Spongouridine

Details

• Internal ID: ea73914a-e27e-4c3e-8690-8458aaee716a
• Taxonomy: Nucleosides, nucleotides, and analogues > Pyrimidine nucleosides
• IUPAC Name: 1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione
• SMILES (Canonical): C1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)O
• SMILES (Isomeric): C1=CN(C(=O)NC1=O)[C@H]2[C@H]([C@@H]([C@H](O2)CO)O)O
• InChI: InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7+,8-/m1/s1
• InChI Key: DRTQHJPVMGBUCF-CCXZUQQUSA-N
• Popularity: 707 references in papers

Physical and Chemical Properties

• Molecular Formula: C₉H₁₂N₂O₆
• Molecular Weight: 244.20 g/mol
• Exact Mass: 244.06953611 g/mol
• Topological Polar Surface Area (TPSA): 119.00 Ų
• XlogP: -2.00
• Atomic LogP (AlogP): -2.85
• H-Bond Acceptor: 7
• H-Bond Donor: 4
• Rotatable Bonds: 2

Synonyms

• 3083-77-0
• Arauridine
• 1-beta-D-Arabinofuranosyluracil
• Uracil arabinoside
• ARABINOFURANOSYLURACIL
• Ara-U
• Spongouridin
• Uracil-beta-D-arabinofuranoside
• Uridine arabinoside
• 1-((2R,3S,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidine-2,4(1H,3H)-dione
• Spongouridine (VAN)
• Arabinosyluracil
• NSC 68928
• 1beta-D-Arabinofuranosyluracil
• 1-beta-D-Arabinofurnosyluracil
• ZK0WMW5NQF
• EINECS 221-386-9
• BRN 0028749
• 2,4(1H,3H)-Pyrimidinedione, 1-beta-D-arabinofuranosyl-
• CHEBI:68346
• Uracil, 1-beta-D-arabinofuranosyl-
• 1-beta-D-Arabinofuranosyl-(1H,3H)-pyrimidine-2,4-dione
• Uracil, 1-beta-D-arabinofuranosyl- (VAN)
• 5-24-06-00136 (Beilstein Handbook Reference)
• 2,4(1H,3H)-Pyrimidinedione, 1-.beta.-D-arabinofuranosyl-
• MFCD00065998
• 1-beta-D-Arabinofuranosylpyrimidine-2,4(1H,3H)-dione (Uracil Arabinoside)
• C9-H12-N2-O6
• NSC-68928
• Uracil 1-|A-D-arabinofuranoside
• Uracil, 1-.beta.-D-arabinofuranosyl-
• 1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione
• UNII-ZK0WMW5NQF
• 1-eta--rabinofuranosyluracl
• 1-?-D-Arabinofuranosyluracil
• SCHEMBL359587
• Uracil 1--D-arabinofuranoside
• Uracil 1-b-D-arabinofuranoside
• CHEMBL1092065
• DTXSID80184832
• DRTQHJPVMGBUCF-CCXZUQQUSA-N
• uracil-1-beta-D-arabinofuranoside
• 1-(beta-D-arabinofuranosyl)uracil
• BCP29295
• HY-N6652
• URACIL ARABINOSIDE [USP-RS]
• HG1013
• s4807
• Uracil 1- beta -D-arabinofuranoside
• AKOS015969693
• CCG-266899
• 1-| cent-D-ARABINOFURANOSYLURACIL
• DS-14592
• LS-158555
• CS-0083204
• SW220050-1
• A820641
• J-700006
• 1-(beta-D-arabinofuranosyl)-pyrimidin-2,4(3H)-dione
• Q27136843
• Uracil 1-beta-D-arabinofuranoside, lymphoma antiproliferative
• 1-.BETA.-D-ARABINOFURANOSYL-2,4(1H,3H)-PYRIMIDINEDIONE
• Uracil arabinoside, European Pharmacopoeia (EP) Reference Standard
• Uracil arabinoside, United States Pharmacopeia (USP) Reference Standard
• 1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)-2-oxolanyl]pyrimidine-2,4-dione
• 1-[(2R,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]pyrimidine-2,4-dione

2D Structure

ADMET Properties (via admetSAR 2)

