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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2009-01-29 12:23:57 UTC

Update Date

2023-02-21 17:17:29 UTC

HMDB ID

HMDB0011601

Secondary Accession Numbers

HMDB11601

Metabolite Identification

Common Name

3-Methylcytosine

Description

3-Methylcytosine belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 3-Methylcytosine has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 3-methylcytosine a potential biomarker for the consumption of these foods. 3-Methylcytosine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on 3-Methylcytosine.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
N3-Methylcytosine	ChEBI

Chemical Formula

C₅H₇N₃O

Average Molecular Weight

125.1286

Monoisotopic Molecular Weight

125.058911861

IUPAC Name

6-amino-1-methyl-1,2-dihydropyrimidin-2-one

Traditional Name

6-amino-1-methylpyrimidin-2-one

CAS Registry Number

4776-08-3

SMILES

CN1C(N)=CC=NC1=O

InChI Identifier

InChI=1S/C5H7N3O/c1-8-4(6)2-3-7-5(8)9/h2-3H,6H2,1H3

InChI Key

KOLPWZCZXAMXKS-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Pyrimidones

Alternative Parents

Substituents

Pyrimidone
Aminopyrimidine
Hydropyrimidine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:39992 )
pyrimidone (CHEBI:39992 )

Ontology

Not Available

Exogenous (HMDB: HMDB0011601)

Food

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Endogenous

Endogenous (HMDB: HMDB0011601)

