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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

2021-09-10 21:09:00 UTC

Update Date

2021-09-26 22:51:19 UTC

HMDB ID

HMDB0243939

Secondary Accession Numbers

None

Metabolite Identification

Common Name

1-Methylcytosine

Description

1-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. 1-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 very few articles have been published on 1-methylcytosine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1-methylcytosine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1-Methylcytosine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1-Methylcytosine hydrochloride	MeSH
N-Methylcytosine	MeSH

Chemical Formula

C₅H₇N₃O

Average Molecular Weight

125.1286

Monoisotopic Molecular Weight

125.058911861

IUPAC Name

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

Traditional Name

1-methylcytosine

CAS Registry Number

Not Available

SMILES

CN1C=CC(N)=NC1=O

InChI Identifier

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

InChI Key

HWPZZUQOWRWFDB-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

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:39624 )
pyrimidone (CHEBI:39624 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (HMDB: HMDB0243939)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

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
logP	-1.4	ALOGPS
logP	-1	ChemAxon
logS	-0.63	ALOGPS
pKa (Strongest Basic)	3.07	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	32.85 m³·mol⁻¹	ChemAxon
Polarizability	12.02 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
DeepCCS	[M+H]+	120.378	30932474
DeepCCS	[M-H]-	117.514	30932474
DeepCCS	[M-2H]-	153.894	30932474
DeepCCS	[M+Na]+	128.938	30932474
AllCCS	[M+H]+	126.9	32859911
AllCCS	[M+H-H2O]+	122.1	32859911
AllCCS	[M+NH4]+	131.4	32859911
AllCCS	[M+Na]+	132.6	32859911
AllCCS	[M-H]-	123.3	32859911
AllCCS	[M+Na-2H]-	125.5	32859911
AllCCS	[M+HCOO]-	127.9	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	8.2087 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.27 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	464.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	292.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	65.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	190.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	53.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	255.8 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	236.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	396.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	544.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	33.8 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	614.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	183.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	196.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	590.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	349.7 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	159.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1-Methylcytosine	CN1C=CC(N)=NC1=O	2371.2	Standard polar	33892256
1-Methylcytosine	CN1C=CC(N)=NC1=O	1448.2	Standard non polar	33892256
1-Methylcytosine	CN1C=CC(N)=NC1=O	1573.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
1-Methylcytosine,1TMS,isomer #1	CN1C=CC(N[Si](C)(C)C)=NC1=O	1617.2	Semi standard non polar	33892256
1-Methylcytosine,1TMS,isomer #1	CN1C=CC(N[Si](C)(C)C)=NC1=O	1680.6	Standard non polar	33892256
1-Methylcytosine,1TMS,isomer #1	CN1C=CC(N[Si](C)(C)C)=NC1=O	2113.4	Standard polar	33892256
1-Methylcytosine,2TMS,isomer #1	CN1C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC1=O	1528.7	Semi standard non polar	33892256
1-Methylcytosine,2TMS,isomer #1	CN1C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC1=O	1695.7	Standard non polar	33892256
1-Methylcytosine,2TMS,isomer #1	CN1C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC1=O	1945.0	Standard polar	33892256
1-Methylcytosine,1TBDMS,isomer #1	CN1C=CC(N[Si](C)(C)C(C)(C)C)=NC1=O	1874.1	Semi standard non polar	33892256
1-Methylcytosine,1TBDMS,isomer #1	CN1C=CC(N[Si](C)(C)C(C)(C)C)=NC1=O	1865.0	Standard non polar	33892256
1-Methylcytosine,1TBDMS,isomer #1	CN1C=CC(N[Si](C)(C)C(C)(C)C)=NC1=O	2236.4	Standard polar	33892256
1-Methylcytosine,2TBDMS,isomer #1	CN1C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC1=O	1979.1	Semi standard non polar	33892256
1-Methylcytosine,2TBDMS,isomer #1	CN1C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC1=O	2113.3	Standard non polar	33892256
1-Methylcytosine,2TBDMS,isomer #1	CN1C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC1=O	2111.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Methylcytosine GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9700000000-09420db81d0679c9995b	2017-08-28	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-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 - 1-Methylcytosine 10V, Positive-QTOF	splash10-004i-0900000000-07242966a29ba15427f7	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methylcytosine 20V, Positive-QTOF	splash10-004i-5900000000-fce74ad01b42e6816d7e	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methylcytosine 40V, Positive-QTOF	splash10-0udi-9000000000-8e48599709f01a2d4bc5	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methylcytosine 10V, Negative-QTOF	splash10-00di-1900000000-921c8371d5a9115991ab	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methylcytosine 20V, Negative-QTOF	splash10-001i-9100000000-aa5765f869a13ca46195	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methylcytosine 40V, Negative-QTOF	splash10-0006-9000000000-40998e6e1274f4a5b51d	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methylcytosine 10V, Positive-QTOF	splash10-004i-1900000000-256ddd7a73c49e197c3b	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methylcytosine 20V, Positive-QTOF	splash10-053r-9100000000-a33b724a51aba6c66f18	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methylcytosine 40V, Positive-QTOF	splash10-0a4i-9000000000-d77a1fa64528cdc87503	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methylcytosine 10V, Negative-QTOF	splash10-00e9-7900000000-e1c3ea3d5bde49531650	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methylcytosine 20V, Negative-QTOF	splash10-0006-9000000000-bc91e49469ef7a9774ca	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Methylcytosine 40V, Negative-QTOF	splash10-0006-9000000000-d1d98a6c79480f7d148f	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

71474

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

1-Methylcytosine

METLIN ID

Not Available

PubChem Compound

79143

PDB ID

Not Available

ChEBI ID

39624

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 1-Methylcytosine (HMDB0243939)

MOL for HMDB0243939 (1-Methylcytosine)

3D MOL for HMDB0243939 (1-Methylcytosine)

3D SDF for HMDB0243939 (1-Methylcytosine)

3D-SDF for HMDB0243939 (1-Methylcytosine)

PDB for HMDB0243939 (1-Methylcytosine)

3D PDB for HMDB0243939 (1-Methylcytosine)

SMILES for HMDB0243939 (1-Methylcytosine)

INCHI for HMDB0243939 (1-Methylcytosine)

Structure for HMDB0243939 (1-Methylcytosine)

3D Structure for HMDB0243939 (1-Methylcytosine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra