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

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2006-08-13 17:08:04 UTC

Update Date

2023-02-21 17:17:00 UTC

HMDB ID

HMDB0004339

Secondary Accession Numbers

HMDB04339

Metabolite Identification

Common Name

2-O-Methylcytosine

Description

2-O-Methylcytosine belongs to the class of organic compounds known as aminopyrimidines and derivatives. These are organic compounds containing an amino group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 2-O-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 2-O-methylcytosine a potential biomarker for the consumption of these foods. 2-O-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 small amount of articles have been published on 2-O-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
4-Amino-2-methoxypyrimidine	ChEBI
O-2-Methylcytosine	ChEBI
2-Methoxy-4-pyrimidinamine	HMDB
2-Methoxy-pyrimidin-4-ylamine	HMDB
O(2)Medc	HMDB, MeSH

Chemical Formula

C₅H₇N₃O

Average Molecular Weight

125.1286

Monoisotopic Molecular Weight

125.058911861

IUPAC Name

2-methoxypyrimidin-4-amine

Traditional Name

4-amino-2-methoxypyrimidine

CAS Registry Number

3289-47-2

SMILES

COC1=NC=CC(N)=N1

InChI Identifier

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

InChI Key

DHYLZDVDOQLEAQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminopyrimidines and derivatives. These are organic compounds containing an amino group attached to a pyrimidine ring. 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

Aminopyrimidines and derivatives

Alternative Parents

Substituents

Aminopyrimidine
Alkyl aryl ether
Imidolactam
Heteroaromatic compound
Azacycle
Ether
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aromatic ether (CHEBI:70854 )
aminopyrimidine (CHEBI:70854 )

Ontology

Not Available

Endogenous (HMDB: HMDB0004339)

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)

