Cytidine

Details

• Internal ID: 830e203b-68dc-4d12-8bf8-5b5a260f8ee1
• Taxonomy: Nucleosides, nucleotides, and analogues > Pyrimidine nucleosides
• IUPAC Name: 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
• SMILES (Canonical): C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)O
• SMILES (Isomeric): C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
• InChI: InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1
• InChI Key: UHDGCWIWMRVCDJ-XVFCMESISA-N
• Popularity: 11,837 references in papers

Physical and Chemical Properties

• Molecular Formula: C₉H₁₃N₃O₅
• Molecular Weight: 243.22 g/mol
• Exact Mass: 243.08552052 g/mol
• Topological Polar Surface Area (TPSA): 129.00 Ų
• XlogP: -2.10
• Atomic LogP (AlogP): -2.56
• H-Bond Acceptor: 8
• H-Bond Donor: 4
• Rotatable Bonds: 2

Synonyms

• 65-46-3
• Cytosine riboside
• 1-beta-D-Ribofuranosylcytosine
• 4-Amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone
• beta-D-Ribofuranoside, cytosine-1
• 1beta-D-Ribofuranosylcytosine
• 4-Amino-1beta-D-ribofuranosyl-2(1H)-pyrimidinone
• CHEBI:17562
• 2(1H)-Pyrimidinone, 4-amino-1-beta-D-ribofuranosyl-
• 5CSZ8459RP
• DTXSID60891552
• 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
• NSC-20258
• 4-amino-1-beta-D-ribofuranosylpyrimidin-2(1H)-one
• 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
• Riboside, Cytosine
• Cytosine Ribonucleoside
• Ribonucleoside, Cytosine
• 4-amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl)pyrimidin-2-one
• 4-amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl)-1,2-dihydropyrimidin-2-one
• RefChem:388908
• DTXCID901030645
• 200-610-9
• 1beta-Ribofuranosylcytosine
• Cytidin
• MFCD00006545
• 1-beta-Ribofuranosylcytosine
• Zytidin
• Cytosine, 1-beta-D-ribofuranosyl-
• 1beta-2'-Ribofuranosylcytosine, d-
• Cyd
• NSC 20258
• cytosine-1beta-D-Ribofuranoside
• 2(1H)-Pyrimidinone, 4-amino-1beta-D-ribofuranosyl-
• 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidin-2-one
• C9H13N3O5
• 4-amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidin-2(1H)-one
• Cytidine; Cytarabine Impurity E
• SMR000058243
• Cytosine-beta-D-riboside
• 1.beta.-Ribofuranosylcytosine
• EINECS 200-610-9
• 1.beta.-D-Ribofuranosylcytosine
• UNII-5CSZ8459RP
• beta-cytidine
• .beta.-D-Ribofuranoside, cytosine-1
• 3h-cytidine
• Cytosine, 1-.beta.-D-ribofuranosyl-
• Posilent (TN)
• CTN
• beta.-D-Ribo-C
• Cytidine, 99%
• 1-b-D-ribosyl-Cytosine
• CYTIDINE [MI]
• Cytosine beta-D-riboside
• CP-C
• 4-Amino-1.beta.-D-ribofuranosyl-2(1H)-pyrimidinone
• CYTIDINE [MART.]
• bmse000190
• bmse000969
• bmse001020
• CYTIDINE [WHO-DD]
• Epitope ID:141494
• 2(1H)-Pyrimidinone, 4-amino-1-.beta.-D-ribofuranosyl-
• SCHEMBL7179
• 1-b-D-Ribofuranosylcytosine
• cytosine-1b-D-Ribofuranoside
• beta-D-ribofuranosyl-cytidine
• MLS000049947
• MLS002207040
• 1-beta-D-ribosyl- (6CI)
• 1-beta-delta-ribosyl-Cytosine
• CHEMBL95606
• GTPL4728
• orb1308081
• SCHEMBL8525830
• 1-beta-D-ribofuranosyl-Cytosine
• cytosine-1b-delta-Ribofuranoside
• SCHEMBL17856892
• SCHEMBL24781031
• SCHEMBL31146639
• 1beta-delta-Ribofuranosylcytosine
• Cytosine-1-beta-D-ribofuranoside
• MSK6801
• 1-beta-delta-Ribofuranosylcytosine
• Cytidine, >=99.0% (HPLC)
• cytosine-1beta-delta-Ribofuranoside
• 1-beta-delta-ribofuranosyl-Cytosine
• HY-B0158
• MMV638723
• s2053
• SBB003195
• AKOS015888568
• CCG-266896
• CS-1989
• DB02097
• NC04070
• SRI-2352_17
• NCGC00093356-08
• NCGC00142483-01
• NCGC00142483-09
• AS-12696
• BP-58628
• ST056938
• SY005417
• DB-029614
• NS00069068
• 65C463
• C00475
• D07769
• EN300-184125
• 1-(beta-D-ribofuranosyl)-4-aminopyrimidin-2-one
• 4-Amino-1-|A-D-ribofuranosyl-2(1H)-pyrimidinone
• 4-Amino-1-b-D-ribofuranosyl-2(1H)-pyrimidinone
• Cytosine -D-riboside;Cytosine-1--D-ribofuranoside
• F226675
• Q422538
• BRD-K71847383-001-07-5
• BRD-K71847383-001-12-5
• 4-Amino-1-.beta.-D-ribofuranosyl-2-(1H)-pyrimidinone
• 4-Amino-1-beta-delta-ribofuranosyl-2(1H)-pyrimidinone
• F0348-2240
• Z1879263740
• 1-(b-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
• 6D2DC474-DD76-4081-8B34-10605C218F49
• 1-(b-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
• 1-(beta-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine
• Cytidine, BioReagent, suitable for cell culture, powder, >=99%

