Modomics - A Database of RNA Modifications

io6A
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 nameN6-(cis-hydroxyisopentenyl)adenosine
IUPAC name(2R,3S,4R,5R)-2-(hydroxymethyl)-5-[6-[(4-hydroxy-3-methylbut-2-enyl)amino]purin-9-yl]oxolane-3,4-diol
Short nameio6A
MODOMICS code new2000000060A
MODOMICS code60A
Synonyms
15896-46-5
28542-78-1
6025-53-2
6-(4-hydroxy-3-methylbut-2-enylamino)-9-beta-d-ribofuranosylpurine
9-(beta-D-Ribofuranosyl)-trans-zeatin
9-ribosylzeatin
Adenosine, N-[(2Z)-4-hydroxy-3-methyl-2-butenyl]-
AKOS030240776
CTK0E7002
CTK8F0844
DTXSID00891556
KS-00000IJE
NS00014570
Q27109360
trans-Zeatinriboside
Zeatin riboside
Zeatin riboside mixed Isomers
Nature of the modified residueNatural
RNAMods code`
Residue unique ID10
Found in RNAYes
Related nucleotides432
Enzymes MiaE (Salmonella typhimurium)
Found in phylogenyEubacteria
Found naturally in RNA typestRNA

Chemical information

Sum formulaC15H21N5O5
Type of moietynucleoside
Degeneracynot applicable
SMILESCC(CO)=CCNc1ncnc2c1nc[n]2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
logP-1.1387
TPSA145.78
Number of atoms25
Number of Hydrogen Bond Acceptors 1 (HBA1)9
Number of Hydrogen Bond Acceptors 2 (HBA2)10
Number of Hydrogen Bond Donors (HBD)5
PDB no exac match , link to the most similar ligand ZIR
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C15H21N5O5/c1-8(4-21)2-3-16-13-10-14(18-6-17-13)20(7-19-10)15-12(24)11(23)9(5-22)25-15/h2,6-7,9,11-12,15,21-24H,3-5H2,1H3,(H,16,17,18)/t9-,11-,12-,15-/m1/s1
InChIKeyGOSWTRUMMSCNCW-SDBHATRESA-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
CC(CO)=CCNc1ncnc2c1ncn2C3OC(CO)C(O)C3O tautomer #0
CC(CO)=CCNc1ncnc2c1ncn2C3OC(CO)C(O)C3O tautomer #1
CC(CO)=CCN=c1nc[nH]c2c1ncn2C3OC(CO)C(O)C3O tautomer #2
CC(CO)=CCN=c1[nH]cnc2c1ncn2C3OC(CO)C(O)C3O tautomer #3
CC(CO)=CCN=C1N=CN=C2C1N=CN2C3OC(CO)C(O)C3O tautomer #4
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
io6A io6A io6A

* 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 mass351.1543
Average mass351.358
[M+H]+352.1621
Product ions220
Normalized LC elution time *2,59 (Kellner 2014)
LC elution order/characteristicsafter m6A (Kellner 2014)

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.


LC-MS Publications

Title Authors Journal Details PubMed Id DOI
Profiling of RNA modifications by multiplexed stable isotope labelling. Kellner S, Neumann J, Rosenkranz D, Lebedeva S, Ketting RF, Zischler H, Schneider D, Helm M. Chem Commun (Camb). [details] 24567952 -

Chemical groups contained

TypeSubtype
otherhydroxyl
otherisopentenyl

Reactions producing N6-(cis-hydroxyisopentenyl)adenosine

Name
i6A:io6A

Reactions starting from N6-(cis-hydroxyisopentenyl)adenosine

Name
io6A:ms2io6A

Last modification of this entry: Sept. 22, 2023