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	73.6 g/L	ALOGPS
logP	0.52	ALOGPS
logP	0.34	ChemAxon
logS	-0.23	ALOGPS
pKa (Strongest Basic)	4.91	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	61.03 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	34.15 m³·mol⁻¹	ChemAxon
Polarizability	12.07 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]+	124.031	31661259
DarkChem	[M-H]-	123.125	31661259
DeepCCS	[M+H]+	126.368	30932474
DeepCCS	[M-H]-	123.024	30932474
DeepCCS	[M-2H]-	160.146	30932474
DeepCCS	[M+Na]+	135.139	30932474
AllCCS	[M+H]+	127.6	32859911
AllCCS	[M+H-H2O]+	122.8	32859911
AllCCS	[M+NH4]+	132.1	32859911
AllCCS	[M+Na]+	133.3	32859911
AllCCS	[M-H]-	123.2	32859911
AllCCS	[M+Na-2H]-	125.4	32859911
AllCCS	[M+HCOO]-	127.8	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.	1.51 minutes	32390414
Predicted by Siyang on May 30, 2022	8.5955 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.57 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	63.8 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	677.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	304.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	77.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	196.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	64.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	296.1 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	247.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	123.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	576.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	36.4 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	644.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	181.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	195.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	424.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	301.9 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	90.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-O-Methylcytosine	COC1=NC=CC(N)=N1	2124.7	Standard polar	33892256
2-O-Methylcytosine	COC1=NC=CC(N)=N1	1225.5	Standard non polar	33892256
2-O-Methylcytosine	COC1=NC=CC(N)=N1	1224.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-O-Methylcytosine,1TMS,isomer #1	COC1=NC=CC(N[Si](C)(C)C)=N1	1432.0	Semi standard non polar	33892256
2-O-Methylcytosine,1TMS,isomer #1	COC1=NC=CC(N[Si](C)(C)C)=N1	1449.9	Standard non polar	33892256
2-O-Methylcytosine,1TMS,isomer #1	COC1=NC=CC(N[Si](C)(C)C)=N1	2206.6	Standard polar	33892256
2-O-Methylcytosine,2TMS,isomer #1	COC1=NC=CC(N([Si](C)(C)C)[Si](C)(C)C)=N1	1408.9	Semi standard non polar	33892256
2-O-Methylcytosine,2TMS,isomer #1	COC1=NC=CC(N([Si](C)(C)C)[Si](C)(C)C)=N1	1523.2	Standard non polar	33892256
2-O-Methylcytosine,2TMS,isomer #1	COC1=NC=CC(N([Si](C)(C)C)[Si](C)(C)C)=N1	2002.5	Standard polar	33892256
2-O-Methylcytosine,1TBDMS,isomer #1	COC1=NC=CC(N[Si](C)(C)C(C)(C)C)=N1	1673.3	Semi standard non polar	33892256
2-O-Methylcytosine,1TBDMS,isomer #1	COC1=NC=CC(N[Si](C)(C)C(C)(C)C)=N1	1639.5	Standard non polar	33892256
2-O-Methylcytosine,1TBDMS,isomer #1	COC1=NC=CC(N[Si](C)(C)C(C)(C)C)=N1	2333.2	Standard polar	33892256
2-O-Methylcytosine,2TBDMS,isomer #1	COC1=NC=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N1	1847.8	Semi standard non polar	33892256
2-O-Methylcytosine,2TBDMS,isomer #1	COC1=NC=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N1	1932.6	Standard non polar	33892256
2-O-Methylcytosine,2TBDMS,isomer #1	COC1=NC=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N1	2152.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2-O-Methylcytosine GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9800000000-51d6332fb202ce69301f	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-O-Methylcytosine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-O-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 - 2-O-Methylcytosine 10V, Positive-QTOF	splash10-004i-0900000000-1bb951b9f83a110d2b8c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methylcytosine 20V, Positive-QTOF	splash10-056r-1900000000-04ddd0fc13028036bb96	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methylcytosine 40V, Positive-QTOF	splash10-0zfr-9100000000-28d888ded8c1951e27dd	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methylcytosine 10V, Negative-QTOF	splash10-00di-0900000000-d894085fe95f3bf03b21	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methylcytosine 20V, Negative-QTOF	splash10-0a4i-9000000000-6cf7c448078bc8360b0b	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methylcytosine 40V, Negative-QTOF	splash10-0a6r-9000000000-5755b8ac13eeb5f1cff7	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methylcytosine 10V, Negative-QTOF	splash10-0avi-9300000000-6806dd55ff204ff61553	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methylcytosine 20V, Negative-QTOF	splash10-006x-9400000000-16ce826c1acf57a439da	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methylcytosine 40V, Negative-QTOF	splash10-014i-9000000000-d27ecb28e0d64b64bb45	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methylcytosine 10V, Positive-QTOF	splash10-004i-0900000000-8d9371432157a6039cca	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methylcytosine 20V, Positive-QTOF	splash10-004i-9800000000-0123eb03801a62b7b6b3	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-O-Methylcytosine 40V, Positive-QTOF	splash10-0f6x-9000000000-75b521ec45dc397b8834	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	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

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

FDB023365

KNApSAcK ID

Not Available

Chemspider ID

141185

KEGG Compound ID

Not Available

BioCyc ID

CPD0-963

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

160679

PDB ID

Not Available

ChEBI ID

70854

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

Motorin Y, Muller S, Behm-Ansmant I, Branlant C: Identification of modified residues in RNAs by reverse transcription-based methods. Methods Enzymol. 2007;425:21-53. [PubMed:17673078 ]
Maden BE, Corbett ME, Heeney PA, Pugh K, Ajuh PM: Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA. Biochimie. 1995;77(1-2):22-9. [PubMed:7599273 ]

Showing metabocard for 2-O-Methylcytosine (HMDB0004339)

MOL for HMDB0004339 (2-O-Methylcytosine)

3D MOL for HMDB0004339 (2-O-Methylcytosine)

3D SDF for HMDB0004339 (2-O-Methylcytosine)

3D-SDF for HMDB0004339 (2-O-Methylcytosine)

PDB for HMDB0004339 (2-O-Methylcytosine)

3D PDB for HMDB0004339 (2-O-Methylcytosine)

SMILES for HMDB0004339 (2-O-Methylcytosine)

INCHI for HMDB0004339 (2-O-Methylcytosine)

Structure for HMDB0004339 (2-O-Methylcytosine)

3D Structure for HMDB0004339 (2-O-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