U.S. Department of Health & Human Services Divider Arrow National Institutes of Health Divider Arrow NCATS

Details

Stereochemistry ABSOLUTE
Molecular Formula C10H15N3O5
Molecular Weight 257.2432
Optical Activity UNSPECIFIED
Defined Stereocenters 4 / 4
E/Z Centers 0
Charge 0

SHOW SMILES / InChI
Structure of 5-METHYLCYTIDINE

SMILES

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

InChI

InChIKey=ZAYHVCMSTBRABG-JXOAFFINSA-N
InChI=1S/C10H15N3O5/c1-4-2-13(10(17)12-8(4)11)9-7(16)6(15)5(3-14)18-9/h2,5-7,9,14-16H,3H2,1H3,(H2,11,12,17)/t5-,6-,7-,9-/m1/s1

HIDE SMILES / InChI

Molecular Formula C10H15N3O5
Molecular Weight 257.2432
Charge 0
Count
Stereochemistry ABSOLUTE
Additional Stereochemistry No
Defined Stereocenters 4 / 4
E/Z Centers 0
Optical Activity UNSPECIFIED

5-methyl cytidine has been indicated in the controlling mechanism for the genetic change, which leads to cancer. Human APOBEC3A (A3A), a polynucleotide cytidine deaminase (PCD) with specificity for single stranded DNA, can extensively deaminate human nuclear DNA. It was discovered that A3A among all human PCDs can deaminate 5-methylcytidine in a variety of single stranded DNA substrates both in vitro and in transfected cells almost as efficiently as cytidine itself. As 5MeCpG deamination hotspots characterize many genes associated with cancer it was made suggestion that A3A is a major player in the onset of cancer.

Approval Year

Targets

Targets

Primary TargetPharmacologyConditionPotency
Target ID: P31941
Gene ID: 100913187|||200315
Gene Symbol: APOBEC3A
Target Organism: Homo sapiens (Human)
Conditions

Conditions

ConditionModalityTargetsHighest PhaseProduct
Diagnostic
Unknown

Approved Use

Unknown
PubMed

PubMed

TitleDatePubMed
Inhibition of urethan induced lung tumour growth in strain A mice by 5-methyl cytidine.
1980
The nature of cancer and the mechanisms of its control: a review.
1980
Monitoring of urinary excretion of modified nucleosides in cancer patients using a set of six monoclonal antibodies.
1992 Jan 31
Immunochemical detection of urinary 5-methyl-2'-deoxycytidine as a potential biologic marker for leukemia.
1995 Jan 31
Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming.
2004 Dec 10
Kilo-scale synthesis process for 2'-O-(2-methoxyethyl)-pyrimidine derivatives.
2005
Global DNA methylation evaluation: potential complementary marker in differential diagnosis of thyroid neoplasia.
2005 Jul
Epigenetic regulation: DNA confers identity but is not enough to maintain it.
2006
The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain.
2006 Jul 21
Modified nucleosides: an accurate tumour marker for clinical diagnosis of cancer, early detection and therapy control.
2006 Jun 5
Incorporation of two modified nucleosides allows selective platination of an oligonucleotide making it suitable for duplex cross-linking.
2007 Aug
DNA methylation and histone acetylation patterns in cultured bovine fibroblasts for nuclear transfer.
2007 Dec
Collision-induced dissociation of cytidine and its derivatives.
2007 Jan
Metabolic signature of breast cancer cell line MCF-7: profiling of modified nucleosides via LC-IT MS coupling.
2007 Nov 29
Postembryonic establishment of megabase-scale gene silencing in nucleolar dominance.
2007 Nov 7
Increased urinary level of oxidized nucleosides in patients with mild-to-moderate Alzheimer's disease.
2007 Sep
Modulation by decitabine of gene expression and growth of osteosarcoma U2OS cells in vitro and in xenografts: identification of apoptotic genes as targets for demethylation.
2007 Sep 10
Functional group and substructure searching as a tool in metabolomics.
2008 Feb 6
Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes.
2008 Jun 27
Modifications in small interfering RNA that separate immunostimulation from RNA interference.
2008 Mar 1
Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1.
2008 May 15
Methylated DNA immunoprecipitation (MeDIP).
2009
Epigenetic differences in cortical neurons from a pair of monozygotic twins discordant for Alzheimer's disease.
2009 Aug 12
A novel method to assess the full genome methylation profile using monoclonal antibody combined with the high throughput based microarray approach.
2009 Aug 16
Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine.
2009 Feb
Specific loss of histone H3 lysine 9 trimethylation and HP1gamma/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD).
2009 Jul
Remodeling of the chromatin structure of the facioscapulohumeral muscular dystrophy (FSHD) locus and upregulation of FSHD-related gene 1 (FRG1) expression during human myogenic differentiation.
2009 Jul 16
DNA methyltransferase-mediated transcriptional silencing in malignant glioma: a combined whole-genome microarray and promoter array analysis.
2009 Jul 23
Frequent long-range epigenetic silencing of protocadherin gene clusters on chromosome 5q31 in Wilms' tumor.
2009 Nov
Titrimetric immunohistochemical evaluation of DNA hypomethylation in uterine tumours.
2009 Nov
Development of a novel output value for quantitative assessment in methylated DNA immunoprecipitation-CpG island microarray analysis.
2009 Oct
Accurate measurement of DNA methylation that is traceable to the international system of units.
2009 Sep 1
Effect of IVF and laser zona dissection on DNA methylation pattern of mouse zygotes.
2009 Sep-Oct
Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus.
2010 Aug
Trichostatin A and 5-azacytidine both cause an increase in global histone H4 acetylation and a decrease in global DNA and H3K9 methylation during mitosis in maize.
2010 Aug 18
Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.
2010 Aug 20
Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase.
2010 Dec
A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress.
2010 Dec 16
Ribonucleoside labeling with Os(VI): a methodological approach to evaluation of RNA methylation by HPLC-ICP-MS.
2010 Feb
Generation of a recombinant single-chain variable fragment (scFv) targeting 5-methyl-2'-deoxycytidine.
2010 Jan
Genome-wide DNA methylation profiling reveals novel epigenetically regulated genes and non-coding RNAs in human testicular cancer.
2010 Jan 19
Altered intra-nuclear organisation of heterochromatin and genes in ICF syndrome.
2010 Jun 29
Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns.
2010 Nov
AutoMeDIP-seq: a high-throughput, whole genome, DNA methylation assay.
2010 Nov
Concomitant heterochromatinisation and down-regulation of gene expression unveils epigenetic silencing of RELB in an aggressive subset of chronic lymphocytic leukemia in males.
2010 Nov 10
Label-free DNA methylation analysis using opto-fluidic ring resonators.
2010 Nov 15
Transcriptome, methylome and genomic variations analysis of ectopic thyroid glands.
2010 Oct 15
Transfer RNA modifications and genes for modifying enzymes in Arabidopsis thaliana.
2010 Sep 14
Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA.
2010 Sep 16
Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome.
2010 Sep 30
Patents

