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 name	N6,N6,2'-O-trimethyladenosine
IUPAC name	(2R,3R,4R,5R)-5-[6-(dimethylamino)purin-9-yl]-2-(hydroxymethyl)-4-methoxyoxolan-3-ol
Short name	m6,6Am
MODOMICS code new	2000009066A
MODOMICS code	066A
Synonyms	(2R,3R,4R,5R)-5-(6-(Dimethylamino)-9H-purin-9-yl)-2-(hydroxymethyl)-4-methoxytetrahydrofuran-3-ol (2R,3R,4R,5R)-5-[6-(dimethylamino)purin-9-yl]-2-(hydroxymethyl)-4-methoxyoxolan-3-ol 30891-53-3 Adenosine, N,N-dimethyl-2'-O-methyl- CTK1B3123 DTXSID30609484 N,N-Dimethyl-2'-O-methyladenosine SCHEMBL667836
Nature of the modified residue	Natural
RNAMods code	η
Residue unique ID	124
Found in RNA	Yes
Related nucleotides	431

Chemical information

Sum formula	C13H19N5O4
Type of moiety	nucleoside
Degeneracy	not applicable
SMILES	CN(C)c1ncnc2c1nc[n]2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1OC
logP	-0.8421
TPSA	105.76
Number of atoms	22
Number of Hydrogen Bond Acceptors 1 (HBA1)	8
Number of Hydrogen Bond Acceptors 2 (HBA2)	9
Number of Hydrogen Bond Donors (HBD)	2
PDB no exac match , link to the most similar ligand	26A
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand	None
InChI	InChI=1S/C13H19N5O4/c1-17(2)11-8-12(15-5-14-11)18(6-16-8)13-10(21-3)9(20)7(4-19)22-13/h5-7,9-10,13,19-20H,4H2,1-3H3/t7-,9-,10-,13-/m1/s1
InChIKey	IPRQAJTUSRLECG-QYVSTXNMSA-N
Search the molecule in external databases	ChEMBL ChemAgora ChEBI PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	20722670
PubChem SIDs	128202375 162507250 226964887 316139573 381998752 405016206 422844072

^* 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

^* 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 mass	309.1437
Average mass	309.321
[M+H]⁺	310.1515
Product ions	164
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

Type	Subtype
methyl group	methyl at O2
methyl group	methyl at other N
methyl group	second methyl at other N

Reactions producing N6,N6,2'-O-trimethyladenosine

Name
m6,6A:m6,6Am
m6Am:m6,6Am

Last modification of this entry: Sept. 22, 2023