NP-MRD: Showing NP-Card for 5-Methylcytosine (NP0002733)

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Record Information

Version

1.0

Created at

2020-11-23 19:39:05 UTC

Updated at

2024-04-19 09:50:52 UTC

NP-MRD ID

NP0002733

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-Methylcytosine

Provided By

BMRB

Description

5-Methylcytosine 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. 5-Methylcytosine exists in all living organisms, ranging from bacteria to humans. 5-Methylcytosine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. 5-Methylcytosine is found in Luffa acutangula. It was first documented in 2005 (PMID: 15748635). Based on a literature review a significant number of articles have been published on 5-Methylcytosine (PMID: 22770225) (PMID: 17984079) (PMID: 29565828) (PMID: 17325422).

Structure

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


     RDKit          2D

 16 16  0  0  0  0  0  0  0  0999 V2000
   -2.0734    0.2942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5869    0.4944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0169    1.8819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4696    2.0821    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3863    0.8948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8729    1.0950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8164   -0.4927    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3298   -0.6929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2401   -2.0804    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2736    1.7808    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8733   -1.1923    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5600    0.0940    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9336    3.0693    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7330   -1.6800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6765   -3.2677    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7267   -2.2806    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  8  2  2  0
  1 10  1  1
  1 11  1  0
  1 12  1  0
  3 13  1  0
  7 14  1  0
  9 15  1  0
  9 16  1  0
M  END
> <DATABASE_ID>
NP0002733

> <DATABASE_NAME>
NP-MRD

> <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

> <FORMULA>
C5H7N3O

> <MOLECULAR_WEIGHT>
125.1286

> <EXACT_MASS>
125.058911861

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
11.885321543269935

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-amino-5-methyl-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-0.63

> <JCHEM_LOGP>
-0.7520553023333332

> <ALOGPS_LOGS>
-1.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.078245303541685

> <JCHEM_PKA_STRONGEST_BASIC>
3.746117471149919

> <JCHEM_POLAR_SURFACE_AREA>
67.48

> <JCHEM_REFRACTIVITY>
42.371900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.91e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-methylcytosine

> <JCHEM_VEBER_RULE>
0

$$$$

View in JSmol

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	MeSH, HMDB
5 Methylcytosine	MeSH, HMDB
5 Methylcytosine monohydrochloride	MeSH, HMDB
5-Methylcytosine monohydrochloride	MeSH, HMDB

Chemical Formula

C₅H₇N₃O

Average Mass

125.1286 Da

Monoisotopic Mass

125.05891 Da

IUPAC Name

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

Traditional Name

5-methylcytosine

CAS Registry Number

Not Available

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

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	[¹H, ] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	Not Available	Not Available	2023-08-15	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	bgnzk@missouri.edu	Not Available	Not Available	2023-08-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Luffa acutangula	LOTUS Database	35616633
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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

Not Available

Substituents

Not Available

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
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

External Links

HMDB ID

HMDB0002894

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

General References

Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C: Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem. 2012 Aug 7;84(15):6429-37. doi: 10.1021/ac300829f. Epub 2012 Jul 17. [PubMed:22770225 ]
Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
Pan L, Yu J, Mi Z, Mo L, Jin H, Yao C, Ren D, Menghe B: A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation). Molecules. 2018 Mar 22;23(4). pii: molecules23040735. doi: 10.3390/molecules23040735. [PubMed:29565828 ]
Pfeifer GP, You YH, Besaratinia A: Mutations induced by ultraviolet light. Mutat Res. 2005 Apr 1;571(1-2):19-31. doi: 10.1016/j.mrfmmm.2004.06.057. Epub 2005 Jan 20. [PubMed:15748635 ]
Widschwendter M: 5-methylcytosine--the fifth base of DNA: the fifth wheel on a car or a highly promising diagnostic and therapeutic target in cancer? Dis Markers. 2007;23(1-2):1-3. doi: 10.1155/2007/860404. [PubMed:17325422 ]

Showing NP-Card for 5-Methylcytosine (NP0002733)

MOL for NP0002733 (5-Methylcytosine)

3D MOL for NP0002733 (5-Methylcytosine)

3D SDF for NP0002733 (5-Methylcytosine)

3D-SDF for NP0002733 (5-Methylcytosine)

PDB for NP0002733 (5-Methylcytosine)

3D PDB for NP0002733 (5-Methylcytosine)

SMILES for NP0002733 (5-Methylcytosine)

INCHI for NP0002733 (5-Methylcytosine)

Structure for NP0002733 (5-Methylcytosine)

3D Structure for NP0002733 (5-Methylcytosine)