Sample Use Guides

In Vivo Use Guide
Unknown
Route of Administration: Unknown
In Vitro Use Guide
Curator's Comment: As several TP53 CpG methylation sites are mutational hotspots in cancer, an oligodeoxynucleotide corresponding to part of exon 8 was synthesized with 5-methylcytidine (5MeC) incorporated at two known sites of methylation in codons 273 and 282. Following incubation with purified myc-His6-tagged A3A (human APOBEC3A (A3A), a polynucleotide cytidine deaminase (PCD)) and recovery of products by standard PCR, both 5MeC and C were readily deaminated in a comparable manner. Given that 5MeC is deaminated by A3A the singularity of 5MeCpG mutation hotspots in cancer probably has more to do with the relative efficiency of T:G mismatch repair compared to highly efficient U:G repair initiated by UNG.
Unknown
Substance Class Chemical
Created
by admin
on Sat Dec 16 09:45:07 GMT 2023
Edited
by admin
on Sat Dec 16 09:45:07 GMT 2023
Record UNII
TL9PB228DC
Record Status Validated (UNII)
Record Version
  • Download
Name Type Language
5-METHYLCYTIDINE
Systematic Name English
4-AMINO-1-.BETA.-D-ARABINOFURANOSYL-5-METHYLPYRIMIDIN-2(1H)-ONE
Systematic Name English
5-METHYL-CYTIDINE
Systematic Name English
NSC-363933
Code English
CYTARABINE IMPURITY I [EP IMPURITY]
Common Name English
CYTIDINE, 5-METHYL-
Systematic Name English
Code System Code Type Description
NSC
363933
Created by admin on Sat Dec 16 09:45:07 GMT 2023 , Edited by admin on Sat Dec 16 09:45:07 GMT 2023
PRIMARY
PUBCHEM
92918
Created by admin on Sat Dec 16 09:45:07 GMT 2023 , Edited by admin on Sat Dec 16 09:45:07 GMT 2023
PRIMARY
CAS
2140-61-6
Created by admin on Sat Dec 16 09:45:07 GMT 2023 , Edited by admin on Sat Dec 16 09:45:07 GMT 2023
PRIMARY
EPA CompTox
DTXSID401016977
Created by admin on Sat Dec 16 09:45:07 GMT 2023 , Edited by admin on Sat Dec 16 09:45:07 GMT 2023
PRIMARY
WIKIPEDIA
5-Methylcytidine
Created by admin on Sat Dec 16 09:45:07 GMT 2023 , Edited by admin on Sat Dec 16 09:45:07 GMT 2023
PRIMARY
FDA UNII
TL9PB228DC
Created by admin on Sat Dec 16 09:45:07 GMT 2023 , Edited by admin on Sat Dec 16 09:45:07 GMT 2023
PRIMARY
ECHA (EC/EINECS)
218-390-8
Created by admin on Sat Dec 16 09:45:07 GMT 2023 , Edited by admin on Sat Dec 16 09:45:07 GMT 2023
PRIMARY
Related Record Type Details
PARENT -> IMPURITY