Summary

Full name2-methylthio-N6-methyladenosine
IUPAC name(2R,3S,4R,5R)-2-(hydroxymethyl)-5-[6-(methylamino)-2-methylsulfanylpurin-9-yl]oxolane-3,4-diol
Short namems2m6A
MODOMICS code621A
Synonyms
13406-51-4
2-Methylthio-N6-methyladenosine
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-[6-(methylamino)-2-methylsulfanylpurin-9-yl]oxolane-3,4-diol
SCHEMBL1961097

Nature of the modified residueNatural
RNAMods code
Residue unique ID5
Found in RNAYes
Related nucleotides377

Chemical information

Sum formulaC12H17N5O4S
Type of moietynucleoside
Degeneracynot applicable
SMILESCNc1nc(SC)nc2c1nc[n]2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
logP-0.7256
TPSA150.85
Number of atoms22
Number of Hydrogen Bond Acceptors 1 (HBA1)9
Number of Hydrogen Bond Acceptors 2 (HBA2)10
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand 26A
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0004044
InChIInChI=1S/C12H17N5O4S/c1-13-9-6-10(16-12(15-9)22-2)17(4-14-6)11-8(20)7(19)5(3-18)21-11/h4-5,7-8,11,18-20H,3H2,1-2H3,(H,13,15,16)/t5-,7-,8-,11-/m1/s1
InChIKeyPHFMCMDFWSZKGD-IOSLPCCCSA-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
CNc1nc(SC)nc2c1ncn2C3OC(CO)C(O)C3O tautomer #0
CNc1nc(SC)nc2c1ncn2C3OC(CO)C(O)C3O tautomer #1
CN=c1nc(SC)[nH]c2c1ncn2C3OC(CO)C(O)C3O tautomer #2
CN=c1[nH]c(SC)nc2c1ncn2C3OC(CO)C(O)C3O tautomer #3
CN=C1N=C(SC)N=C2C1N=CN2C3OC(CO)C(O)C3O tautomer #4

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
ms2m6A ms2m6A ms2m6A

* 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 mass327.1001
Average mass327.359
[M+H]+328.1079
Product ions196
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
heavy atomthiomethyl
methyl groupmethyl at other N

Reactions producing 2-methylthio-N6-methyladenosine

Name
m6A:ms2m6A

Last modification of this entry: Sept. 29, 2021


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