Summary

Full name5-aminomethyl-2-geranylthiouridine
Short namenm5ges2U
MODOMICS code21510U
Nature of the modified residueNatural
RNAMods codeΔ
Residue unique ID169
Found in RNAYes
Related nucleotides385

Chemical information

Sum formulaC20H31N3O5S
Type of moietynucleoside
Degeneracynot applicable
SMILESCC(C)=CCC/C(/C)=C/CSc1nc(=O)c(CN)c[n]1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
logP1.7986
TPSA156.13
Number of atoms29
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)4
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/C20H31N3O5S/c1-12(2)5-4-6-13(3)7-8-29-20-22-18(27)14(9-21)10-23(20)19-17(26)16(25)15(11-24)28-19/h5,7,10,15-17,19,24-26H,4,6,8-9,11,21H2,1-3H3/b13-7+/t15-,16-,17-,19-/m1/s1
InChIKeySOFILOWAOSHASN-JCPZAAIZSA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 

* 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


Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
nm5ges2U nm5ges2U nm5ges2U

* 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 mass425.1984
Average mass425.542
[M+H]+426.2062
Product ions294
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
aminoalkylaminomethyl
sulphurthio
hydrocarbongeranyl

Reactions producing 5-aminomethyl-2-geranylthiouridine

Name
ges2U:nm5ges2U
cmnm5ges2U:nm5ges2U
nm5s2U:nm5ges2U

Reactions starting from 5-aminomethyl-2-geranylthiouridine

Name
nm5ges2U:mnm5ges2U

Last modification of this entry: Sept. 29, 2021


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