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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (5) Show 5 proteins XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2006-05-22 15:12:17 UTC

Update Date

2023-02-21 17:16:29 UTC

HMDB ID

HMDB0002894

Secondary Accession Numbers

HMDB02894

Metabolite Identification

Common Name

5-Methylcytosine

Description

5-Methylcytosine is a methylated nucleotide base found in eukaryotic DNA. In animals, the DNA methylation of cytosine to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In plants, the methylated sequence is CpNpGp, where N can be any base. -- Pubchem; 5-Methylcytosine is a methylated form of cytosine in which a methyl group is attached to carbon 5, altering its structure without altering its base-pairing properties. -- Wikipedia ; 5-Methylcytosine is an epigenetic modification formed by the action of DNA methyltransferases. In bacteria, 5-methylcytosine can be found at a variety of sites, and is often used as a marker to protect DNA from being cut by native methylation-sensitive restriction enzymes. In plants, 5-methylcytosine occurs at both CpG and CpNpG sequences. In fungi and animals, 5-methylcytosine predominately occurs at CpG dinucleotides. Although most eukaryotes methylate only a small percentage of these sites, in vertebrates 70-80% of CpG cytosines are methylated. -- Wikipedia .

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-5-methyl-2(1H)-pyrimidinone	ChEBI
4-Amino-5-methyl-2-pyrimidinol	ChEBI
4-Amino-5-methyl-2-(1H)-pyrimidinone	HMDB
5-Methyl-cytosine	HMDB
5-Methylcytosine>96	HMDB
Monohydrochloride, 5-methylcytosine	HMDB
5 Methylcytosine	HMDB
5 Methylcytosine monohydrochloride	HMDB
5-Methylcytosine monohydrochloride	HMDB

Chemical Formula

C₅H₇N₃O

Average Molecular Weight

125.1286

Monoisotopic Molecular Weight

125.058911861

IUPAC Name

6-amino-5-methyl-1,2-dihydropyrimidin-2-one

Traditional Name

5-methylcytosine

CAS Registry Number

554-01-8

SMILES

CC1=C(N)NC(=O)N=C1

InChI Identifier

InChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)

InChI Key

LRSASMSXMSNRBT-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl 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

