ContaminantDB: 5-Methylcytidine

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-05-25 18:09:34 UTC

Update Date

2016-11-09 01:17:20 UTC

Accession Number

CHEM021668

Identification

Common Name

5-Methylcytidine

Class

Small Molecule

Description

Contaminant Sources

FooDB Chemicals
HMDB Contaminants - Urine

Contaminant Type

Not Available

Chemical Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
5-Methyl-cytidine	HMDB
5-Methylcytidine	HMDB

Chemical Formula

C₁₀H₁₅N₃O₅

Average Molecular Mass

257.243 g/mol

Monoisotopic Mass

257.101 g/mol

CAS Registry Number

2140-61-6

IUPAC Name

4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one

Traditional Name

5-methylcytidine

SMILES

CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)N=C1N

InChI Identifier

InChI=1S/C10H15N3O5/c1-4-2-13(10(17)12-8(4)11)9-7(16)6(15)5(3-14)18-9/h2,5-7,9,14-16H,3H2,1H3,(H2,11,12,17)/t5-,6-,7-,9-/m1/s1

InChI Key

ZAYHVCMSTBRABG-JXOAFFINSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Hydroxypyrimidine
Hydropyrimidine
Monosaccharide
Pyrimidine
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organic nitrogen compound
Hydrocarbon derivative
Primary alcohol
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

methylcytidine (CHEBI:20607 )

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	20.8 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-2.4	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	0.14	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	128.61 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	58.9 m³·mol⁻¹	ChemAxon
Polarizability	24.54 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0adl-9420000000-0b05b3fff49a937e78cb	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-001i-6921100000-895058c6ba83f084d86e	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_6) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_7) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004i-0900000000-01346f227c58c4e64dd3	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-004i-0900000000-25d8b3fb44e47bc7f544	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-004i-1900000000-0ad90898ddb462fa200b	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-004i-4900000000-ff34d9c361d96f5aa2de	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-004i-0900000000-0366c638ef303f3731b3	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-004i-0900000000-f936466105072c9b573c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-056r-0950000000-10971ba54196bbfdfc8d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0090000000-d8be738cdc4e54477227	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0gi0-1490000000-f34a1cb7ce97d538cb7a	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0avi-1960000000-da3e8a4eb805781bcbc6	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0002-9000000000-0a9ca0be7ac354db9478	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0910000000-960e39cedc554f014863	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-2900000000-2ecbb224dc501d648886	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-056r-5900000000-55a400dd7cd5fcd9ea3d	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0950000000-0275ab78e34a521999fb	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-3920000000-50690663d91d4d14a39c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-007p-9200000000-978b587a0b7b22774839	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0ab9-0890000000-24f0c238f60d3c00adbb	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-006y-9700000000-c0edbd46e86d76296c58	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0005-9200000000-9358476776cf6eec42c1	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-a1c51dd1d9ae2dee6e38	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-1910000000-f366741e71fc5efb780d	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a7i-8900000000-f063ff1fc5cb2b980e9e	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum