Gracillin

Details

• Internal ID: 7b4a7dfd-786e-4bc9-a90e-dd991df946b3
• Taxonomy: Lipids and lipid-like molecules > Steroids and steroid derivatives > Steroidal glycosides > Steroidal saponins
• IUPAC Name: (2S,3R,4R,5R,6S)-2-[(2R,3R,4S,5R,6R)-5-hydroxy-6-(hydroxymethyl)-2-[(1S,2S,4S,5'R,6R,7S,8R,9S,12S,13R,16S)-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.02,9.04,8.013,18]icos-18-ene-6,2'-oxane]-16-yl]oxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-3-yl]oxy-6-methyloxane-3,4,5-triol
• SMILES (Canonical): CC1CCC2(C(C3C(O2)CC4C3(CCC5C4CC=C6C5(CCC(C6)OC7C(C(C(C(O7)CO)O)OC8C(C(C(C(O8)CO)O)O)O)OC9C(C(C(C(O9)C)O)O)O)C)C)C)OC1
• SMILES (Isomeric): C[C@@H]1CC[C@@]2([C@H]([C@H]3[C@@H](O2)C[C@@H]4[C@@]3(CC[C@H]5[C@H]4CC=C6[C@@]5(CC[C@@H](C6)O[C@H]7[C@@H]([C@H]([C@@H]([C@H](O7)CO)O)O[C@H]8[C@@H]([C@H]([C@@H]([C@H](O8)CO)O)O)O)O[C@H]9[C@@H]([C@@H]([C@H]([C@@H](O9)C)O)O)O)C)C)C)OC1
• InChI: InChI=1S/C45H72O17/c1-19-8-13-45(55-18-19)20(2)30-27(62-45)15-26-24-7-6-22-14-23(9-11-43(22,4)25(24)10-12-44(26,30)5)57-42-39(61-40-36(53)34(51)31(48)21(3)56-40)38(33(50)29(17-47)59-42)60-41-37(54)35(52)32(49)28(16-46)58-41/h6,19-21,23-42,46-54H,7-18H2,1-5H3/t19-,20+,21+,23+,24-,25+,26+,27+,28-,29-,30+,31+,32-,33-,34-,35+,36-,37-,38+,39-,40+,41+,42-,43+,44+,45-/m1/s1
• InChI Key: YQEMAEKYNNOCBY-IEMDQPGHSA-N
• Popularity: 27 references in papers

Physical and Chemical Properties

• Molecular Formula: C₄₅H₇₂O₁₇
• Molecular Weight: 885.00 g/mol
• Exact Mass: 884.47695082 g/mol
• Topological Polar Surface Area (TPSA): 256.00 Ų
• XlogP: 1.40
• Atomic LogP (AlogP): 0.21
• H-Bond Acceptor: 17
• H-Bond Donor: 9
• Rotatable Bonds: 8

Synonyms

• 19083-00-2
• CCRIS 4124
• NSC 698787
• CHEBI:5528
• (2S,3R,4R,5R,6S)-2-[(2R,3R,4S,5R,6R)-5-hydroxy-6-(hydroxymethyl)-2-[(1S,2S,4S,5'R,6R,7S,8R,9S,12S,13R,16S)-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.02,9.04,8.013,18]icos-18-ene-6,2'-oxane]-16-yl]oxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-3-yl]oxy-6-methyloxane-3,4,5-triol
• 2-[5-Hydroxy-6-(hydroxymethyl)-2-[(1S,2S,4S,5'R,6R,7S,8R,9S,12S,13R,16S)-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.02,9.04,8.013,18]icos-18-ene-6,2'-oxane]-16-yl]oxy-4-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-3-yl]oxy-6-methyloxane-3,4,5-triol
• beta-D-Glucopyranoside, (3beta,25R)-spirost-5-en-3-yl O-6-deoxy-alpha-L-mannopyranosyl-(1-2)-O-(beta-D-glucopyranosyl-(1-3))-
• C45H72O17
• C45-H72-O17
• CHEMBL500045
• SCHEMBL4661659
• DTXSID301031114
• HY-N0706
• s3915
• AKOS032962645
• CCG-270556
• CS-5792
• AS-74972
• LS-188489
• C08901
• Q1541130
• Diosgenyl rhamnopyranosyl-1-2-(glucopyranosyl-1-3)glucopyranoside
• beta-D-Glucopyranoside, (3beta,25R)-spirost-5-en-3-yl O-6-deoxy-alpha-L-mannopyranosyl-(1-->2)-O-[beta-D-glucopyranosyl-(1-->3)]-

2D Structure

ADMET Properties (via admetSAR 2)