Hydroxypyrimidines

Alternative Parents

Substituents

Hydroxypyrimidine
Imidolactam
Hydropyrimidine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidines (CHEBI:27551 )
a small molecule (CPD0-2018 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	270 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	34.5 mg/mL	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	8.91 g/L	ALOGPS
logP	-0.63	ALOGPS
logP	-0.75	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	10.08	ChemAxon
pKa (Strongest Basic)	3.75	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	67.48 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	42.37 m³·mol⁻¹	ChemAxon
Polarizability	11.89 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]+	125.073	31661259
DarkChem	[M-H]-	121.64	31661259
DeepCCS	[M+H]+	130.045	30932474
DeepCCS	[M-H]-	126.313	30932474
DeepCCS	[M-2H]-	163.75	30932474
DeepCCS	[M+Na]+	139.193	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]-	122.8	32859911
AllCCS	[M+Na-2H]-	125.0	32859911
AllCCS	[M+HCOO]-	127.4	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.	1.52 minutes	32390414
Predicted by Siyang on May 30, 2022	8.4481 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.95 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	110.1 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	440.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	309.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	66.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	201.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	55.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	279.0 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	244.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	683.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	561.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	40.5 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	627.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	191.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	221.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	679.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	401.5 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	229.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Methylcytosine	CC1=C(N)NC(=O)N=C1	2505.6	Standard polar	33892256
5-Methylcytosine	CC1=C(N)NC(=O)N=C1	1502.8	Standard non polar	33892256
5-Methylcytosine	CC1=C(N)NC(=O)N=C1	1675.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Methylcytosine,1TMS,isomer #1	CC1=C(N[Si](C)(C)C)[NH]C(=O)N=C1	1595.7	Semi standard non polar	33892256
5-Methylcytosine,1TMS,isomer #1	CC1=C(N[Si](C)(C)C)[NH]C(=O)N=C1	1622.0	Standard non polar	33892256
5-Methylcytosine,1TMS,isomer #1	CC1=C(N[Si](C)(C)C)[NH]C(=O)N=C1	2246.3	Standard polar	33892256
5-Methylcytosine,1TMS,isomer #2	CC1=C(N)N([Si](C)(C)C)C(=O)N=C1	1555.7	Semi standard non polar	33892256
5-Methylcytosine,1TMS,isomer #2	CC1=C(N)N([Si](C)(C)C)C(=O)N=C1	1598.6	Standard non polar	33892256
5-Methylcytosine,1TMS,isomer #2	CC1=C(N)N([Si](C)(C)C)C(=O)N=C1	2274.5	Standard polar	33892256
5-Methylcytosine,2TMS,isomer #1	CC1=C(N[Si](C)(C)C)N([Si](C)(C)C)C(=O)N=C1	1688.3	Semi standard non polar	33892256
5-Methylcytosine,2TMS,isomer #1	CC1=C(N[Si](C)(C)C)N([Si](C)(C)C)C(=O)N=C1	1727.5	Standard non polar	33892256
5-Methylcytosine,2TMS,isomer #1	CC1=C(N[Si](C)(C)C)N([Si](C)(C)C)C(=O)N=C1	2014.7	Standard polar	33892256
5-Methylcytosine,2TMS,isomer #2	CC1=C(N([Si](C)(C)C)[Si](C)(C)C)[NH]C(=O)N=C1	1540.5	Semi standard non polar	33892256
5-Methylcytosine,2TMS,isomer #2	CC1=C(N([Si](C)(C)C)[Si](C)(C)C)[NH]C(=O)N=C1	1671.8	Standard non polar	33892256
5-Methylcytosine,2TMS,isomer #2	CC1=C(N([Si](C)(C)C)[Si](C)(C)C)[NH]C(=O)N=C1	2058.4	Standard polar	33892256
5-Methylcytosine,3TMS,isomer #1	CC1=C(N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)C(=O)N=C1	1756.7	Semi standard non polar	33892256
5-Methylcytosine,3TMS,isomer #1	CC1=C(N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)C(=O)N=C1	1789.4	Standard non polar	33892256
5-Methylcytosine,3TMS,isomer #1	CC1=C(N([Si](C)(C)C)[Si](C)(C)C)N([Si](C)(C)C)C(=O)N=C1	1829.2	Standard polar	33892256
5-Methylcytosine,1TBDMS,isomer #1	CC1=C(N[Si](C)(C)C(C)(C)C)[NH]C(=O)N=C1	1830.8	Semi standard non polar	33892256
5-Methylcytosine,1TBDMS,isomer #1	CC1=C(N[Si](C)(C)C(C)(C)C)[NH]C(=O)N=C1	1825.9	Standard non polar	33892256
5-Methylcytosine,1TBDMS,isomer #1	CC1=C(N[Si](C)(C)C(C)(C)C)[NH]C(=O)N=C1	2366.8	Standard polar	33892256
5-Methylcytosine,1TBDMS,isomer #2	CC1=C(N)N([Si](C)(C)C(C)(C)C)C(=O)N=C1	1795.4	Semi standard non polar	33892256
5-Methylcytosine,1TBDMS,isomer #2	CC1=C(N)N([Si](C)(C)C(C)(C)C)C(=O)N=C1	1803.8	Standard non polar	33892256
5-Methylcytosine,1TBDMS,isomer #2	CC1=C(N)N([Si](C)(C)C(C)(C)C)C(=O)N=C1	2348.2	Standard polar	33892256
5-Methylcytosine,2TBDMS,isomer #1	CC1=C(N[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N=C1	2099.8	Semi standard non polar	33892256
5-Methylcytosine,2TBDMS,isomer #1	CC1=C(N[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N=C1	2109.4	Standard non polar	33892256
5-Methylcytosine,2TBDMS,isomer #1	CC1=C(N[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N=C1	2170.1	Standard polar	33892256
5-Methylcytosine,2TBDMS,isomer #2	CC1=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[NH]C(=O)N=C1	1991.8	Semi standard non polar	33892256
5-Methylcytosine,2TBDMS,isomer #2	CC1=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[NH]C(=O)N=C1	2091.4	Standard non polar	33892256
