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	2'-O-methylinosine
IUPAC name	9-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-1H-purin-6-one
Short name	Im
MODOMICS code new	2000000909A
MODOMICS code	09A
Synonyms	2-Chloro-6-fluorobenzotrichloride 2'-O-METHYL-D-INOSINE 2?O-Methylinosine 2'-(o-Methyl)-inosine 2'-O-methylinosine 2'-O-Methyl-inosine 2-(O-METHYL)-INOSINE 3881-21-8 3'-O-Methyl-Inosine 881M218 9-[(2R,3R,4R,5R)-4-HYDROXY-5-(HYDROXYMETHYL)-3-METHOXYOXOLAN-2-YL]-1H-PURIN-6-ONE 9-((2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxytetrahydrofuran-2-yl)-1H-purin-6(9H)-one 9-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxy-tetrahydrofuran-2-yl]-3H-purin-6-one 9-((2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxytetrahydrofuran-2-yl)-9H-purin-6-ol 9-[(2R,3R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxy-oxolan-2-yl]-3H-purin-6-one AC-8215 AKOS025402340 AN-8215 CHEBI:68467 CID10062287 CTK8F4496 DTXSID00435030 HPHXOIULGYVAKW-IOSLPCCCSA-N J-700080 MFCD01631008 NS00014739 Q15632692 SCHEMBL658713 VZ21766 ZINC34149906
Nature of the modified residue	Natural
RNAMods code	≤
Residue unique ID	128
Found in RNA	Yes
Related nucleotides	367

Chemical information

Sum formula	C11H14N4O5
Type of moiety	nucleoside
Degeneracy	not applicable
SMILES	CO[C@H]1[C@H]([n]2cnc3c2nc[nH]c3=O)O[C@H](CO)[C@H]1O
logP	-1.6148
TPSA	122.49
Number of atoms	20
Number of Hydrogen Bond Acceptors 1 (HBA1)	7
Number of Hydrogen Bond Acceptors 2 (HBA2)	8
Number of Hydrogen Bond Donors (HBD)	3
PDB no exac match , link to the most similar ligand	NOS
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand	None
InChI	InChI=1S/C11H14N4O5/c1-19-8-7(17)5(2-16)20-11(8)15-4-14-6-9(15)12-3-13-10(6)18/h3-5,7-8,11,16-17H,2H2,1H3,(H,12,13,18)/t5-,7-,8-,11-/m1/s1
InChIKey	HPHXOIULGYVAKW-IOSLPCCCSA-N
Search the molecule in external databases	ChEMBL ChemAgora ChEBI PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	135412763
PubChem SIDs	15046798 44179318 79570041 126617342 126664468 128093780 160645712 163129407 206253751 222493929 223669264 225075322 226956609 252225444 260399922 274825940 304738027 310276821 310917173 312244632 312343725 315373926 315965342 316538429 316900028 322091962 341124652 341321993 341844340 342465016 347661073 349025873 363671141 375118961 375540692 377991419 381990237 385011995 385533581 385644302 386480618 387100400 389340052 419542663 438549127 441092157 442862468 443520498

^* 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(n2cnc3c2ncnc3O)OC(CO)C1O tautomer #0 COC1C(n2cnc3c2[nH]cnc3=O)OC(CO)C1O tautomer #1 COC1C(n2cnc3c2nc[nH]c3=O)OC(CO)C1O tautomer #2 COC1C(n2cnc3c2ncnc3O)OC(CO)C1O tautomer #3 COC1C(N2C=NC3C2=NC=NC3=O)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	282.0964
Average mass	282.253
[M+H]⁺	283.1042
Product ions	137
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
other	keto

Reactions producing 2'-O-methylinosine

Name
I:Im
Am:Im

Reactions starting from 2'-O-methylinosine

Name
Im:m1Im

Last modification of this entry: Sept. 22, 2023