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

Summary

Full name1,2'-O-dimethyladenosine
IUPAC name(2R,3R,4R,5R)-2-(hydroxymethyl)-5-(6-imino-1-methylpurin-9-yl)-4-methoxyoxolan-3-ol
Short namem1Am
MODOMICS code new2000000901A
MODOMICS code01A
Synonyms
1-N-,2'-O-dimethyladenosine
2'-O-methyl-1-methyl-adenosine
(2R,3R,4R,5R)-2-(hydroxymethyl)-5-(6-imino-1-methylpurin-9-yl)-4-methoxyoxolan-3-ol
DJONVIMMDYQLKR-WOUKDFQISA-N
SCHEMBL20580140

Nature of the modified residueNatural
RNAMods codeœ
Residue unique ID32
Found in RNAYes
Related nucleotides340

Chemical information

Sum formulaC12H17N5O4
Type of moietynucleoside
Degeneracynot applicable
SMILESCO[C@H]1[C@H]([n]2c3nc[n](c(=N)c3nc2)C)O[C@H](CO)[C@H]1O
logP-1.3854
TPSA118.41
Number of atoms21
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)3
PDB no exac match , link to the most similar ligand PUR
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C12H17N5O4/c1-16-4-15-11-7(10(16)13)14-5-17(11)12-9(20-2)8(19)6(3-18)21-12/h4-6,8-9,12-13,18-19H,3H2,1-2H3/t6-,8-,9-,12-/m1/s1
InChIKeyDJONVIMMDYQLKR-WOUKDFQISA-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


Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
m1Am m1Am m1Am

* 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 mass295.1281
Average mass295.294
[M+H]+296.1359
Product ions150
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.

Reactions producing 1,2'-O-dimethyladenosine

Name
m1A:m1Am
Am:m1Am

Last modification of this entry: Sept. 22, 2023