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	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	25.5 g/L	ALOGPS
logP	-0.77	ALOGPS
logP	-0.92	ChemAxon
logS	-0.69	ALOGPS
pKa (Strongest Basic)	3.75	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	58.69 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	42.91 m³·mol⁻¹	ChemAxon
Polarizability	11.83 Å³	ChemAxon
Number of Rings	1	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]+	124.807	31661259
DarkChem	[M-H]-	121.915	31661259
DeepCCS	[M+H]+	119.765	30932474
DeepCCS	[M-H]-	116.667	30932474
DeepCCS	[M-2H]-	153.177	30932474
DeepCCS	[M+Na]+	128.326	30932474
AllCCS	[M+H]+	126.8	32859911
AllCCS	[M+H-H2O]+	122.0	32859911
AllCCS	[M+NH4]+	131.2	32859911
AllCCS	[M+Na]+	132.5	32859911
AllCCS	[M-H]-	121.9	32859911
AllCCS	[M+Na-2H]-	124.1	32859911
AllCCS	[M+HCOO]-	126.5	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.	1.58 minutes	32390414
Predicted by Siyang on May 30, 2022	8.1653 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.99 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	60.9 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	422.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	300.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	62.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	195.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	54.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	262.9 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	239.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	280.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	535.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	33.5 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	601.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	188.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	198.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	633.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	353.4 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	166.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Methylcytosine	CN1C(N)=CC=NC1=O	2401.7	Standard polar	33892256
3-Methylcytosine	CN1C(N)=CC=NC1=O	1482.8	Standard non polar	33892256
3-Methylcytosine	CN1C(N)=CC=NC1=O	1647.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Methylcytosine,1TMS,isomer #1	CN1C(N[Si](C)(C)C)=CC=NC1=O	1618.3	Semi standard non polar	33892256
3-Methylcytosine,1TMS,isomer #1	CN1C(N[Si](C)(C)C)=CC=NC1=O	1628.2	Standard non polar	33892256
3-Methylcytosine,1TMS,isomer #1	CN1C(N[Si](C)(C)C)=CC=NC1=O	2064.7	Standard polar	33892256
3-Methylcytosine,2TMS,isomer #1	CN1C(N([Si](C)(C)C)[Si](C)(C)C)=CC=NC1=O	1585.7	Semi standard non polar	33892256
3-Methylcytosine,2TMS,isomer #1	CN1C(N([Si](C)(C)C)[Si](C)(C)C)=CC=NC1=O	1677.5	Standard non polar	33892256
3-Methylcytosine,2TMS,isomer #1	CN1C(N([Si](C)(C)C)[Si](C)(C)C)=CC=NC1=O	1927.9	Standard polar	33892256
3-Methylcytosine,1TBDMS,isomer #1	CN1C(N[Si](C)(C)C(C)(C)C)=CC=NC1=O	1908.8	Semi standard non polar	33892256
3-Methylcytosine,1TBDMS,isomer #1	CN1C(N[Si](C)(C)C(C)(C)C)=CC=NC1=O	1814.5	Standard non polar	33892256
3-Methylcytosine,1TBDMS,isomer #1	CN1C(N[Si](C)(C)C(C)(C)C)=CC=NC1=O	2196.4	Standard polar	33892256
3-Methylcytosine,2TBDMS,isomer #1	CN1C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=CC=NC1=O	2036.8	Semi standard non polar	33892256
3-Methylcytosine,2TBDMS,isomer #1	CN1C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=CC=NC1=O	2110.5	Standard non polar	33892256
3-Methylcytosine,2TBDMS,isomer #1	CN1C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=CC=NC1=O	2099.3	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylcytosine GC-MS (Non-derivatized) - 70eV, Positive	splash10-00b9-9600000000-1844a081213b3ead252d	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylcytosine 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 - 3-Methylcytosine 10V, Positive-QTOF	splash10-004i-0900000000-068a24b689fa566d73ff	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytosine 20V, Positive-QTOF	splash10-056r-5900000000-65cc3c0f336953b85086	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytosine 40V, Positive-QTOF	splash10-0fr6-9000000000-e5737f8d7b89ece805cf	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytosine 10V, Negative-QTOF	splash10-00di-1900000000-7e25edf95b9a8b79baa0	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytosine 20V, Negative-QTOF	splash10-01bd-9200000000-985e6cb391c32bf22431	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytosine 40V, Negative-QTOF	splash10-0006-9000000000-6b4b0a748e1d9e56a4fe	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytosine 10V, Negative-QTOF	splash10-00di-2900000000-51269272bcc03c3bc735	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytosine 20V, Negative-QTOF	splash10-014l-9100000000-a4b14dbc3fe350637533	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytosine 40V, Negative-QTOF	splash10-014l-9000000000-5bff62817b63d65f94d5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytosine 10V, Positive-QTOF	splash10-004i-1900000000-512940c3012d0f1a2515	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytosine 20V, Positive-QTOF	splash10-004l-9500000000-8c17f35bf9905c92dbcc	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylcytosine 40V, Positive-QTOF	splash10-0uxr-9000000000-9701d242da20bc1926e9	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

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

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Asthma	33739820	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Asthma	33739820	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028312

KNApSAcK ID

Not Available

Chemspider ID

123940

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Methylcytosine

METLIN ID

Not Available

PubChem Compound

140523

PDB ID

Not Available

ChEBI ID

39992

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

Sedgwick B, Bates PA, Paik J, Jacobs SC, Lindahl T: Repair of alkylated DNA: recent advances. DNA Repair (Amst). 2007 Apr 1;6(4):429-42. Epub 2006 Nov 16. [PubMed:17112791 ]

Showing metabocard for 3-Methylcytosine (HMDB0011601)

MOL for HMDB0011601 (3-Methylcytosine)

3D MOL for HMDB0011601 (3-Methylcytosine)

3D SDF for HMDB0011601 (3-Methylcytosine)

3D-SDF for HMDB0011601 (3-Methylcytosine)

PDB for HMDB0011601 (3-Methylcytosine)

3D PDB for HMDB0011601 (3-Methylcytosine)

SMILES for HMDB0011601 (3-Methylcytosine)

INCHI for HMDB0011601 (3-Methylcytosine)

Structure for HMDB0011601 (3-Methylcytosine)

3D Structure for HMDB0011601 (3-Methylcytosine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra