Summary

Full name5-methylcytidine
IUPAC name4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one
Short namem5C
MODOMICS code5C
Synonyms
140M616
2140-61-6
21917-99-7
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one
4-amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-methylpyrimidin-2(1H)-one
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methyl-pyrimidin-2-one
5-methyl-cytidine
5-Methylcytidine
5-Methylcytidine, 98% - 250MG 250mg
5-Methylcytidine, >=99%
5-Methyl-D-cytidine
AC1L3P3S
AC1Q6C23
AC-32357
Adenosine receptor agonist, 13
AJ-55618
AKOS015841917
AKOS015896918
AM83948
ANW-24421
AR-1G9002
BDBM200216
BRD-K65963527-001-01-8
C016568
CHEBI:20607
CHEMBL72086
CID92918
CS-0061684
CTK4E6675
Cytidine, 5-methyl-
Cytidine,5-methyl-
DS-8104
DTXSID401016977
EINECS 218-390-8
HY-113135
J-700100
M1931
m5C
MFCD00006548
NS00049274
NSC 363933
Q238546
s6138
SB35398
SC-21988
SCHEMBL41572
ST24044891
TL9PB228DC
TR-010033
UNII-TL9PB228DC
ZAYHVCMSTBRABG-JXOAFFINSA-N
ZINC6069529

Nature of the modified residueNatural
RNAMods code?
Residue unique ID18
Found in RNAYes
Related nucleotides186
Enzymes Dnmt2 (Homo sapiens)
Dnmt2 (Geobacter sulfurreducens)
EfmM (Enterococcus faecium)
Nop2 (Saccharomyces cerevisiae)
Rcm1 (Saccharomyces cerevisiae)
RlmI (Escherichia coli)
RlmO (Thermus thermophilus)
RsmB (Escherichia coli)
RsmF (Escherichia coli)
RsmF (Thermus thermophilus)
Trm4 (Saccharomyces cerevisiae)
Trm4 (Homo sapiens)
Trm4 (Pyrococcus abyssi)
Found in phylogenyEubacteria, Eukaryota
Found naturally in RNA typesmRNA, other, pre-tRNA, rRNA, tRNA

Chemical information

Sum formulaC10H15N3O5
Type of moietynucleoside
Degeneracynot applicable
PubChem ID92918
SMILESCc1c(N)nc(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c1
logP-1.6734
TPSA130.83
Number of atoms18
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)8
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand LKC
HMDB (Human Metabolome Database) exact match HMDB0000982
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000982
InChIInChI=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
InChIKeyZAYHVCMSTBRABG-JXOAFFINSA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs
815326
10225671
14774542
24896915
29214844
44423697
57335431
75800430
87560073
91721514
103145862
103271758
104408709
117588044
129876515
134224800
135052146
135566007
137355391
151981336
152036337
160657129
160791922
162219849
162814992
172087712
223564789
223998396
226426571
241178151
242081427
245818154
249759710
249864163
250002515
250220429
251881229
252228290
252374069
252410161
254758636
255470550
257912919
273528946
275952070
307086811
310140474
310276661
312225981
312343744
316468249
318590040
319492509
321933318
322082902
341113669
341161674
341838841
342526804
347244535
348274963
348902041
354309139
355042688
355133158
355209175
363669363
371430445
374062076
374168277
375147464
375294029
375670696
375987065
375987316
376125548
378020099
381019030
381385316
383236855
384407875
385646582
386482968
387183040
388623471
404640182
404759472
404825303
405534879
406528657
419508928
433774779
433775277
433776078
433776347
433776727
434699392
435375272
439442517
440703486
440822249
441394237
441656420
443498293
443556463

* Chemical properties calculated with Open Babel - O'Boyle et al. Open Babel: An open chemical toolbox. J Cheminform 3, 33 (2011) (link)


Download Structures

2D   .png .mol .mol2 .sdf .pdb .smi
3D   .mol .mol2 .sdf .pdb

Tautomers

Tautomers SMILES
Cc1c(=N)[nH]c(=O)n(C2C(O)C(O)C(CO)O2)c1 tautomer #0
Cc1c(N)nc(=O)n(C2C(O)C(O)C(CO)O2)c1 tautomer #1
Cc1c(=N)nc(O)n(C2C(O)C(O)C(CO)O2)c1 tautomer #2

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
m5C m5C m5C

* CYP Metabolic sites predicted with SMARTCyp. SMARTCyp is a method for prediction of which sites in a molecule that are most liable to metabolism by Cytochrome P450. It has been shown to be applicable to metabolism by the isoforms 1A2, 2A6, 2B6, 2C8, 2C19, 2E1, and 3A4 (CYP3A4), and specific models for the isoform 2C9 (CYP2C9) and isoform 2D6 (CYP2D6). CYP3A4, CYP2D6, and CYP2C9 are the three of the most important enzymes in drug metabolism since they are involved in the metabolism of more than half of the drugs used today. The three top-ranked atoms are highlighted. See: SmartCYP and SmartCYP - background; Patrik Rydberg, David E. Gloriam, Lars Olsen, The SMARTCyp cytochrome P450 metabolism prediction server, Bioinformatics, Volume 26, Issue 23, 1 December 2010, Pages 2988–2989 (link)


LC-MS Information

Monoisotopic mass257.1012
Average mass257.243
[M+H]+258.109
Product ions126
Normalized LC elution time *0,82 (Kellner 2014); 0,84 (Kellner 2014)
LC elution order/characteristicsbetween U and G (Kellner 2014, Kellner 2014)

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.


LC-MS Publications

Title Authors Journal Details PubMed Id DOI
Profiling of RNA modifications by multiplexed stable isotope labelling. Kellner S, Neumann J, Rosenkranz D, Lebedeva S, Ketting RF, Zischler H, Schneider D, Helm M. Chem Commun (Camb). [details] 24567952 -
Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Su D, Chan CT, Gu C, Lim KS, Chionh YH, McBee ME, Russell BS, Babu IR, Begley TJ, Dedon PC... Nat Protoc [details] 24625781 -
Absolute and relative quantification of RNA modifications via biosynthetic isotopomers. Kellner S, Ochel A, Thuring K, Spenkuch F, Neumann J, Sharma S, Entian KD, Schneider D, Helm M... Nucleic Acids Res [details] 25129236 -

Chemical groups contained

TypeSubtype
methyl groupmethyl at aromatic C

Reactions producing 5-methylcytidine

Name
C:m5C

Reactions starting from 5-methylcytidine

Name
m5C:m5Cm

Publications

Title Authors Journal Details PubMed Id DOI
A map of 5-methylcytosine residues in Trypanosoma brucei tRNA revealed by sodium bisulfite sequencing. Militello KT, Chen LM, Ackerman SE, Mandarano AH, Valentine EL Mol Biochem Parasitol [details] 24389163 10.1016

Last modification of this entry: Sept. 29, 2021


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