Daphnorin

Details

• Internal ID: 1bdf5f22-7262-4733-a35e-8620a1b1bac3
• Taxonomy: Phenylpropanoids and polyketides > Coumarins and derivatives > Coumarin glycosides
• IUPAC Name: 6-methoxy-3-(2-oxochromen-7-yl)oxy-7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-2-one
• SMILES (Canonical): COC1=C(C=C2C(=C1)C=C(C(=O)O2)OC3=CC4=C(C=C3)C=CC(=O)O4)OC5C(C(C(C(O5)CO)O)O)O
• SMILES (Isomeric): COC1=C(C=C2C(=C1)C=C(C(=O)O2)OC3=CC4=C(C=C3)C=CC(=O)O4)O[C@H]5[C@@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O
• InChI: InChI=1S/C25H22O12/c1-32-16-6-12-7-18(33-13-4-2-11-3-5-20(27)34-14(11)8-13)24(31)35-15(12)9-17(16)36-25-23(30)22(29)21(28)19(10-26)37-25/h2-9,19,21-23,25-26,28-30H,10H2,1H3/t19-,21-,22+,23-,25-/m1/s1
• InChI Key: WYIIRKFHBPIFQZ-FGBFUVBKSA-N
• Popularity: 8 references in papers

Physical and Chemical Properties

• Molecular Formula: C₂₅H₂₂O₁₂
• Molecular Weight: 514.40 g/mol
• Exact Mass: 514.11112613 g/mol
• Topological Polar Surface Area (TPSA): 170.00 Ų
• XlogP: 1.40
• Atomic LogP (AlogP): 0.88
• H-Bond Acceptor: 12
• H-Bond Donor: 4
• Rotatable Bonds: 6

Synonyms

• MLS002472896
• SMR001397007
• 55806-40-1
• cid_185819
• CHEMBL1209491
• BDBM89206
• DTXSID60971207
• HMS2205G09
• NCGC00247451-01
• 6-methoxy-3-(2-oxochromen-7-yl)oxy-7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-2-one
• 6-Methoxy-2-oxo-3-[(2-oxo-2H-1-benzopyran-7-yl)oxy]-2H-1-benzopyran-7-yl hexopyranoside
• 3-(2-ketochromen-7-yl)oxy-6-methoxy-7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-methylol-tetrahydropyran-2-yl]oxy-coumarin
• 6-methoxy-3-[(2-oxo-1-benzopyran-7-yl)oxy]-7-[[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)-2-oxanyl]oxy]-1-benzopyran-2-one
• 7-[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-methoxy-3-(2-oxidanylidenechromen-7-yl)oxy-chromen-2-one

2D Structure

ADMET Properties (via admetSAR 2)

Target	Value	Probability (raw)	Probability (%)
Human Intestinal Absorption	-	0.6646	66.46%
Caco-2	-	0.8864	88.64%
Blood Brain Barrier	-	0.8000	80.00%
Human oral bioavailability	-	0.6143	61.43%
Subcellular localzation	Mitochondria	0.4931	49.31%
OATP2B1 inhibitior	-	0.8371	83.71%
OATP1B1 inhibitior	+	0.8221	82.21%
OATP1B3 inhibitior	+	0.9819	98.19%
MATE1 inhibitior	-	0.8800	88.00%
OCT2 inhibitior	-	0.7500	75.00%
BSEP inhibitior	+	0.7837	78.37%
P-glycoprotein inhibitior	+	0.6226	62.26%
P-glycoprotein substrate	-	0.7398	73.98%
CYP3A4 substrate	+	0.5816	58.16%
CYP2C9 substrate	-	0.8282	82.82%
CYP2D6 substrate	-	0.8494	84.94%
CYP3A4 inhibition	-	0.9139	91.39%
CYP2C9 inhibition	-	0.9155	91.55%
CYP2C19 inhibition	-	0.9229	92.29%
CYP2D6 inhibition	-	0.9528	95.28%
CYP1A2 inhibition	-	0.9085	90.85%
CYP2C8 inhibition	+	0.4665	46.65%
CYP inhibitory promiscuity	-	0.8980	89.80%
UGT catelyzed	-	0.5000	50.00%
Carcinogenicity (binary)	-	0.9900	99.00%
Carcinogenicity (trinary)	Non-required	0.6959	69.59%
Eye corrosion	-	0.9895	98.95%
Eye irritation	-	0.9488	94.88%
Skin irritation	-	0.8333	83.33%
Skin corrosion	-	0.9572	95.72%
Ames mutagenesis	-	0.6900	69.00%
Human Ether-a-go-go-Related Gene inhibition	-	0.4226	42.26%
Micronuclear	+	0.6133	61.33%
Hepatotoxicity	-	0.7942	79.42%
skin sensitisation	-	0.9208	92.08%
Respiratory toxicity	-	0.5111	51.11%
Reproductive toxicity	+	0.7889	78.89%
Mitochondrial toxicity	+	0.5875	58.75%
Nephrotoxicity	-	0.6374	63.74%
Acute Oral Toxicity (c)	III	0.6568	65.68%
Estrogen receptor binding	+	0.8138	81.38%
Androgen receptor binding	+	0.6761	67.61%
Thyroid receptor binding	-	0.5000	50.00%
Glucocorticoid receptor binding	+	0.7562	75.62%
Aromatase binding	-	0.5785	57.85%
PPAR gamma	+	0.7075	70.75%
Honey bee toxicity	-	0.8177	81.77%
Biodegradation	-	0.9000	90.00%
Crustacea aquatic toxicity	-	0.6749	67.49%
Fish aquatic toxicity	+	0.7298	72.98%

