Summary

Full name5-aminomethyluridine
IUPAC name5-(aminomethyl)-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione
Short namenm5U
MODOMICS code510U
Synonyms
190448-73-8
5-(aminomethyl)-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione
5-aminomethyluridine
5-(Aminomethyl)uridine
J3.618.759J
SCHEMBL1665190

Nature of the modified residueNatural
RNAMods code
Residue unique ID115
Found in RNAYes
Related nucleotides355
Enzymes MnmCD (Escherichia coli)
MnmE (Escherichia coli)
MnmE (Chlorobium tepidum)
MnmE (Nostoc sp.)
MnmE (Thermotoga maritima)
MnmG (Escherichia coli)
MnmG (Chlorobium tepidum)
MnmG (Aquifex aeolicus)
Found in phylogenyEubacteria, Eukaryota

Chemical information

Sum formulaC10H15N3O6
Type of moietynucleoside
Degeneracynot applicable
SMILESNCc1c(=O)[nH]c(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c1
logP-2.6929
TPSA150.8
Number of atoms19
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)8
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/C10H15N3O6/c11-1-4-2-13(10(18)12-8(4)17)9-7(16)6(15)5(3-14)19-9/h2,5-7,9,14-16H,1,3,11H2,(H,12,17,18)/t5-,6-,7-,9-/m1/s1
InChIKeyZQVNMALZHZYKQM-JXOAFFINSA-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
NCc1c(=O)[nH]c(=O)n(C2C(O)C(O)C(CO)O2)c1 tautomer #0
NCc1c(O)nc(=O)n(C2C(O)C(O)C(CO)O2)c1 tautomer #1
NCc1c(=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
nm5U nm5U nm5U

* 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 mass273.0961
Average mass273.243
[M+H]+274.1039
Product ions142
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.

Chemical groups contained

TypeSubtype
methyl groupmethyl at aromatic C
otherprimary amine

Reactions producing 5-aminomethyluridine

Name
cmnm5U:nm5U
U:nm5U

Reactions starting from 5-aminomethyluridine

Name
nm5U:mnm5U
nm5U:nm5s2U
nm5U:inm5U

Last modification of this entry: Sept. 29, 2021


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