Summary

Full name5,2'-O-dimethyluridine
IUPAC name1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione
Short namem5Um
MODOMICS code05U
Synonyms
114952-97-5
1-(2-O-Methyl-beta-D-ribofuranosyl)thymine
1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione
1-((2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxytetrahydrofuran-2-yl)-5-methylpyrimidine-2,4(1H,3H)-dione
1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxy-tetrahydrofuran-2-yl]-5-methyl-pyrimidine-2,4-dione
2NULL-O-Methyl-5-Methyluridine
2'-Ome-5-Me Uridine
2'-O-Methyl-5- methyl uridine
2'-O-methyl-5-methyluridine
2`-O-Methyl-5-methyluridine 5,2`-O-Dimethyluridine
2'-O-Methylribothymidine
2/'-O-Methylribothymidine
486M094
4-Hydroxy-5-methyl-1-(2-O-methylpentofuranosyl)pyrimidin-2(1H)-one
5,2'-O-Dimethyluridine
55486-09-4
5-M-2'-OMeUridine
5-Me-2'-OMe Uridine
5-Me-2'-O-Me-U
5-METHYL-2-O-METHYLURIDINE
5-Methyl-2'-O-methyl-uridine
5-Methyl-2'-O-methyluridine
5,O2'-dimethyl-uridine
6339-35-1
AC1L4SES
AC1Q69E9
AC-32269
AIDS339890
AKOS015914616
AN-40323
AR-1G8873
AS-17244
C11H16N2O6
CHEBI:19226
CID191372
CM-321
CS-0100727
CTK4A8986
DB-021465
DTXSID20970832
I14-41207
J-700099
KS-00000NC5
MFCD03788700
Q27109137
SCHEMBL62321
TL8006552
TM
U006
Uridine, 5-methyl-2'-O-methyl-
Uridine,5-methyl-2-O-methyl- (9CI)
YHRRPHCORALGKQ-FDDDBJFASA-N
ZINC21302775

Nature of the modified residueNatural
RNAMods code\
Residue unique ID122
Found in RNAYes
Related nucleotides296
Found naturally in RNA typestRNA

Chemical information

Sum formulaC11H16N2O6
Type of moietynucleoside
Degeneracynot applicable
SMILESCO[C@H]1[C@H]([n]2c(=O)[nH]c(=O)c(C)c2)O[C@H](CO)[C@H]1O
logP-1.8894
TPSA113.78
Number of atoms19
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 38T
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000884
InChIInChI=1S/C11H16N2O6/c1-5-3-13(11(17)12-9(5)16)10-8(18-2)7(15)6(4-14)19-10/h3,6-8,10,14-15H,4H2,1-2H3,(H,12,16,17)/t6-,7-,8-,10-/m1/s1
InChIKeyYHRRPHCORALGKQ-FDDDBJFASA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs
10261303
10587069
15491421
33512563
49836355
53529579
57396642
62132567
91750453
103145733
113450917
117584594
126686410
129797353
135168801
135373342
135668178
152054035
162186519
162777304
179680401
202540640
222561031
223673850
226443846
249716237
249764422
252219134
252225473
252257262
252374574
252447623
252452567
255470455
272773112
275951975
300403061
310276876
312237487
312343743
313189000
315378078
316893845
318022624
319195650
322082217
341126317
341716758
341849610
342582002
346421668
347266372
347725211
348122964
349122001
354270379
355046202
355101025
363671137
364167554
374053599
375136064
375554667
375944841
376152120
381366504
383533390
384407692
384527835
385383111
385663813
386500329
388827370
404623130
419580324
434699440
436407220
438515878
439790868
440084720
440703573
440822375
441395341
441656416
443512436
443512449

* 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(n2c(=O)[nH]c(=O)c(C)c2)OC(CO)C1O tautomer #0
COC1C(n2c(O)nc(=O)c(C)c2)OC(CO)C1O tautomer #1
COC1C(n2c(=O)nc(O)c(C)c2)OC(CO)C1O tautomer #2

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
m5Um m5Um m5Um

* 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 mass272.1008
Average mass272.255
[M+H]+273.1086
Product ions127
Normalized LC elution time * not available
LC elution order/characteristics not available

* 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
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 -

Chemical groups contained

TypeSubtype
methyl groupmethyl at O2
methyl groupmethyl at aromatic C

Reactions producing 5,2'-O-dimethyluridine

Name
m5U:m5Um

Last modification of this entry: Sept. 29, 2021


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