Target	Value	Probability (raw)	Probability (%)
Human Intestinal Absorption	-	0.8841	88.41%
Caco-2	-	0.9536	95.36%
Blood Brain Barrier	+	0.6000	60.00%
Human oral bioavailability	-	0.8714	87.14%
Subcellular localzation	Nucleus	0.5714	57.14%
OATP2B1 inhibitior	-	1.0000	100.00%
OATP1B1 inhibitior	+	0.9391	93.91%
OATP1B3 inhibitior	+	0.9510	95.10%
MATE1 inhibitior	-	1.0000	100.00%
OCT2 inhibitior	-	1.0000	100.00%
BSEP inhibitior	-	0.9679	96.79%
P-glycoprotein inhibitior	-	0.9599	95.99%
P-glycoprotein substrate	-	0.9745	97.45%
CYP3A4 substrate	-	0.6070	60.70%
CYP2C9 substrate	-	0.5918	59.18%
CYP2D6 substrate	-	0.8725	87.25%
CYP3A4 inhibition	-	0.9617	96.17%
CYP2C9 inhibition	-	0.9626	96.26%
CYP2C19 inhibition	-	0.9462	94.62%
CYP2D6 inhibition	-	0.9381	93.81%
CYP1A2 inhibition	-	0.9301	93.01%
CYP2C8 inhibition	-	0.9795	97.95%
CYP inhibitory promiscuity	-	0.9781	97.81%
UGT catelyzed	+	0.7000	70.00%
Carcinogenicity (binary)	-	0.8800	88.00%
Carcinogenicity (trinary)	Non-required	0.4917	49.17%
Eye corrosion	-	0.9904	99.04%
Eye irritation	-	0.9557	95.57%
Skin irritation	-	0.7975	79.75%
Skin corrosion	-	0.9508	95.08%
Ames mutagenesis	-	0.7900	79.00%
Human Ether-a-go-go-Related Gene inhibition	-	0.7552	75.52%
Micronuclear	+	1.0000	100.00%
Hepatotoxicity	+	0.8000	80.00%
skin sensitisation	-	0.8829	88.29%
Respiratory toxicity	+	0.7444	74.44%
Reproductive toxicity	+	0.9778	97.78%
Mitochondrial toxicity	+	0.9250	92.50%
Nephrotoxicity	-	0.6439	64.39%
Acute Oral Toxicity (c)	III	0.6185	61.85%
Estrogen receptor binding	-	0.6636	66.36%
Androgen receptor binding	+	0.7304	73.04%
Thyroid receptor binding	-	0.6698	66.98%
Glucocorticoid receptor binding	+	0.6553	65.53%
Aromatase binding	-	0.6036	60.36%
PPAR gamma	+	0.6937	69.37%
Honey bee toxicity	-	0.9214	92.14%
Biodegradation	-	0.6750	67.50%
Crustacea aquatic toxicity	-	0.7500	75.00%
Fish aquatic toxicity	-	0.8321	83.21%

Targets

Proven Targets:

No proven targets yet!

Predicted Targets (via Super-PRED):

CHEMBL ID	UniProt ID	Name	Probability	Model accuracy
CHEMBL3251	P19838	Nuclear factor NF-kappa-B p105 subunit	95.41%	96.09%
CHEMBL4016	P42262	Glutamate receptor ionotropic, AMPA 2	93.47%	86.92%
CHEMBL226	P30542	Adenosine A1 receptor	92.94%	95.93%
CHEMBL2581	P07339	Cathepsin D	92.85%	98.95%
CHEMBL4203	Q9HAZ1	Dual specificity protein kinase CLK4	86.17%	94.45%
CHEMBL2635	P51452	Dual specificity protein phosphatase 3	83.88%	94.00%
CHEMBL5619	P27695	DNA-(apurinic or apyrimidinic site) lyase	83.44%	91.11%
CHEMBL2123	P51582	Pyrimidinergic receptor P2Y4	82.79%	93.39%
CHEMBL255	P29275	Adenosine A2b receptor	81.49%	98.59%
CHEMBL1806	P11388	DNA topoisomerase II alpha	80.99%	89.00%
CHEMBL3137262	O60341	LSD1/CoREST complex	80.72%	97.09%

Plants that contains it

• Lepisorus contortus

Cross-Links

• PubChem: 18323
• NPASS: NPC89051
• ChEMBL: CHEMBL1092065
• LOTUS: LTS0097578
• wikiData: Q27136843