Garcinone D

Details

• Internal ID: 6afe363c-042a-4ec7-9071-5772bfbf614b
• Taxonomy: Organoheterocyclic compounds > Benzopyrans > 1-benzopyrans > Xanthones > 8-prenylated xanthones
• IUPAC Name: 1,3,6-trihydroxy-8-(3-hydroxy-3-methylbutyl)-7-methoxy-2-(3-methylbut-2-enyl)xanthen-9-one
• SMILES (Canonical): CC(=CCC1=C(C2=C(C=C1O)OC3=C(C2=O)C(=C(C(=C3)O)OC)CCC(C)(C)O)O)C
• SMILES (Isomeric): CC(=CCC1=C(C2=C(C=C1O)OC3=C(C2=O)C(=C(C(=C3)O)OC)CCC(C)(C)O)O)C
• InChI: InChI=1S/C24H28O7/c1-12(2)6-7-13-15(25)10-18-20(21(13)27)22(28)19-14(8-9-24(3,4)29)23(30-5)16(26)11-17(19)31-18/h6,10-11,25-27,29H,7-9H2,1-5H3
• InChI Key: TYALNCRUIKOKGP-UHFFFAOYSA-N
• Popularity: 18 references in papers

Physical and Chemical Properties

• Molecular Formula: C₂₄H₂₈O₇
• Molecular Weight: 428.50 g/mol
• Exact Mass: 428.18350323 g/mol
• Topological Polar Surface Area (TPSA): 116.00 Ų
• XlogP: 4.90
• Atomic LogP (AlogP): 4.28
• H-Bond Acceptor: 7
• H-Bond Donor: 4
• Rotatable Bonds: 6

Synonyms

• 107390-08-9
• 1,3,6-trihydroxy-8-(3-hydroxy-3-methylbutyl)-7-methoxy-2-(3-methylbut-2-enyl)xanthen-9-one
• CHEMBL462879
• 1,3,6-TRIHYDROXY-8-(3-HYDROXY-3-METHYLBUTYL)-7-METHOXY-2-(3-METHYLBUT-2-EN-1-YL)-9H-XANTHEN-9-ONE
• Garcinone-D
• D05YJR
• Garcinia mangostana (Mangosteen)
• DTXSID00420547
• HY-N6953
• BDBM50250510
• AKOS037514656
• MS-27582
• CS-0027732
• FT-0686619
• A14800
• F82147
• Q-100046
• 1,3,6-trihydroxy-8-(3-hydroxy-3-methyl-butyl)-7-methoxy-2-(3-methylbut-2-enyl)xanthen-9-one
• 9H-Xanthen-9-one, 1,3,6-trihydroxy-8-(3-hydroxy-3-methylbutyl)-7-methoxy-2-(3-methyl-2-butenyl)-

2D Structure

ADMET Properties (via admetSAR 2)