2D Structure

ADMET Properties (via admetSAR 2)

Target	Value	Probability (raw)	Probability (%)
Human Intestinal Absorption	-	0.5214	52.14%
Caco-2	-	0.9072	90.72%
Blood Brain Barrier	+	0.8500	85.00%
Human oral bioavailability	-	0.8571	85.71%
Subcellular localzation	Nucleus	0.4886	48.86%
OATP2B1 inhibitior	-	1.0000	100.00%
OATP1B1 inhibitior	+	0.9461	94.61%
OATP1B3 inhibitior	+	0.9506	95.06%
MATE1 inhibitior	-	1.0000	100.00%
OCT2 inhibitior	-	1.0000	100.00%
BSEP inhibitior	-	0.9797	97.97%
P-glycoprotein inhibitior	-	0.9526	95.26%
P-glycoprotein substrate	-	0.9737	97.37%
CYP3A4 substrate	-	0.6285	62.85%
CYP2C9 substrate	-	0.8000	80.00%
CYP2D6 substrate	-	0.8777	87.77%
CYP3A4 inhibition	-	0.9609	96.09%
CYP2C9 inhibition	-	0.9638	96.38%
CYP2C19 inhibition	-	0.9489	94.89%
CYP2D6 inhibition	-	0.9497	94.97%
CYP1A2 inhibition	-	0.9543	95.43%
CYP2C8 inhibition	-	0.9860	98.60%
CYP inhibitory promiscuity	-	0.9810	98.10%
UGT catelyzed	+	0.7000	70.00%
Carcinogenicity (binary)	-	0.9700	97.00%
Carcinogenicity (trinary)	Danger	0.4707	47.07%
Eye corrosion	-	0.9899	98.99%
Eye irritation	-	0.9761	97.61%
Skin irritation	-	0.7802	78.02%
Skin corrosion	-	0.9438	94.38%
Ames mutagenesis	-	1.0000	100.00%
Human Ether-a-go-go-Related Gene inhibition	-	0.7018	70.18%
Micronuclear	+	1.0000	100.00%
Hepatotoxicity	+	0.9502	95.02%
skin sensitisation	-	0.8566	85.66%
Respiratory toxicity	+	0.9556	95.56%
Reproductive toxicity	+	1.0000	100.00%
Mitochondrial toxicity	+	0.9875	98.75%
Nephrotoxicity	+	0.4497	44.97%
Acute Oral Toxicity (c)	III	0.7926	79.26%
Estrogen receptor binding	-	0.5448	54.48%
Androgen receptor binding	+	0.8696	86.96%
Thyroid receptor binding	+	0.5416	54.16%
Glucocorticoid receptor binding	+	0.6838	68.38%
Aromatase binding	+	0.5341	53.41%
PPAR gamma	+	0.7112	71.12%
Honey bee toxicity	-	0.9394	93.94%
Biodegradation	-	0.9000	90.00%
Crustacea aquatic toxicity	-	0.7100	71.00%
Fish aquatic toxicity	-	0.9006	90.06%

Targets

Proven Targets:

CHEMBL ID	UniProt ID	Name	Min activity	Assay type	Source
CHEMBL5023	Q00987	p53-binding protein Mdm-2	20 nM	IC50	via Super-PRED
CHEMBL1293235	P02545	Prelamin-A/C	39.8 nM	Potency	via Super-PRED
CHEMBL2842	P42345	Serine/threonine-protein kinase mTOR	73.6 nM	Potency	via Super-PRED

Predicted Targets (via Super-PRED):

CHEMBL ID	UniProt ID	Name	Probability	Model accuracy
CHEMBL226	P30542	Adenosine A1 receptor	96.07%	95.93%
CHEMBL3251	P19838	Nuclear factor NF-kappa-B p105 subunit	95.60%	96.09%
CHEMBL3137261	O14744	PRMT5/MEP50 complex	92.18%	100.00%
CHEMBL2140	P48775	Tryptophan 2,3-dioxygenase	89.22%	98.46%
CHEMBL2635	P51452	Dual specificity protein phosphatase 3	87.92%	94.00%
CHEMBL3137262	O60341	LSD1/CoREST complex	84.35%	97.09%
CHEMBL5619	P27695	DNA-(apurinic or apyrimidinic site) lyase	83.43%	91.11%
CHEMBL2581	P07339	Cathepsin D	82.97%	98.95%
CHEMBL1293249	Q13887	Kruppel-like factor 5	81.83%	86.33%

Plants that contains it

• Arabidopsis thaliana
• Capsicum annuum
• Castanopsis fissa
• Euryale ferox
• Fritillaria cirrhosa
• Fritillaria delavayi
• Fritillaria pallidiflora
• Fritillaria przewalskii
• Fritillaria taipaiensis
• Fritillaria thunbergii
• Fritillaria unibracteata
• Fritillaria verticillata
• Fritillaria walujewii
• Ginkgo biloba
• Isatis tinctoria
• Morinda citrifolia
• Panax notoginseng
• Persicaria tinctoria
• Pinellia ternata
• Typha angustifolia
• Typha orientalis
• Ziziphus jujuba

Cross-Links

• PubChem: 6175
• NPASS: NPC62927
• ChEMBL: CHEMBL95606
• LOTUS: LTS0273945
• wikiData: Q105030172