Modomics - A Database of RNA Modifications

The molecule is shown in a ball-and-stick representation with the following colors for atoms :

⬤ Hydrogen (H): white ⬤ Carbon (C): gray ⬤ Oxygen (O): red ⬤ Phosphorus (P): orange ⬤ Nitrogen (N): blue ⬤ Selenium (Se): gold ⬤ Sulfur (S): yellow

Summary

Full name	5,2'-O-dimethyluridine
IUPAC name	1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione
Short name	m5Um
MODOMICS code new	2000000905U
MODOMICS code	05U
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 residue	Natural
RNAMods code	\
Residue unique ID	122
Found in RNA	Yes
Related nucleotides	296
Found naturally in RNA types	tRNA

Chemical information

Sum formula	C11H16N2O6
Type of moiety	nucleoside
Degeneracy	not applicable
SMILES	CO[C@H]1[C@H]([n]2c(=O)[nH]c(=O)c(C)c2)O[C@H](CO)[C@H]1O
logP	-1.8894
TPSA	113.78
Number of atoms	19
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 exact match, link to the most similar ligand	None
InChI	InChI=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
InChIKey	YHRRPHCORALGKQ-FDDDBJFASA-N
Search the molecule in external databases	ChEMBL ChemAgora ChEBI PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	191372
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

^* 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 mass	272.1008
Average mass	272.255
[M+H]⁺	273.1086
Product ions	127
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

Type	Subtype
methyl group	methyl at O2
methyl group	methyl at aromatic C

Reactions producing 5,2'-O-dimethyluridine

Name
m5U:m5Um

Last modification of this entry: Sept. 22, 2023