Target	Value	Probability (raw)	Probability (%)
Human Intestinal Absorption	+	0.9711	97.11%
Caco-2	+	0.5926	59.26%
Blood Brain Barrier	+	0.5500	55.00%
Human oral bioavailability	+	0.6286	62.86%
Subcellular localzation	Mitochondria	0.5279	52.79%
OATP2B1 inhibitior	-	0.7062	70.62%
OATP1B1 inhibitior	+	0.9138	91.38%
OATP1B3 inhibitior	+	0.9178	91.78%
MATE1 inhibitior	-	0.7600	76.00%
OCT2 inhibitior	-	0.8500	85.00%
BSEP inhibitior	+	0.6160	61.60%
P-glycoprotein inhibitior	-	0.4520	45.20%
P-glycoprotein substrate	-	0.6917	69.17%
CYP3A4 substrate	+	0.5967	59.67%
CYP2C9 substrate	-	0.5948	59.48%
CYP2D6 substrate	-	0.8240	82.40%
CYP3A4 inhibition	-	0.6398	63.98%
CYP2C9 inhibition	+	0.5407	54.07%
CYP2C19 inhibition	+	0.5707	57.07%
CYP2D6 inhibition	-	0.6475	64.75%
CYP1A2 inhibition	+	0.7353	73.53%
CYP2C8 inhibition	+	0.5449	54.49%
CYP inhibitory promiscuity	+	0.5000	50.00%
UGT catelyzed	+	0.7000	70.00%
Carcinogenicity (binary)	-	0.9800	98.00%
Carcinogenicity (trinary)	Non-required	0.7007	70.07%
Eye corrosion	-	0.9914	99.14%
Eye irritation	-	0.6648	66.48%
Skin irritation	-	0.7136	71.36%
Skin corrosion	-	0.9281	92.81%
Ames mutagenesis	+	0.5400	54.00%
Human Ether-a-go-go-Related Gene inhibition	-	0.3738	37.38%
Micronuclear	-	0.7400	74.00%
Hepatotoxicity	-	0.5968	59.68%
skin sensitisation	-	0.8016	80.16%
Respiratory toxicity	+	0.7000	70.00%
Reproductive toxicity	+	0.9556	95.56%
Mitochondrial toxicity	+	0.8000	80.00%
Nephrotoxicity	-	0.9273	92.73%
Acute Oral Toxicity (c)	III	0.4975	49.75%
Estrogen receptor binding	+	0.9041	90.41%
Androgen receptor binding	+	0.6763	67.63%
Thyroid receptor binding	+	0.5558	55.58%
Glucocorticoid receptor binding	+	0.8723	87.23%
Aromatase binding	+	0.7870	78.70%
PPAR gamma	+	0.8804	88.04%
Honey bee toxicity	-	0.7594	75.94%
Biodegradation	-	0.8000	80.00%
Crustacea aquatic toxicity	-	0.5200	52.00%
Fish aquatic toxicity	+	0.9639	96.39%

Targets

Proven Targets:

CHEMBL ID	UniProt ID	Name	Min activity	Assay type	Source
CHEMBL1978	P11511	Cytochrome P450 19A1	5200 nM	IC50	PMID: 18558747
CHEMBL5533	Q04206	Nuclear factor NF-kappa-B p65 subunit	3200 nM	IC50	PMID: 19839614

Predicted Targets (via Super-PRED):

CHEMBL ID	UniProt ID	Name	Probability	Model accuracy
CHEMBL5619	P27695	DNA-(apurinic or apyrimidinic site) lyase	99.55%	91.11%
CHEMBL3401	O75469	Pregnane X receptor	95.11%	94.73%
CHEMBL4203	Q9HAZ1	Dual specificity protein kinase CLK4	94.50%	94.45%
CHEMBL1293249	Q13887	Kruppel-like factor 5	94.08%	86.33%
CHEMBL2581	P07339	Cathepsin D	94.00%	98.95%
CHEMBL2635	P51452	Dual specificity protein phosphatase 3	91.75%	94.00%
CHEMBL1293267	Q9HC97	G-protein coupled receptor 35	91.53%	89.34%
CHEMBL4793	Q86TI2	Dipeptidyl peptidase IX	88.79%	96.95%
CHEMBL215	P09917	Arachidonate 5-lipoxygenase	88.55%	92.68%
CHEMBL4016	P42262	Glutamate receptor ionotropic, AMPA 2	88.54%	86.92%
CHEMBL1806	P11388	DNA topoisomerase II alpha	88.10%	89.00%
CHEMBL3060	Q9Y345	Glycine transporter 2	87.36%	99.17%
CHEMBL3192	Q9BY41	Histone deacetylase 8	84.47%	93.99%
CHEMBL4261	Q16665	Hypoxia-inducible factor 1 alpha	83.81%	85.14%
CHEMBL3194	P02766	Transthyretin	82.79%	90.71%
CHEMBL3108638	O15164	Transcription intermediary factor 1-alpha	80.72%	95.56%
CHEMBL5163	Q9NY46	Sodium channel protein type III alpha subunit	80.00%	96.90%

Plants that contains it

• Aster bellidiastrum
• Caragana halodendron
• Cratoxylum cochinchinense
• Davallia divaricata
• Dolomiaea souliei
• Eucalyptus camaldulensis
• Garcinia dulcis
• Garcinia mangostana
• Garcinia morella
• Ligularia vellerea
• Lonicera hypoleuca
• Nicotiana sylvestris
• Serpocaulon triseriale

Cross-Links

• PubChem: 5495926
• NPASS: NPC61010
• ChEMBL: CHEMBL462879
• LOTUS: LTS0006332
• wikiData: Q72480078