Summary

Full name5-methyluridine
IUPAC name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione
Short namem5U
MODOMICS code5U
Synonyms
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)-2-oxolanyl]-5-methylpyrimidine-2,4-dione
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione
1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-methylpyrimidine-2,4(1H,3H)-dione
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methyl-pyrimidine-2,4-dione
1-[(2R,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione
1-((2R,3R,4S,5R)-TETRAHYDRO-3,4-DIHYDROXY-5-(HYDROXYMETHYL)FURAN-2-YL)-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE
1463-10-1
1-[(4S,2R,3R,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,3-dihydropyrimidine-2,4-dione
172163-66-5
180000-19-5
1-b-D-Ribofuranosylthymine
1-beta-delta-Ribofuranosylthymine
1-(beta-D-ribofuranosyl)thymine
1-.beta.-D-Ribofuranosylthymine
2,4(1H,3H)-Pyrimidinedione, 5-methyl-1-.beta.-D-ribofuranosyl-
38T
463M101
5-methyl-1-beta-delta-ribofuranosyl-2,4(1H,3H)-Pyrimidinedione
5-methyl-1-beta-D-ribofuranosyl-2,4(1H,3H)-Pyrimidinedione
5-methyl-Uridine
5-Methyluridine
5-METHYLURIDINE 5'-MONOPHOSPHATE
5-Methyluridine, 97%
5-Methyluridine, 99% - 25G 25g
5-Methyluridine, powder
5MU
5MU-5MU-5MU
A808481
AC1L9HXX
AC-8172
ACT03080
AJ-43265
AKOS015896830
AM83947
ANW-21004
Arabinosylthymine
b-D-Ribofuranoside thymine-1
beta-delta-Ribofuranoside
beta-delta-Ribofuranoside thymine-1
beta-D-Ribofuranoside
.beta.-D-Ribofuranoside, thymine-1
.beta.-D-Ribofuranosylthymine
bmse000759
C10-H14-N2-O6
C10H14N2O6
CHEBI:30821
CHEBI:45996
CHEMBL106175
CID445408
CJ-10312
CM0074
CS-W010160
CTK0H4640
DB-030334
DS-18476
DTXSID20163348
DWRXFEITVBNRMK-JXOAFFINSA-N
EINECS 215-973-9
Epitope ID:141497
HY-W009444
I14-2705
J-700101
KS-00000NGX
KSC174M4B
M1405
MFCD00006535
NS00024786
PubChem14166
Q425078
ribosylthymidine
Ribosylthymine
Ribothymidine
RL01838
s6156
SC-09124
SCHEMBL29298
ST2406328
STL507242
Thymine ribofuranoside
Thymine ribonucleoside
Thymine riboside
thymine-1 beta-delta-Ribofuranosylthymine
thymine-1 beta-D-Ribofuranosylthymine
TL8001022
UNII-ZS1409014A
Uridine, 5-methyl-
uridine-1'-14C-5-methyl-
uridine-1,3-15N2-5-methyl-
ZINC2583634
ZS1409014A

Nature of the modified residueNatural
RNAMods codeT
Residue unique ID12
Found in RNAYes
Related nucleotides194
Enzymes RlmC (Escherichia coli)
RlmC (Pyrococcus abyssi)
RlmCD (Bacillus subtilis)
RlmD (Escherichia coli)
RlmFO (Mycoplasma capricolum)
Trm2 (Saccharomyces cerevisiae)
TrmA (Escherichia coli)
TrmFO (Bacillus subtilis)
TrmFO (Thermus thermophilus)
TrmU54 (Pyrococcus abyssi)
Found in phylogenyArchaea, Eubacteria, Eukaryota
Found naturally in RNA typesrRNA, tRNA

Chemical information

Sum formulaC10H14N2O6
Type of moietynucleoside
Degeneracynot applicable
PubChem ID445408
SMILESCc1c(=O)[nH]c(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c1
logP-2.5435
TPSA124.78
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)4
PDB no exac match , link to the most similar ligand 5HT
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000497
InChIInChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,9-/m1/s1
InChIKeyDWRXFEITVBNRMK-JXOAFFINSA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs
811760
7885419
7885420
10299694
14798888
15540847
24878114
24897297
26522141
36888129
49831022
57404680
79682760
87325314
87573355
91664129
103321563
104634233
111677887
123059576
126631895
127797981
128124569
131299320
135051664
141238813
143489897
152036249
152226275
152242406
160788505
162226445
163303417
163802399
165235680
172087417
174527562
175442902
179652968
193126152
202549687
211535896
222293359
223438479
223495666
223552436
223742464
226416409
241032854
242082282
249492811
249826821
250003690
250208908
251866533
252225474
252257266
252375466
252409227
252452552
255401169
256572848
275456594
275871922
310277198
312225942
312343745
313079932
315443704
315723806
316412317
316893421
316893487
316897883
316970838
318038377
319223523
319478449
321932735
322081905
336198155
341112032
341189150
341834407
342526803
346435583
346712717
348274887
348776451
354285801
354746060
355132903
355219437
363669354
368509978
374018418
375136887
375555675
375986861
375987485
376152446
376212454
376653182
381018117
381320088
381394233
385633325
386227352
386623959
387087042
388666495
402403814
404622930
404640197
404760963
404824386
419578555
433706334
433774999
433775261
433829835
434138698
434695123
438444098
438500009
439507873
440820643
441091019
441390339
441567455
442112791

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

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
m5U m5U m5U

* 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]+259.093
Product ions127
Normalized LC elution time *1 (Kellner 2014, Kellner 2014)
LC elution order/characteristicsco-eluting with 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 -

Comments

Alternative name is ribosylthymidine.

Chemical groups contained

TypeSubtype
methyl groupmethyl at aromatic C

Reactions producing 5-methyluridine

Name
U:m5U

Reactions starting from 5-methyluridine

Name
m5U:m5Um
m5U:m5s2U

Last modification of this entry: Sept. 29, 2021


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