Modomics - A Database of RNA Modifications

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 name	5-formylcytidine
IUPAC name	4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxopyrimidine-5-carbaldehyde
Short name	f5C
MODOMICS code new	2000000071C
MODOMICS code	71C
Synonyms	148608-53-1 259823-22-8 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxopyrimidine-5-carbaldehyde 4-Amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-2-oxo-1,2-dihydropyrimidine-5-carbaldehyde 5-Formylcytidine AC1L31O6 CID132842 CTK0I2055 Cytidine, 5-formyl- cytidine, 6-formyl- DTXSID00164035 SCHEMBL453966
Nature of the modified residue	Natural
RNAMods code	>
Residue unique ID	31
Found in RNA	Yes
Related nucleotides	232
Enzymes	ALKBH1 (Homo sapiens)
Found naturally in RNA types	tRNA

Chemical information

Sum formula	C10H13N3O6
Type of moiety	nucleoside
Degeneracy	not applicable
SMILES	Nc1nc(=O)[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)cc1C=O
logP	-2.1693
TPSA	147.9
Number of atoms	19
Number of Hydrogen Bond Acceptors 1 (HBA1)	8
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	LKC
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand	None
InChI	InChI=1S/C10H13N3O6/c11-8-4(2-14)1-13(10(18)12-8)9-7(17)6(16)5(3-15)19-9/h1-2,5-7,9,15-17H,3H2,(H2,11,12,18)/t5-,6-,7-,9-/m1/s1
InChIKey	OCMSXKMNYAHJMU-JXOAFFINSA-N
Search the molecule in external databases	ChEMBL ChemAgora ChEBI PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	132842
PubChem SIDs	10243209 16413044 29310879 50909792 57344277 104378339 128789250 135088642 162477636 226774032 241037393 273115965 315724488 316892629 316892819 319154100 341246688 347752853 355132154 381984416 383002991 389479182 405016558 415829224 435892036 439613175 441007051 441169428

^* 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)cc1C=O tautomer #0 Nc1nc(=O)n(C2OC(CO)C(O)C2O)cc1C=O tautomer #1 N=c1nc(O)n(C2OC(CO)C(O)C2O)cc1C=O tautomer #2
Tautomer image	Show Image

Predicted CYP Metabolic Sites

CYP3A4	CYP2D6	CYP2C9

^* 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 mass	271.0804
Average mass	271.227
[M+H]⁺	272.0882
Product ions	140
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.

Chemical groups contained

Type	Subtype
other	formyl

Reactions producing 5-formylcytidine

Name
C:f5C
hm5C:f5C

Reactions starting from 5-formylcytidine

Name
f5C:f5Cm

Last modification of this entry: Sept. 22, 2023