Summary

Full name2'-O-methyluridine
IUPAC name1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]pyrimidine-2,4-dione
Short nameUm
MODOMICS code0U
Synonyms
1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]pyrimidine-2,4-dione
1-((2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxytetrahydrofuran-2-yl)pyrimidine-2,4(1H,3H)-dione
1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxy-tetrahydrofuran-2-yl]pyrimidine-2,4-dione
140M763
2 inverted exclamation marka-O-Methyluridine
2' -O-Methyluridine
2140-76-3
21919-02-8
2'-Methyoxy uridine
2NULL-O-Methyl uridine
2'-O-Methyl Uridine
2-O-Methyluridine
2'-O-methyl-uridine
2'-O-Methyluridine
2/'-O-Methyluridine
2'-O-Methyluridine, 99% - 1G 1g
2'-o-Methyluridine, AldrichCPR
399VZB6TMB
4-Hydroxy-1-(2-O-methylpentofuranosyl)pyrimidin-2(1H)-one
AC1L2SDP
AJ-55450
AKOS015850961
AKOS015919383
AN-15690
ANW-24423
AR-1E4536
AS-12177
C10H14N2O6
CHEBI:19227
CID102212
CJ-12848
CM-320
CS-W012540
CTK1A2705
DB-006206
DTXSID10943959
J-700070
Jsp004357
KSC202O0L
M-1525
MFCD00056054
O(2')-Methyluridine
O2'-Methyluridine
Q15632791
RP29162
RW1284
SCHEMBL25866
ST2403033
SXUXMRMBWZCMEN-ZOQUXTDFSA-N
TL8006287
um
UNII-399VZB6TMB
Uridine, 2'-O-methyl-
ZINC5998208

Nature of the modified residueNatural
RNAMods codeJ
Residue unique ID50
Found in RNAYes
Related nucleotides205
Enzymes AviRb (Streptomyces viridochromogenes)
MRM2 (Homo sapiens)
Mrm2 (Saccharomyces cerevisiae)
Nop1 (Saccharomyces cerevisiae)
RlmE (Escherichia coli)
Spb1 (Saccharomyces cerevisiae)
Trm44 (Saccharomyces cerevisiae)
TrmJ (Escherichia coli)
TrmL (Escherichia coli)
aTrm56 (Pyrococcus horikoshii)
Found in phylogenyArchaea, Eubacteria, Eukaryota
Found naturally in RNA typesrRNA, snRNA, snoRNA, tRNA

Chemical information

Sum formulaC10H14N2O6
Type of moietynucleoside
Degeneracynot applicable
SMILESCO[C@H]1[C@H]([n]2ccc(=O)[nH]c2=O)O[C@H](CO)[C@H]1O
logP-2.1978
TPSA113.78
Number of atoms18
Number of Hydrogen Bond Acceptors 1 (HBA1)6
Number of Hydrogen Bond Acceptors 2 (HBA2)7
Number of Hydrogen Bond Donors (HBD)3
PDB no exac match , link to the most similar ligand URI
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000296
InChIInChI=1S/C10H14N2O6/c1-17-8-7(15)5(4-13)18-9(8)12-3-2-6(14)11-10(12)16/h2-3,5,7-9,13,15H,4H2,1H3,(H,11,14,16)/t5-,7-,8-,9-/m1/s1
InChIKeySXUXMRMBWZCMEN-ZOQUXTDFSA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs
10232469
14819530
44432149
49836090
50265554
57337603
91750291
96022813
103121401
104366298
126670798
129304264
135059796
135668170
136990985
140033897
151990380
152058802
152226274
160791924
162174561
162247716
162497384
163803927
164031795
174560182
201503735
223498202
223564621
223664197
223834798
226413856
249716236
249823573
249951665
250200717
252219133
252315137
252375465
252391303
252410164
252450043
252452566
255402313
257895261
273518002
275871730
310277200
310825929
312237488
312343715
313079671
313188999
315442302
316541920
318044642
319473225
321933319
322082003
329793623
341113091
341244236
341836043
342465009
347248266
348902061
354266518
355102242
355256432
363671416
364130203
375136062
375554670
375611445
377501972
377950396
381020367
383533385
384418537
384501009
385642110
386478383
388747073
404623002
404825306
419580325
433711928
434694284
436407216
438515814
441091025
441394937
441579668
442064917
443499250

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

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
Um Um Um

* 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 mass258.0852
Average mass258.228
[M+H]+259.0926
Product ions113
Normalized LC elution time *1,10 (Kellner 2014); 1,09 (Kellner 2014)
LC elution order/characteristicsbetween G and A (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-methyluridine

Name
U:Um

Reactions starting from 2'-O-methyluridine

Name
Um:cmnm5Um
Um:s2Um

Last modification of this entry: Sept. 29, 2021


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