Showing Compound 5-Methyldeoxycytidine (FDB022917)

Record Information

Version

1.0

Creation date

2011-09-21 00:21:41 UTC

Update date

2015-07-21 06:57:25 UTC

Primary ID

FDB022917

Secondary Accession Numbers

Not Available

Chemical Information

FooDB Name

5-Methyldeoxycytidine

Description

5-Methyldeoxycytidine is a dinucleotide. Methylation of cytosine-guanine dinucleotide sequences (CpG dinucleotides) catalyzed by DNA methyltransferase, particularly in the 5′-promoter regions of mammalian genes, forms 5-methyldeoxycytidine (5-mdc) whose levels may regulate gene expression. Levels of 5-mdc and the expression of nm23-H1 (an anti-metastatic gene identified in and human cancer lines) are highly correlated with human hepatoma cells with different invasion activities. DNA hypermethylation is a common finding in malignant cells and has been explored as a therapeutic target for hypomethylating agents. The levels of 5-mdc in the urine of patients with breast cancer is not significantly different than controls. (PMID: 17044778, 17264127, 16799933) [HMDB]

CAS Number

838-07-3

Structure

MOL SDF PDB SMILES InChI

Synonyms

Predicted Properties

Property	Value	Source
Water Solubility	10.8 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-1.5	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	0.41	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	108.38 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	57.39 m³·mol⁻¹	ChemAxon
Polarizability	23.34 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Chemical Formula

C10H15N3O4

IUPAC name

4-amino-1-[(2R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one

InChI Identifier

InChI=1S/C10H15N3O4/c1-5-3-13(10(16)12-9(5)11)8-2-6(15)7(4-14)17-8/h3,6-8,14-15H,2,4H2,1H3,(H2,11,12,16)/t6?,7-,8-/m1/s1

InChI Key

LUCHPKXVUGJYGU-SPDVFEMOSA-N

Isomeric SMILES

CC1=CN([C@H]2CC(O)[C@@H](CO)O2)C(=O)N=C1N

Average Molecular Weight

241.2438

Monoisotopic Molecular Weight

241.106255983

Classification

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Disposition

Source:

Endogenous

Physico-Chemical Properties

Physico-Chemical Properties - Experimental

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Property	Value	Reference
Boiling Point	Not Available
Charge	Not Available
Density	Not Available
Experimental logP	Not Available
Experimental pKa	Not Available
Experimental Water Solubility	Not Available
Isoelectric point	Not Available
Mass Composition	Not Available
Melting Point	Not Available
Optical Rotation	Not Available

Showing 1 to 10 of 14 entries

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
Predicted GC-MS	5-Methyldeoxycytidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0006-9420000000-4af773e99af76af961ea	Spectrum
Predicted GC-MS	5-Methyldeoxycytidine, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0006-9014000000-1fd11a88c9a0762a6b1d	Spectrum
Predicted GC-MS	5-Methyldeoxycytidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-d1d23649ec4fa9201eba	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-2900000000-d21a1bb287e1d523b6c2	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-3900000000-b4f3cca0a164fdbc5031	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4j-0920000000-6aa55dc948aac874e1a0	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0uk9-2920000000-6d51e08eb5820a748902	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-007p-9400000000-77fb64e0199129096777	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00dl-0970000000-a011cf5a5c3613811717	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00dl-9600000000-ee60e868c938ff348f09	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-006y-9500000000-81204e67016c197ad16f	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-a1c51dd1d9ae2dee6e38	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00b9-2900000000-7c9c6f54bbfba0acc135	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0059-6900000000-9559671d86d852719546	2021-09-24	View Spectrum

NMR

Not Available

External Links

ChemSpider ID

12719

ChEMBL ID

Not Available

KEGG Compound ID

C03592

Pubchem Compound ID

13279

Pubchem Substance ID

Not Available

ChEBI ID

27964

Phenol-Explorer ID

Not Available

DrugBank ID

Not Available

HMDB ID

HMDB02224

CRC / DFC (Dictionary of Food Compounds) ID

Not Available

EAFUS ID

Not Available

Dr. Duke ID

Not Available

BIGG ID

Not Available

KNApSAcK ID

Not Available

HET ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

Flavornet ID

Not Available

GoodScent ID

Not Available

SuperScent ID

Not Available

Wikipedia ID

Not Available

Phenol-Explorer Metabolite ID

Not Available

Duplicate IDS

Not Available

Old DFC IDS

Not Available

Associated Foods

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Food	Content Range	Average	Reference

Anatidae	Expected but not quantified	Not Available	HMDB
Beefalo	Expected but not quantified	Not Available	HMDB
Bison	Expected but not quantified	Not Available	HMDB
Buffalo	Expected but not quantified	Not Available	HMDB
Cattle (Beef, Veal)	Expected but not quantified	Not Available	HMDB
Chicken	Expected but not quantified	Not Available	HMDB
Columbidae (Dove, Pigeon)	Expected but not quantified	Not Available	HMDB
Deer	Expected but not quantified	Not Available	HMDB
Domestic goat	Expected but not quantified	Not Available	HMDB
Domestic pig	Expected but not quantified	Not Available	HMDB