Summary

Full name2'-O-methylcytidine
IUPAC name4-amino-1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]pyrimidin-2-one
Short nameCm
MODOMICS code0C
Synonyms
2140-72-9
2NULL-O-Methylcytidine
2'-O-Methyl cytidine
2''-O-Methylcytidine
2'-O-Methylcytidine
2/'-O-Methylcytidine
2'-O-METHYL-CYTIDINE
2-O-METHYLCYTIDINE 1G
2-O-METHYLCYTIDINE 200MG
2'-O-Methylcytidine =98.0% (by HPLC, titration analysis)
2'-O-Methylcytidine, 99% - 1G 1g
4-amino-1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]pyrimidin-2-one
4-amino-1-((2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxytetrahydrofuran-2-yl)pyrimidin-2(1H)-one
4-amino-1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxy-tetrahydrofuran-2-yl]pyrimidin-2-one
4-Amino-1-((2R,3R,4S,5R)-4-hydroxy-5-hydroxymethyl-3-methoxy-tetrahydro-furan-2-yl)-1H-pyrimidin-2-one
4-Imino-1-(2-O-methylpentofuranosyl)-1,4-dihydropyrimidin-2-ol
58970-16-4
5XD9IH2G27
AB0011995
AC1L45EF
AIDS338901
AJ-55451
AK-54700
AKOS015850975
AKOS015896935
ANW-54599
BRD-K23276845-001-01-1
C10H15N3O5
CHEBI:19228
CHEMBL176605
CID150971
CJ-12849
CM-782
CTK1A1816
Cytidine, 2'-O-methyl-
DS-14587
DTXSID50943958
M-3929
MFCD00056067
O-2-Methylcytidine
O(2')-Methylcytidine
O2'-Methylcytidine
PubChem11055
Q15632793
RFCQJGFZUQFYRF-ZOQUXTDFSA-N
RP29164
SC-23539
SCHEMBL64632
TC-071340
TL8001776
UNII-5XD9IH2G27
ZB1481
ZINC5998209

Nature of the modified residueNatural
RNAMods codeB
Residue unique ID84
Found in RNAYes
Related nucleotides201
Enzymes Nop1 (Saccharomyces cerevisiae)
RlmM (Escherichia coli)
RsmI (Escherichia coli)
Trm13 (Saccharomyces cerevisiae)
Trm7 (Saccharomyces cerevisiae)
TrmJ (Escherichia coli)
TrmJ (Sulfolobus acidocaldarius)
TrmL (Escherichia coli)
aTrm56 (Pyrococcus abyssi)
Found in phylogenyEubacteria, Eukaryota
Found naturally in RNA typesrRNA, snRNA, tRNA

Chemical information

Sum formulaC10H15N3O5
Type of moietynucleoside
Degeneracynot applicable
PubChem ID150971
SMILESCO[C@H]1[C@H]([n]2ccc(N)nc2=O)O[C@H](CO)[C@H]1O
logP-1.3277
TPSA119.83
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)3
PDB no exac match , link to the most similar ligand AR3
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000089
InChIInChI=1S/C10H15N3O5/c1-17-8-7(15)5(4-14)18-9(8)13-3-2-6(11)12-10(13)16/h2-3,5,7-9,14-15H,4H2,1H3,(H2,11,12,16)/t5-,7-,8-,9-/m1/s1
InChIKeyRFCQJGFZUQFYRF-ZOQUXTDFSA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs
801056
10250947
15416822
29214868
46227564
49831747
57347190
77346497
91749329
103441186
104429828
126664465
129120328
135108104
135585796
136911144
143236511
151990394
152036354
152245336
160657122
160822097
162175374
162496560
163383576
164229403
174560184
175423279
185987991
223379288
223498203
223564622
223792906
226445864
241101737
249721735
249759708
249982662
250200716
251900509
252225442
252256384
252314595
252410163
255410879
257895262
273518004
275876015
297447005
312237489
312599979
315442304
316538427
316961327
316967635
318050292
319455920
321933324
322089326
340561650
341246747
342465010
346692074
348902055
355102238
355215592
363671139
363909403
371640619
374045231
375322429
375628575
376131879
376738012
378019845
381018174
381385313
381933237
383212602
383533389
384501008
385642111
386478384
388827357
402322406
402322407
402403354
404623000
404825315
406587671
406670241
419580315
434694283
438515816
439452479
441087783
441412899
441579669
443498294
443555473

* 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
COC1C(n2ccc(=N)[nH]c2=O)OC(CO)C1O tautomer #0
COC1C(n2ccc(N)nc2=O)OC(CO)C1O tautomer #1
COC1C(n2ccc(=N)nc2O)OC(CO)C1O tautomer #2

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
Cm Cm Cm

* 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]+258.1082
Product ions112
Normalized LC elution time *0,90 (Kellner 2014); 0,92 (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 O2

Reactions producing 2'-O-methylcytidine

Name
C:Cm

Reactions starting from 2'-O-methylcytidine

Name
Cm:m4Cm
Cm:m5Cm
Cm:ac4Cm
Cm:f5Cm

Last modification of this entry: Sept. 29, 2021


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