Targets

Proven Targets:

CHEMBL ID	UniProt ID	Name	Min activity	Assay type	Source
CHEMBL1993	P26358	DNA (cytosine-5)-methyltransferase 1	7560 nM	IC50	PMID: 19128055
CHEMBL1287622	Q9Y468	Lethal(3)malignant brain tumor-like protein 1	31622.8 nM	Potency	PMID: 13678412
CHEMBL1075138	Q9NUW8	Tyrosyl-DNA phosphodiesterase 1	25118.9 nM	Potency	PMID: 26005918

Predicted Targets (via Super-PRED):

CHEMBL ID	UniProt ID	Name	Probability	Model accuracy
CHEMBL220	P22303	Acetylcholinesterase	98.32%	94.45%
CHEMBL5619	P27695	DNA-(apurinic or apyrimidinic site) lyase	97.57%	91.11%
CHEMBL2635	P51452	Dual specificity protein phosphatase 3	96.11%	94.00%
CHEMBL4016	P42262	Glutamate receptor ionotropic, AMPA 2	91.64%	86.92%
CHEMBL3108638	O15164	Transcription intermediary factor 1-alpha	91.51%	95.56%
CHEMBL3060	Q9Y345	Glycine transporter 2	91.47%	99.17%
CHEMBL2581	P07339	Cathepsin D	91.31%	98.95%
CHEMBL3137262	O60341	LSD1/CoREST complex	89.77%	97.09%
CHEMBL3251	P19838	Nuclear factor NF-kappa-B p105 subunit	89.39%	96.09%
CHEMBL4261	Q16665	Hypoxia-inducible factor 1 alpha	89.12%	85.14%
CHEMBL1075094	Q16236	Nuclear factor erythroid 2-related factor 2	88.43%	96.00%
CHEMBL4208	P20618	Proteasome component C5	88.16%	90.00%
CHEMBL1293249	Q13887	Kruppel-like factor 5	85.55%	86.33%
CHEMBL3401	O75469	Pregnane X receptor	84.61%	94.73%
CHEMBL3880	P07900	Heat shock protein HSP 90-alpha	81.54%	96.21%
CHEMBL5608	Q16288	NT-3 growth factor receptor	80.65%	95.89%
CHEMBL3714130	P46095	G-protein coupled receptor 6	80.18%	97.36%

Plants that contains it

• Daphne genkwa
• Daphne mezereum
• Edgeworthia chrysantha
• Lawsonia inermis
• Ruta corsica
• Stellera chamaejasme
• Wikstroemia retusa

Cross-Links

• PubChem: 185819
• NPASS: NPC284810
• ChEMBL: CHEMBL1209491
• LOTUS: LTS0178249
• wikiData: Q82954645