Modomics - A Database of RNA Modifications

hm6A
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-hydroxymethyladenosine
IUPAC name(2R,3S,4R,5R)-2-(hydroxymethyl)-5-[6-(hydroxymethylamino)purin-9-yl]oxolane-3,4-diol
Short namehm6A
MODOMICS code new2000000068A
MODOMICS code68A
Synonyms
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-[6-(hydroxymethylamino)purin-9-yl]oxolane-3,4-diol
6295-09-6
6-N-Methylhydroxylaminopurine riboside
98897-14-4
AC1L2RKY
AC1Q4Y5C
AR-1K0050
CCRIS 2561
CID127187
CTK5I0115
DTXSID60913006
LS-188893
n6-hydroxymethyladenosine
N(6)-Hydroxymethyladenosine
N6-(Hydroxymethyl)adenosine
N-(Hydroxymethyl)-9-pentofuranosyl-9H-purin-6-amine
n-(hydroxymethyl)adenosine
SCHEMBL18740390
ZDSMLAYSJRQEGM-IOSLPCCCSA-N
Nature of the modified residueNatural
RNAMods codeϪ
Residue unique ID176
Found in RNAYes
Related nucleotides436
Enzymes FTO (Homo sapiens)
Found in phylogenyEukaryota
Found naturally in RNA typesmRNA

Chemical information

Sum formulaC11H15N5O5
Type of moietynucleoside
Degeneracynot applicable
SMILESO[C@H]1[C@H]([n]2cnc3c(NCO)ncnc23)O[C@H](CO)[C@H]1O
logP-2.1275
TPSA145.78
Number of atoms21
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 26A
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C11H15N5O5/c17-1-5-7(19)8(20)11(21-5)16-3-14-6-9(15-4-18)12-2-13-10(6)16/h2-3,5,7-8,11,17-20H,1,4H2,(H,12,13,15)/t5-,7-,8-,11-/m1/s1
InChIKeyZDSMLAYSJRQEGM-IOSLPCCCSA-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
OC1C(n2cnc3c(NCO)ncnc23)OC(CO)C1O tautomer #0
OC1C(n2cnc3c(NCO)ncnc23)OC(CO)C1O tautomer #1
OC1C(n2cnc3c(=NCO)nc[nH]c23)OC(CO)C1O tautomer #2
OC1C(n2cnc3c(=NCO)[nH]cnc23)OC(CO)C1O tautomer #3
OC1C(N2C=NC3C(=NCO)N=CN=C23)OC(CO)C1O tautomer #4
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
hm6A hm6A hm6A

* 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 mass297.1073
Average mass297.267
[M+H]+298.1151
Product ions268/136
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 N6-hydroxymethyladenosine

Name
m6A:hm6A

Reactions starting from N6-hydroxymethyladenosine

Name
hm6A:f6A

Publications

Title Authors Journal Details PubMed Id DOI
FTO-mediated formation of N(6)-hydroxymethyladenosine and N(6)-formyladenosine in mammalian RNA. Fu Y, Jia G, Pang X, Wang RN, Wang X, Li CJ, Smemo S, Dai Q, Bailey KA, Nobrega MA, Han KL, Cui Q, He C... Nat Commun [details] 23653210 -

Last modification of this entry: Sept. 22, 2023