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


Full name2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine
IUPAC name(2R,3S,4R,5R)-2-(hydroxymethyl)-5-[6-[(4-hydroxy-3-methylbut-2-enyl)amino]-2-methylsulfanylpurin-9-yl]oxolane-3,4-diol
Short namems2io6A
MODOMICS code new2000002160A
MODOMICS code2160A
Adenosine, N-[(2Z)-4-hydroxy-3-methyl-2-butenyl]-2-(methylthio)-
Nature of the modified residueNatural
RNAMods code
Residue unique ID126
Found in RNAYes
Related nucleotides375
Enzymes MiaE (Salmonella typhimurium)
Found in phylogenyEubacteria
Found naturally in RNA typestRNA

Chemical information

Sum formulaC16H23N5O5S
Type of moietynucleoside
Degeneracynot applicable
Number of atoms27
Number of Hydrogen Bond Acceptors 1 (HBA1)10
Number of Hydrogen Bond Acceptors 2 (HBA2)11
Number of Hydrogen Bond Donors (HBD)5
PDB no exac match , link to the most similar ligand ZIR
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
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 SMILES
CC(CO)=CCNc1nc(SC)nc2c1ncn2C3OC(CO)C(O)C3O tautomer #0
CC(CO)=CCNc1nc(SC)nc2c1ncn2C3OC(CO)C(O)C3O tautomer #1
CC(CO)=CCN=c1nc(SC)[nH]c2c1ncn2C3OC(CO)C(O)C3O tautomer #2
CC(CO)=CCN=c1[nH]c(SC)nc2c1ncn2C3OC(CO)C(O)C3O tautomer #3
CC(CO)=CCN=C1N=C(SC)N=C2C1N=CN2C3OC(CO)C(O)C3O tautomer #4
Tautomer image Show Image

Predicted CYP Metabolic Sites

ms2io6A ms2io6A ms2io6A

* 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 mass397.142
Average mass397.449
Product ions266
Normalized LC elution time *3,19 (Kellner 2014)
LC elution order/characteristicsafter m6A (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 -

Chemical groups contained

heavy atomthiomethyl

Reactions producing 2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine


Last modification of this entry: Sept. 22, 2023