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	N6,2'-O-dimethyladenosine
IUPAC name	(2R,3R,4R,5R)-2-(hydroxymethyl)-4-methoxy-5-[6-(methylamino)purin-9-yl]oxolan-3-ol
Short name	m6Am
MODOMICS code new	2000000906A
MODOMICS code	06A
Synonyms	(2R,3R,4R,5R)-2-(hydroxymethyl)-4-methoxy-5-[6-(methylamino)purin-9-yl]oxolan-3-ol 3-Glucosaminoglycan sulfate 3GS 57817-83-1 57821-29-1 AC1O57LU Adenosine, N-methyl-2'-O-methyl- Aterina C007858 C12-H17-N5-O4 CID6453528 DTXSID50206530 Glucuronyl glucosamine glycan sulfate Glucuronyl glucosaminoglycan sulfate Glucuronylglucosamine-glicane sulfate Glucuronylglucosamineglicane sulfate glucuronylglucosaminoglycan sulfate Gluparin KRX-101 LEV25J2GTV Luzone N,2'-O-Dimethyladenosine n6,2'-O-dimethyladenosine n6-methyl-2'-o-methyladenosine N6,O2'-Dimethyladenosine N(6),O(2)-Dimethyladenosine Provenal SCHEMBL665209 Sulodexide Sulodexide [INN] Sulodexido Sulodexido [INN-Spanish] Sulodexidum Sulodexidum [INN-Latin] Treparin UNII-75HGV0062C UNII-LEV25J2GTV Vessel Vessel 2F Vessel Due F ZLA0007 zlchem 6
Nature of the modified residue	Natural
RNAMods code	χ
Residue unique ID	82
Found in RNA	Yes
Related nucleotides	430
Found naturally in RNA types	snRNA

Chemical information

Sum formula	C12H17N5O4
Type of moiety	nucleoside
Degeneracy	not applicable
SMILES	CO[C@H]1[C@H]([n]2cnc3c2ncnc3NC)O[C@H](CO)[C@H]1O
logP	-0.7934
TPSA	114.55
Number of atoms	21
Number of Hydrogen Bond Acceptors 1 (HBA1)	8
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	26A
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand	None
InChI	InChI=1S/C12H17N5O4/c1-13-10-7-11(15-4-14-10)17(5-16-7)12-9(20-2)8(19)6(3-18)21-12/h4-6,8-9,12,18-19H,3H2,1-2H3,(H,13,14,15)/t6-,8-,9-,12-/m1/s1
InChIKey	GRYSXUXXBDSYRT-WOUKDFQISA-N
Search the molecule in external databases	ChEMBL ChemAgora ChEBI PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	6453528
PubChem SIDs	11972838 14771674 43044373 50387517 57370569 114532677 127997598 134222413 135194157 136023842 226962616 315766835 316892495 319328982 319328983 319549370 341718300 355189907 389148469 426111568 434261793 434370223 435892274 439479428 439540413 439645230 441079236 441415567 443564629

^* 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	COC1C(n2cnc3c2ncnc3NC)OC(CO)C1O tautomer #0 COC1C(n2cnc3c2ncnc3NC)OC(CO)C1O tautomer #1 COC1C(n2cnc3c2[nH]cnc3=NC)OC(CO)C1O tautomer #2 COC1C(n2cnc3c2nc[nH]c3=NC)OC(CO)C1O tautomer #3 COC1C(N2C=NC3C2=NC=NC3=NC)OC(CO)C1O tautomer #4
Tautomer image	Show Image

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	295.1281
Average mass	295.294
[M+H]⁺	296.1359
Product ions	150
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

Reactions producing N6,2'-O-dimethyladenosine

Name
m6A:m6Am
Am:m6Am

Reactions starting from N6,2'-O-dimethyladenosine

Name
m6Am:m6,6Am

Last modification of this entry: Sept. 22, 2023