5-Methylcytosine,2TBDMS,isomer #2	CC1=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[NH]C(=O)N=C1	2188.5	Standard polar	33892256
5-Methylcytosine,3TBDMS,isomer #1	CC1=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N=C1	2336.9	Semi standard non polar	33892256
5-Methylcytosine,3TBDMS,isomer #1	CC1=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N=C1	2397.1	Standard non polar	33892256
5-Methylcytosine,3TBDMS,isomer #1	CC1=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N=C1	2164.5	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - 5-Methylcytosine GC-MS (1 TMS)	splash10-001i-4900000000-73c143c463607343e59d	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Methylcytosine GC-MS (2 TMS)	splash10-0udi-3950000000-332af504e32034e6ea67	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Methylcytosine GC-MS (3 TMS)	splash10-0059-3934000000-6eb3288b70641721809a	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Methylcytosine GC-EI-TOF (Non-derivatized)	splash10-0udi-2970000000-9bae58e66a60384a4b47	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Methylcytosine GC-EI-TOF (Non-derivatized)	splash10-0udi-1890000000-547f8dd8c93c7e653e8c	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Methylcytosine GC-EI-TOF (Non-derivatized)	splash10-0udi-1960000000-eb731b2f4381755effcf	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Methylcytosine GC-EI-TOF (Non-derivatized)	splash10-0fk9-8970000000-8e71ebdb5a55e2426344	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Methylcytosine GC-MS (Non-derivatized)	splash10-001i-4900000000-73c143c463607343e59d	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Methylcytosine GC-MS (Non-derivatized)	splash10-0udi-3950000000-332af504e32034e6ea67	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Methylcytosine GC-MS (Non-derivatized)	splash10-0059-3934000000-6eb3288b70641721809a	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytosine GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-6900000000-cb2ceeb7f5bd935faa19	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Methylcytosine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-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
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine , negative-QTOF	splash10-0089-9600000000-aa86d3c38a48514c2a4d	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine LC-ESI-QQ , positive-QTOF	splash10-004i-0900000000-045ecf28f36874a7b146	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine LC-ESI-QQ , positive-QTOF	splash10-004i-0900000000-17d0aa6deb42e4974069	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine LC-ESI-QQ , positive-QTOF	splash10-0a59-6900000000-2ba4efb5ece00114fe13	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine LC-ESI-QQ , positive-QTOF	splash10-0a59-9300000000-1a71fa46d7b0fd6269f3	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine LC-ESI-QQ , positive-QTOF	splash10-0zgi-9000000000-61088abf446eafee8dd2	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine LC-ESI-QTOF , positive-QTOF	splash10-004i-0900000000-a1c6199ce762a7fb6855	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine LC-ESI-QTOF , positive-QTOF	splash10-004i-1900000000-e85c44ed5cd560d17d60	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine , positive-QTOF	splash10-004i-0900000000-7ce4adb73357e05cc8b5	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine 10V, Positive-QTOF	splash10-004i-3900000000-b2832b699d97e3d2bfaa	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine 10V, Negative-QTOF	splash10-008c-9300000000-7427dfe8792596330411	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine 35V, Positive-QTOF	splash10-004i-0900000000-bb76593a12a5655ad756	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine 20V, Negative-QTOF	splash10-0006-9000000000-011e24f4e333703cb5cb	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine 35V, Positive-QTOF	splash10-004i-0900000000-a84f7e26153cb2255dc5	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine 35V, Positive-QTOF	splash10-004i-0900000000-7e7dde0bdedd7250d617	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine 10V, Positive-QTOF	splash10-004i-0900000000-bb789d0a4d3bce440b9a	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine 30V, Positive-QTOF	splash10-004i-1900000000-e85c44ed5cd560d17d60	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine 40V, Negative-QTOF	splash10-0006-9000000000-efc3476af90e31d453f8	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 5-Methylcytosine 20V, Positive-QTOF	splash10-0a7i-5900000000-e991fa239913a7dfb67d	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytosine 10V, Positive-QTOF	splash10-004i-0900000000-63ea0e71e72b5a60804b	2015-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytosine 20V, Positive-QTOF	splash10-004i-5900000000-8b8c84afdb6f620a4706	2015-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytosine 40V, Positive-QTOF	splash10-0pb9-9300000000-a069a5c69d4eb3143d95	2015-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytosine 10V, Negative-QTOF	splash10-00di-1900000000-04225473bccf83af00d8	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytosine 20V, Negative-QTOF	splash10-00e9-9500000000-e5c525a63af7fcf81390	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Methylcytosine 40V, Negative-QTOF	splash10-0006-9000000000-8eb88ca79a619c9357ae	2015-09-15	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