Target	Value	Probability (raw)	Probability (%)
Human Intestinal Absorption	+	0.7196	71.96%
Caco-2	-	0.8872	88.72%
Blood Brain Barrier	-	0.7000	70.00%
Human oral bioavailability	-	0.8000	80.00%
Subcellular localzation	Mitochondria	0.7739	77.39%
OATP2B1 inhibitior	-	1.0000	100.00%
OATP1B1 inhibitior	+	0.8977	89.77%
OATP1B3 inhibitior	+	0.8663	86.63%
MATE1 inhibitior	-	0.9800	98.00%
OCT2 inhibitior	-	0.5750	57.50%
BSEP inhibitior	+	0.8203	82.03%
P-glycoprotein inhibitior	+	0.7178	71.78%
P-glycoprotein substrate	+	0.5000	50.00%
CYP3A4 substrate	+	0.7431	74.31%
CYP2C9 substrate	-	0.8054	80.54%
CYP2D6 substrate	-	0.8216	82.16%
CYP3A4 inhibition	-	0.9460	94.60%
CYP2C9 inhibition	-	0.9118	91.18%
CYP2C19 inhibition	-	0.9113	91.13%
CYP2D6 inhibition	-	0.9360	93.60%
CYP1A2 inhibition	-	0.8848	88.48%
CYP2C8 inhibition	+	0.7490	74.90%
CYP inhibitory promiscuity	-	0.8774	87.74%
UGT catelyzed	-	0.7000	70.00%
Carcinogenicity (binary)	-	0.9900	99.00%
Carcinogenicity (trinary)	Non-required	0.5291	52.91%
Eye corrosion	-	0.9892	98.92%
Eye irritation	-	0.9127	91.27%
Skin irritation	-	0.5662	56.62%
Skin corrosion	-	0.9438	94.38%
Ames mutagenesis	-	1.0000	100.00%
Human Ether-a-go-go-Related Gene inhibition	+	0.7474	74.74%
Micronuclear	-	0.8800	88.00%
Hepatotoxicity	-	1.0000	100.00%
skin sensitisation	-	0.9240	92.40%
Respiratory toxicity	+	0.7556	75.56%
Reproductive toxicity	+	0.8667	86.67%
Mitochondrial toxicity	-	0.5375	53.75%
Nephrotoxicity	-	0.7977	79.77%
Acute Oral Toxicity (c)	III	0.4459	44.59%
Estrogen receptor binding	+	0.8631	86.31%
Androgen receptor binding	+	0.7222	72.22%
Thyroid receptor binding	-	0.5746	57.46%
Glucocorticoid receptor binding	-	0.5909	59.09%
Aromatase binding	+	0.6681	66.81%
PPAR gamma	+	0.7225	72.25%
Honey bee toxicity	-	0.5749	57.49%
Biodegradation	-	0.8500	85.00%
Crustacea aquatic toxicity	-	0.5100	51.00%
Fish aquatic toxicity	+	0.9442	94.42%

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	98.72%	96.09%
CHEMBL5619	P27695	DNA-(apurinic or apyrimidinic site) lyase	98.17%	91.11%
CHEMBL226	P30542	Adenosine A1 receptor	96.60%	95.93%
CHEMBL3137262	O60341	LSD1/CoREST complex	94.87%	97.09%
CHEMBL1994	P08235	Mineralocorticoid receptor	93.56%	100.00%
CHEMBL1806	P11388	DNA topoisomerase II alpha	90.44%	89.00%
CHEMBL1907603	Q05586	Glutamate NMDA receptor; GRIN1/GRIN2B	89.31%	95.89%
CHEMBL4203	Q9HAZ1	Dual specificity protein kinase CLK4	89.24%	94.45%
CHEMBL5608	Q16288	NT-3 growth factor receptor	88.25%	95.89%
CHEMBL4681	P42330	Aldo-keto-reductase family 1 member C3	87.17%	89.05%
CHEMBL5255	O00206	Toll-like receptor 4	86.84%	92.50%
CHEMBL237	P41145	Kappa opioid receptor	86.31%	98.10%
CHEMBL1293249	Q13887	Kruppel-like factor 5	86.24%	86.33%
CHEMBL253	P34972	Cannabinoid CB2 receptor	86.20%	97.25%
CHEMBL4187	Q99250	Sodium channel protein type II alpha subunit	85.49%	95.50%
CHEMBL1821	P08173	Muscarinic acetylcholine receptor M4	84.07%	94.08%
CHEMBL3359	P21462	Formyl peptide receptor 1	83.91%	93.56%
CHEMBL2581	P07339	Cathepsin D	82.39%	98.95%
CHEMBL218	P21554	Cannabinoid CB1 receptor	81.56%	96.61%
CHEMBL2274	Q9H228	Sphingosine 1-phosphate receptor Edg-8	81.22%	100.00%
CHEMBL1907602	P06493	Cyclin-dependent kinase 1/cyclin B1	80.99%	91.24%
CHEMBL2635	P51452	Dual specificity protein phosphatase 3	80.80%	94.00%

Plants that contains it

• Clintonia udensis
• Dioscorea collettii
• Dioscorea collettii var. hypoglauca
• Dioscorea communis
• Dioscorea futschauensis
• Dioscorea gracillima
• Dioscorea nipponica
• Dioscorea panthaica
• Dioscorea pseudojaponica
• Dioscorea spongiosa
• Dioscorea zingiberensis
• Dracaena cochinchinensis
• Dracaena concinna
• Dracaena draco
• Lilium regale
• Paris mairei
• Paris polyphylla
• Paris polyphylla var. chinensis
• Phragmites australis
• Polygonatum kingianum
• Polygonatum zanlanscianense
• Smilax china
• Tribulus terrestris
• Triteleia hyacinthina

Cross-Links

• PubChem: 159861
• NPASS: NPC300557
• ChEMBL: CHEMBL500045
• LOTUS: LTS0264846
• wikiData: Q1541130