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-carbamoylmethyluridine
IUPAC name	2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetamide
Short name	ncm5U
MODOMICS code new	2000000053U
MODOMICS code	53U
Synonyms	2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetamide 2-(2,4-dioxo-1-beta-D-ribofuranosyl-1,2,3,4-tetrahydro-pyrimidin-5-yl)-acetamide 29569-30-0 5-(2-amino-2-oxoethyl)uridine 5-Carbamoylmethyluridine 5-(Carbamoylmethyl)uridine 5-Cbmu 5-uridinacetamide AC1MIVNF C11-H15-N3-7 C11H15N37 CHEBI:62005 CID3080754 CTK4G3508 DTXSID60183742 Q27131521 SCHEMBL157977 Uridine, 5-(2-amino-2-oxoethyl)- Uridine,5-(2-amino-2-oxoethyl)-
Nature of the modified residue	Natural
RNAMods code	&
Residue unique ID	43
Found in RNA	Yes
Related nucleotides	356
Found in phylogeny	Eukaryota
Found naturally in RNA types	tRNA

Chemical information

Sum formula	C11H15N3O7
Type of moiety	nucleoside
Degeneracy	not applicable
SMILES	NC(Cc1c(=O)[nH]c(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c1)=O
logP	-3.1238
TPSA	167.87
Number of atoms	21
Number of Hydrogen Bond Acceptors 1 (HBA1)	8
Number of Hydrogen Bond Acceptors 2 (HBA2)	9
Number of Hydrogen Bond Donors (HBD)	5
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/C11H15N3O7/c12-6(16)1-4-2-14(11(20)13-9(4)19)10-8(18)7(17)5(3-15)21-10/h2,5,7-8,10,15,17-18H,1,3H2,(H2,12,16)(H,13,19,20)/t5-,7-,8-,10-/m1/s1
InChIKey	ZYEWPVTXYBLWRT-VPCXQMTMSA-N
Search the molecule in external databases	ChEMBL ChemAgora ChEBI PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	3080754
PubChem SIDs	36411682 57354414 78025875 111681184 121270247 135260234 162831825 226521758 272889046 312242188 315744121 316893738 319287650 341251600 348954762 354311264 385670905 386507463 389283175 419562796 439539400 441393598

^* 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

NC(Cc1c(=O)[nH]c(=O)n(C2C(O)C(O)C(CO)O2)c1)=O tautomer #0
NC(C=C1C(=O)NC(=O)N(C2C(O)C(O)C(CO)O2)C1)=O tautomer #1
NC(=Cc1c(=O)[nH]c(=O)n(C2C(O)C(O)C(CO)O2)c1)O tautomer #2
NC(Cc1c(O)nc(=O)n(C2C(O)C(O)C(CO)O2)c1)=O tautomer #3
NC(C=C1C(O)=NC(=O)N(C2C(O)C(O)C(CO)O2)C1)=O tautomer #4
NC(Cc1c(=O)nc(O)n(C2C(O)C(O)C(CO)O2)c1)=O tautomer #5
NC(C=C1C(=O)N=C(O)N(C2C(O)C(O)C(CO)O2)C1)=O tautomer #6
N=C(C=C1C(=O)NC(=O)N(C2C(O)C(O)C(CO)O2)C1)O tautomer #7
N=C(Cc1c(=O)[nH]c(=O)n(C2C(O)C(O)C(CO)O2)c1)O tautomer #8
NC(=Cc1c(O)nc(=O)n(C2C(O)C(O)C(CO)O2)c1)O tautomer #9
NC(=Cc1c(=O)nc(O)n(C2C(O)C(O)C(CO)O2)c1)O tautomer #10
N=C(C=C1C(O)=NC(=O)N(C2C(O)C(O)C(CO)O2)C1)O tautomer #11
N=C(Cc1c(O)nc(=O)n(C2C(O)C(O)C(CO)O2)c1)O tautomer #12
N=C(C=C1C(=O)N=C(O)N(C2C(O)C(O)C(CO)O2)C1)O tautomer #13
N=C(Cc1c(=O)nc(O)n(C2C(O)C(O)C(CO)O2)c1)O tautomer #14

Tautomer image

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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	301.091
Average mass	301.253
[M+H]⁺	302.0988
Product ions	170/153/125
Normalized LC elution time^*	0,50 (Kellner 2014)
LC elution order/characteristics	between C and U (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	-

Chemical groups contained

Type	Subtype
methyl group	methyl at aromatic C
other	carbamoyl

Reactions producing 5-carbamoylmethyluridine

Name
U:ncm5U

Reactions starting from 5-carbamoylmethyluridine

Name
ncm5U:ncm5Um
ncm5U:nchm5U
ncm5U:ncm5s2U

Last modification of this entry: Sept. 22, 2023