Modomics - A Database of RNA Modifications

m1A
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 name1-methyladenosine
IUPAC name(2R,3S,4R,5R)-2-(hydroxymethyl)-5-(6-imino-1-methylpurin-9-yl)oxolane-3,4-diol
Short namem1A
MODOMICS code new2000000001A
MODOMICS code1A
Synonyms
15763-06-1
1-Methyladenosine
1-Methyladenosine, 98% - 250MG 250mg
(2R,3R,4S,5R)-2-(6-Amino-1-methyl-1H-purin-9(2H)-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-(6-imino-1-methyl-1H-purin-9(6H)-yl)tetrahydrofuran-3,4-diol
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-(6-imino-1-methyl-6,9-dihydro-1H-purin-9-yl)oxolane-3,4-diol
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-(6-imino-1-methylpurin-9-yl)oxolane-3,4-diol
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-(6-imino-1-methyl-purin-9-yl)tetrahydrofuran-3,4-diol
AC1L1DAV
AC-32347
Adenosine, 1-methyl-
Adenosine, 1-methyl- (VAN) (8CI)
Adenosine, N,6-didehydro-1,6-dihydro-1-methyl-
Adenosine, N,6-didehydro-1,6-dihydro-1-methyl- (9CI)
Adenosine, N,6-didehydro-1,9-dihydro-1-methyl-
AKOS030241121
alpha-Vetivone
C02494
C11-H15-N5-O4
CHEBI:16020
CHEMBL1866485
CID27476
CS-0059513
CTK8F3395
DTXSID30864632
GFYLSDSUCHVORB-IOSLPCCCSA-N
HY-113081
K-4948
M1A
MFCD00038421
N1-Methyladenosine
N(1)-methyladenosine
N1-Methyl-D-adenosine
NCGC00163305-01
NS00099498
NSC 92165
Q161643
SCHEMBL19553541
ZINC100053615
Nature of the modified residueNatural
RNAMods code"
Residue unique ID83
Found in RNAYes
Related nucleotides204
Enzymes Bmt2 (Saccharomyces cerevisiae)
KamB (Streptomyces sp. DSM 40477)
NpmA (Escherichia coli)
Rrp8 (Saccharomyces cerevisiae)
TRMT10C (Homo sapiens)
Trm61 (Saccharomyces cerevisiae)
TrmI (Pyrococcus abyssi)
TrmI (Thermus thermophilus)
TrmI (Mycobacterium tuberculosis)
TrmK (Bacillus subtilis)
Trmt61A (Homo sapiens)
Trmt61B (Homo sapiens)
Found in phylogenyArchaea, Eubacteria, Eukaryota
Found naturally in RNA typesrRNA, tRNA

Chemical information

Sum formulaC11H15N5O4
Type of moietynucleoside
Degeneracynot applicable
PubChem ID27476
SMILESC[n]1c(=N)c2c([n]([C@H]3[C@H](O)[C@H](O)[C@@H](CO)O3)cn2)nc1
logP-2.0395
TPSA129.41
Number of atoms20
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand M1A
HMDB (Human Metabolome Database) exact match None
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C11H15N5O4/c1-15-3-14-10-6(9(15)12)13-4-16(10)11-8(19)7(18)5(2-17)20-11/h3-5,7-8,11-12,17-19H,2H2,1H3/t5-,7-,8-,11-/m1/s1
InChIKeyGFYLSDSUCHVORB-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


Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
m1A m1A m1A

* 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 mass281.1124
Average mass281.268
[M+H]+282.1202
Product ions150
Normalized LC elution time *0,64 (Kellner 2014); 0,72 (Kellner 2014)
LC elution order/characteristicsbetween U and G (Kellner 2014, 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 -
Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Su D, Chan CT, Gu C, Lim KS, Chionh YH, McBee ME, Russell BS, Babu IR, Begley TJ, Dedon PC... Nat Protoc [details] 24625781 -
Absolute and relative quantification of RNA modifications via biosynthetic isotopomers. Kellner S, Ochel A, Thuring K, Spenkuch F, Neumann J, Sharma S, Entian KD, Schneider D, Helm M... Nucleic Acids Res [details] 25129236 -

Comments

m1A has a positive charge at neutral pH.

Chemical groups contained

TypeSubtype
methyl groupmethyl at aromatic N

Reactions producing 1-methyladenosine

Name
A:m1A

Reactions starting from 1-methyladenosine

Name
m1A:m1I
m1A:m1Am
m1A:A

Last modification of this entry: Sept. 22, 2023