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

Cytoplasm (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Fibroblasts

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

FDB004432

KNApSAcK ID

Not Available

Chemspider ID

58551

KEGG Compound ID

C02376

BioCyc ID

CPD0-2018

BiGG ID

Not Available

Wikipedia Link

5-Methylcytosine

METLIN ID

3247

PubChem Compound

65040

PDB ID

Not Available

ChEBI ID

27551

Food Biomarker Ontology

Not Available

VMH ID

5MTC

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Umetani, Hideki. Method for preparing 5-methylcytosine. Jpn. Kokai Tokkyo Koho (2006), 8 pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Pfeifer GP, You YH, Besaratinia A: Mutations induced by ultraviolet light. Mutat Res. 2005 Apr 1;571(1-2):19-31. Epub 2005 Jan 20. [PubMed:15748635 ]

Enzymes

Enzyme Details

1. DNA (cytosine-5)-methyltransferase 3A

General function:: Involved in DNA binding
Specific function:: Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. It modifies DNA in a non-processive manner and also methylates non-CpG sites. May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. Plays a role in paternal and maternal imprinting. Required for methylation of most imprinted loci in germ cells. Acts as a transcriptional corepressor for ZNF238. Can actively repress transcription through the recruitment of HDAC activity (By similarity).
Gene Name:: DNMT3A
Uniprot ID:: Q9Y6K1
Molecular weight:: 101857.595

Enzyme Details

2. DNA (cytosine-5)-methyltransferase 3B

General function:: Involved in DNA binding
Specific function:: Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 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. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1.
Gene Name:: DNMT3B
Uniprot ID:: Q9UBC3
Molecular weight:: 81309.795

Enzyme Details

3. tRNA (cytosine(38)-C(5))-methyltransferase

General function:: Involved in DNA binding
Specific function:: Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp).
Gene Name:: TRDMT1
Uniprot ID:: O14717
Molecular weight:: 44596.17

Enzyme Details

4. tRNA (cytosine(34)-C(5))-methyltransferase

General function:: Involved in tRNA (cytosine-5-)-methyltransferase activity
Specific function:: RNA methyltransferase that methylates tRNAs, and possibly RNA polymerase III transcripts. Methylates cytosine to 5-methylcytosine (m5C) at position 34 of intron-containing tRNA(Leu)(CAA) precursors. Not able to modify tRNAs at positions 48 or 49. May act downstream of Myc to regulate epidermal cell growth and proliferation. Required for proper spindle assembly and chromosome segregation, independently of its methyltransferase activity.
Gene Name:: NSUN2
Uniprot ID:: Q08J23
Molecular weight:: 82392.405

Enzyme Details

5. Cytosine-specific methyltransferase

General function:: Involved in DNA binding
Specific function:: S-adenosyl-L-methionine + DNA = S-adenosyl-L- homocysteine + DNA containing 5-methylcytosine
Gene Name:: Not Available
Uniprot ID:: Q59FP7
Molecular weight:: 182018.2

Showing metabocard for 5-Methylcytosine (HMDB0002894)

MOL for HMDB0002894 (5-Methylcytosine)

3D MOL for HMDB0002894 (5-Methylcytosine)

3D SDF for HMDB0002894 (5-Methylcytosine)

3D-SDF for HMDB0002894 (5-Methylcytosine)

PDB for HMDB0002894 (5-Methylcytosine)

3D PDB for HMDB0002894 (5-Methylcytosine)

SMILES for HMDB0002894 (5-Methylcytosine)

INCHI for HMDB0002894 (5-Methylcytosine)

Structure for HMDB0002894 (5-Methylcytosine)

3D Structure for HMDB0002894 (5-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

Enzymes