Metabolomics Structure Database

MDLMOL SDF CSV TSV

MW REGNO:	37025
Common Name:	Deoxycytidine
Systematic Name:	4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
RefMet Name:	Deoxycytidine
Synonyms:	[PubChem Synonyms]
Exact Mass:	227.0906 (neutral)    Calculate m/z: (Choose adduct) [M+H]+ [M+H-H2O]+ [M.]+ [M+2H]2+ [M+3H]3+ [M+4H]4+ [M+K]+ [M+2K]2+ [M-H+2K]+ [M+Na]+ [M+2Na]2+ [M-H+2Na]+ [M+Li]+ [M+2Li]2+ [M+NH4]+ [M-H]- [M-2H]2- [M-3H]3- [M-4H]4- [M+Cl]- [M+OAc]- [M+HCOO]- M(neutral)
Formula:	C9H13N3O4
InChIKey:	CKTSBUTUHBMZGZ-SHYZEUOFSA-N
ClassyFire superclass:	Nucleosides, nucleotides, and analogues
ClassyFire class:	Pyrimidine nucleosides
ClassyFire subclass:	Pyrimidine 2'-deoxyribonucleosides
ClassyFire direct parent:	Pyrimidine 2'-deoxyribonucleosides
Massbank MS spectra:	View MS spectra
NP-MRD NMR spectra:	View NMR spectra
SMILES:	c1cn([C@H]2C[C@@H]([C@@H](CO)O2)O)c(=O)nc1N
Studies:	Available studies (via RefMet name)

Select appropriate tab below to view additional details:

All Database Links Calculated Properties Human Pathways

External database links:

PubChem CID:	13711
CHEBI ID:	15698
HMDB ID:	HMDB0000014
KEGG ID:	C00881
Chemspider ID:	13117
METLIN ID:	3367
MetaCyc ID:	DEOXYCYTIDINE
NP-MRD ID(NMR):	NP0000493
Plant Metabolite Hub(Pmhub):	MS000000121

Calculated physicochemical properties (?):

Heavy Atoms:	16
Rings:	2
Aromatic Rings:	1
Rotatable Bonds:	2
van der Waals Molecular volume:	188.88 Å3 molecule-1
Toplogical Polar Sufrace Area:	112.67 Å2 molecule-1
Hydrogen Bond Donors:	3
Hydrogen Bond Acceptors:	6
logP:	0.22
Molar Refractivity:	56.15
Fraction sp3 Carbons:	0.56
sp3 Carbons:	5

Human Pathway links:

HMDB and KEGG pathways containing this metabolite

REACTOME pathways containing this metabolite

References

LIPID MAPS classification: "Update of the LIPID MAPS comprehensive classification system for lipids", Fahy E, Subramaniam S, Murphy RC, Nishijima M, Raetz CR, Shimizu T, Spener F, van Meer G, Wakelam MJ, and Dennis EA, J. Lipid Res. (2009) 50: S9-S14. DOI: 10.1194/jlr.R800095-JLR200
ClassyFire classification: "ClassyFire: automated chemical classification with a comprehensive, computable taxonomy", Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS, J. Cheminformatics (2016) 8:61. DOI: 10.1186/s13321-016-0174-y
NPClassifier classification: "NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products", Kim HW, Wang M, Leber CA, Nothias LF, Reher R, Kang KB, van der Hooft JJJ, Dorrestein PC, Gerwick WH and Cottrell GW. J Nat Prod. 2021 Nov 26;84(11):2795-2807.DOI: 10.1021/acs.jnatprod.1c00399.