Metabolomics Structure Database

MDLMOL SDF CSV TSV

MW REGNO:	43237
Common Name:	Cytarabine
Systematic Name:	4-amino-1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
RefMet Name:	Cytarabine
Synonyms:	[PubChem Synonyms]
Exact Mass:	243.0855 (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:	C9H13N3O5
InChIKey:	UHDGCWIWMRVCDJ-CCXZUQQUSA-N
ClassyFire superclass:	Nucleosides, nucleotides, and analogues
ClassyFire class:	Pyrimidine nucleosides
ClassyFire subclass:	Pyrimidine nucleosides
ClassyFire direct parent:	Aromatic heteromonocyclic compounds
Massbank MS spectra:	View MS spectra
NP-MRD NMR spectra:	View NMR spectra
SMILES:	c1cn([C@H]2[C@H]([C@@H]([C@@H](CO)O2)O)O)c(=O)nc1N
Studies:	Available studies (via RefMet name)

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All Database Links Calculated Properties Human Pathways

External database links:

PubChem CID:	6253
CHEBI ID:	28680
HMDB ID:	HMDB0015122
KEGG ID:	C02961
Chemspider ID:	6017
NP-MRD ID(NMR):	NP0000033
EPA CompTox DB:	DTXCID80196738

Calculated physicochemical properties (?):

Heavy Atoms:	17
Rings:	2
Aromatic Rings:	1
Rotatable Bonds:	2
van der Waals Molecular volume:	197.67 Å3 molecule-1
Toplogical Polar Sufrace Area:	132.90 Å2 molecule-1
Hydrogen Bond Donors:	4
Hydrogen Bond Acceptors:	7
logP:	-0.52
Molar Refractivity:	58.05
Fraction sp3 Carbons:	0.56
sp3 Carbons:	5

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.