Modomics - A Database of RNA Modifications

Summary

Full name5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine
IUPAC name[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-methylphosphinic acid
Short name45A
MODOMICS code 5000000009A
Synonyms
[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-methylphosphinic acid
45A
{[5-(6-amino-9h-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(methyl)phosphinic acid
5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine
ABM
AC1L9HEX
adenosine 5'-methylphosphonate
Adenosine-5'-methylphosphonate hemihydrate
ALPHA-METHYLENE ADENOSINE MONOPHOSPHATE
AP2
CID445093
DB02798
methyl phosphonic acid adenosine ester
NS00069557
phosphomethylphosphonic acid adenosyl ester
PXSSQXBLDTZHLF-IOSLPCCCSA-N
Q27454412
SCHEMBL9751898
Nature of the modified residueUnnatural
RNAMods code
Residue unique ID298
Found in RNAYes

Chemical information

Sum formulaC11H16N5O6P
Type of moietynucleotide
Degeneracynot aplicable
PubChem ID445093
SMILESCP(OC[C@@H]1[C@@H](O)[C@@H](O)[C@H]([n]2c3c(c(ncn3)N)nc2)O1)(=O)[O-]
logP-1.1405000000000003
TPSA165.84
Number of atoms39
Number of Hydrogen Bond Acceptors 1 (HBA1)10
Number of Hydrogen Bond Acceptors 2 (HBA2)11
Number of Hydrogen Bond Donors (HBD)4
InChIInChI=1S/C11H16N5O6P/c1-23(19,20)21-2-5-7(17)8(18)11(22-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H,19,20)(H2,12,13,14)/p-1/t5-,7-,8-,11-/m1/s1
InChIKeyPXSSQXBLDTZHLF-IOSLPCCCSA-M
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
CP(OCC1C(O)C(O)C(n2c3c(c(ncn3)N)nc2)O1)(=O)[O-] tautomer #0

CP(OCC1C(O)C(O)C(n2c3c(c(ncn3)N)nc2)O1)(=O)[O-] tautomer #1

CP(OCC1C(O)C(O)C(n2c3c(c(nc[nH]3)=N)nc2)O1)(=O)[O-] tautomer #2

CP(OCC1C(O)C(O)C(n2c3c(c([nH]cn3)=N)nc2)O1)(=O)[O-] tautomer #3

CP(OCC1C(O)C(O)C(N2C=3C(C(N=CN3)=N)N=C2)O1)(=O)[O-] tautomer #4


Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
45A 45A 45A

* 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 massNone
Average mass345.248
[M+H]+ not available
Product ions not available
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.

Last modification of this entry: Sept. 20, 2023