Modomics - A Database of RNA Modifications

msms2i6A
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 name2- methylthiomethylenethio-N6-isopentenyl-adenosine
Short namemsms2i6A
MODOMICS code new2000021161A
MODOMICS code21161A
Nature of the modified residueNatural
RNAMods code£
Residue unique ID182
Found in RNAYes
Related nucleotides372

Chemical information

Sum formulaC17H25N5O4S2
Type of moietynucleoside
Degeneracynot applicable
SMILESCC(C)=CCNc1nc(SCSC)nc2c1nc[n]2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
logP1.3015
TPSA176.15
Number of atoms28
Number of Hydrogen Bond Acceptors 1 (HBA1)10
Number of Hydrogen Bond Acceptors 2 (HBA2)11
Number of Hydrogen Bond Donors (HBD)4
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
InChIInChI=1S/C17H25N5O4S2/c1-9(2)4-5-18-14-11-15(21-17(20-14)28-8-27-3)22(7-19-11)16-13(25)12(24)10(6-23)26-16/h4,7,10,12-13,16,23-25H,5-6,8H2,1-3H3,(H,18,20,21)/t10-,12-,13-,16-/m1/s1
InChIKeyNFWRNKCNTZDCAI-XNIJJKJLSA-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

Tautomers

Tautomers SMILES
CC(C)=CCNc1nc(SCSC)nc2c1ncn2C3OC(CO)C(O)C3O tautomer #0
CC(C)=CCNc1nc(SCSC)nc2c1ncn2C3OC(CO)C(O)C3O tautomer #1
CC(C)=CCN=c1nc(SCSC)[nH]c2c1ncn2C3OC(CO)C(O)C3O tautomer #2
CC(C)=CCN=c1[nH]c(SCSC)nc2c1ncn2C3OC(CO)C(O)C3O tautomer #3
CC(C)=CCN=C1N=C(SCSC)N=C2C1N=CN2C3OC(CO)C(O)C3O tautomer #4
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
msms2i6A msms2i6A msms2i6A

* 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 mass427.1347
Average mass427.542
[M+H]+428.0
Product ions not available
Normalized LC elution time *3.56
LC elution order/characteristicsafter m6A

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.

Publications

Title Authors Journal Details PubMed Id DOI
A vastly increased chemical variety of RNA modifications that includes a thioacetal structure Dal Magro C, Keller P, Kotter A, Werner S, Duarte V, Marchand V, Ignarski M, Freiwald A, Müller RU, Dieterich C, Motorin Y, Butter F, Atta M, Helm M. Angew. Chem. Int. Ed. [details] 29624844 10.1002/anie.201713188

Last modification of this entry: Sept. 22, 2023