Modomics - A Database of RNA Modifications

hm5C
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 name5-hydroxymethylcytidine
IUPAC name4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)pyrimidin-2-one
Short namehm5C
MODOMICS code new2000000051C
MODOMICS code51C
Synonyms
19235-17-7
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)pyrimidin-2-one
4-amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-(hydroxymethyl)pyrimidin-2(1H)-one
5-hydroxymethyl cytidine
5-hydroxymethylcytidine
5-(Hydroxymethyl)cytidine
BRD-K68006081-001-01-1
Cytidine, 5-(hydroxymethyl)-
SCHEMBL156036
Nature of the modified residueNatural
RNAMods code∅
Residue unique ID119
Found in RNAYes
Related nucleotides254
Enzymes ALKBH1 (Homo sapiens)

Chemical information

Sum formulaC10H15N3O6
Type of moietynucleoside
Degeneracynot applicable
SMILESNc1nc(=O)[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)cc1CO
logP-2.4895
TPSA151.06
Number of atoms19
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)5
PDB no exac match , link to the most similar ligand LKC
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C10H15N3O6/c11-8-4(2-14)1-13(10(18)12-8)9-7(17)6(16)5(3-15)19-9/h1,5-7,9,14-17H,2-3H2,(H2,11,12,18)/t5-,6-,7-,9-/m1/s1
InChIKeyNFEXJLMYXXIWPI-JXOAFFINSA-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
N=c1[nH]c(=O)n(C2OC(CO)C(O)C2O)cc1CO tautomer #0
Nc1nc(=O)n(C2OC(CO)C(O)C2O)cc1CO tautomer #1
N=c1nc(O)n(C2OC(CO)C(O)C2O)cc1CO tautomer #2
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
hm5C hm5C hm5C

* 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 mass273.0961
Average mass273.243
[M+H]+274.1039
Product ions142
Normalized LC elution time *0,52 (Kellner 2014)
LC elution order/characteristicsbetween C and U (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
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 -

Chemical groups contained

TypeSubtype
otherhydroxymethyl

Reactions producing 5-hydroxymethylcytidine

Name
C:hm5C
m5C:hm5C

Reactions starting from 5-hydroxymethylcytidine

Name
hm5C:f5Cm
hm5C:f5C

Last modification of this entry: Sept. 22, 2023