Summary

Full name5-carbamoylmethyluridine
IUPAC name2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetamide
Short namencm5U
MODOMICS code53U
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 residueNatural
RNAMods code&
Residue unique ID43
Found in RNAYes
Related nucleotides356
Found in phylogenyEukaryota
Found naturally in RNA typestRNA

Chemical information

Sum formulaC11H15N3O7
Type of moietynucleoside
Degeneracynot applicable
SMILESNC(Cc1c(=O)[nH]c(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c1)=O
logP-3.1238
TPSA167.87
Number of atoms21
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 exac match, link to the most similar ligand HMDB0000884
InChIInChI=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
InChIKeyZYEWPVTXYBLWRT-VPCXQMTMSA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs

* 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 Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
ncm5U ncm5U ncm5U

* 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 mass301.091
Average mass301.253
[M+H]+302.0988
Product ions170/153/125
Normalized LC elution time *0,50 (Kellner 2014)
LC elution order/characteristicsbetween 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

TypeSubtype
methyl groupmethyl at aromatic C
othercarbamoyl

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. 29, 2021


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