Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]
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 ]
Saba HI, Wijermans PW: Decitabine in myelodysplastic syndromes. Semin Hematol. 2005 Jul;42(3 Suppl 2):S23-31. [PubMed:16015501 ]
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 ]
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 ]
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 ]

Showing metabocard for Decitabine (HMDB0015391)

MOL for HMDB0015391 (Decitabine)

3D MOL for HMDB0015391 (Decitabine)

3D SDF for HMDB0015391 (Decitabine)

3D-SDF for HMDB0015391 (Decitabine)

PDB for HMDB0015391 (Decitabine)

3D PDB for HMDB0015391 (Decitabine)

SMILES for HMDB0015391 (Decitabine)

INCHI for HMDB0015391 (Decitabine)

Structure for HMDB0015391 (Decitabine)

3D Structure for HMDB0015391 (Decitabine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

References

References