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Gardenifolin E

Family: Rubiaceae
Kingdom: Plantae
Class: Lignan

Canonical Smiles	COC(=O)/C(=C(\c1cc(OC)c2c(c1)[C@@H](CO)[C@H](O2)c1ccc(c(c1)OC)O)/C)/C
InChI	InChI=1S/C23H26O7/c1-12(13(2)23(26)29-5)15-8-16-17(11-24)21(30-22(16)20(10-15)28-4)14-6-7-18(25)19(9-14)27-3/h6-10,17,21,24-25H,11H2,1-5H3/b13-12-/t17-,21-/m1/s1
InChIKey	LDXYOYLFYDQQRY-LAEXESCWSA-N
Formula	C₂₃H₂₆O₇
HBA	7
HBD	2
MW	414.45
Rotatable Bonds	6
TPSA	94.45
LogP	3.59
Number Rings	3
Number Aromatic Rings	2
Heavy Atom Count	30
Formal Charge	0
Fraction CSP3	0.35
Exact Mass	414.17
Number of Lipinski Rule Violations	0

#	Species	Family	Kingdom	NCBI Taxonomy ID
1	Gardenia ternifolia	Rubiaceae	Plantae	1237590

Showing of synonyms

Tshitenge DT, Feineis D, et al. (2017). Gardenifolins A-H, Scalemic Neolignans from Gardenia ternifolia: Chiral Resolution, Configurational Assignment, and Cytotoxic Activities against the HeLa Cancer Cell Line.. Journal of natural products,2017, 80(5), 1604-1614. [View] [PubMed]

No compound-protein relationship available.

SMILES: c1cccc(c12)OC(C2)c3ccccc3

Level: 1

Mol. Weight: 196.25 g/mol

SMILES: C1COc(c12)cccc2

Level: 0

Mol. Weight: 120.15 g/mol

SMILES: c1ccccc1

Level: 0

Mol. Weight: 78.11 g/mol

Cytotoxic

Absorption

Caco-2 (logPapp): -4.6
Human Oral Bioavailability 20%: Non-Bioavailable
Human Intestinal Absorption: Absorbed
Madin-Darby Canine Kidney: -4.730
Human Oral Bioavailability 50%: Non-Bioavailable
P-Glycoprotein Inhibitor: Inhibitor
P-Glycoprotein Substrate: Non-Substrate
Skin Permeability: -2.54

Distribution

Blood-Brain Barrier (CNS): -
Blood-Brain Barrier: Penetrable
Fraction Unbound (Human): 1.070
Plasma Protein Binding: 78.96
Steady State Volume of Distribution: -

Metabolism

Breast Cancer Resistance Protein: Non-Inhibitor
CYP 1A2 Inhibitor: Non-Inhibitor
CYP 1A2 Substrate: Substrate
CYP 2C19 Inhibitor: Inhibitor
CYP 2C19 Substrate: Non-Substrate
CYP 2C9 Inhibitor: Inhibitor
CYP 2C9 Substrate: Substrate
CYP 2D6 Inhibitor: Non-Inhibitor
CYP 2D6 Substrate: Non-Substrate
CYP 3A4 Inhibitor: Inhibitor
CYP 3A4 Substrate: Substrate
OATP1B1: Non-Inhibitor
OATP1B3: Non-Inhibitor

Excretion

Clearance: 10.190
Organic Cation Transporter 2: Non-Inhibitor
Half-Life of Drug: -

Toxicity

AMES Mutagenesis: Safe
Avian: Safe
Bee: Toxic
Bioconcentration Factor: 0.970
Biodegradation: Safe
Carcinogenesis: Safe
Crustacean: Toxic
Liver Injury I (DILI): Safe
Eye Corrosion: Safe
Eye Irritation: Safe
Maximum Tolerated Dose: 0.600
Liver Injury II: Toxic
hERG Blockers: Safe
Daphnia Maga: 5.790
Micronucleos: Toxic
NR-AhR: Safe
NR-AR: Safe
NR-AR-LBD: Safe
NR-Aromatase: Safe
NR-ER: Safe
NR-ER-LBD: Safe
NR-GR: Toxic
NR-PPAR-gamma: Safe
NR-TR: Safe
T. Pyriformis: -30.270
Rat (Acute): 2.290
Rat (Chronic Oral): 2.750
Fathead Minnow: 4.990
Respiratory Disease: Toxic
Skin Sensitisation: Safe
SR-ARE: Safe
SR-ATAD5: Safe
SR-HSE: Safe
SR-MMP: Toxic
SR-p53: Safe

General Properties

Boiling Point: 454.290
Hydration Free Energy: -4.320
Log(D) at pH=7.4: 3.610
Log(P): 2.58
Log S: -4.51
Log(Vapor Pressure): -8.45
Melting Point: 129.93
pKa Acid: 8.75
pKa Basic: 4.04

Protein Name	UniProt ID	Entry Name	Species	#Pharmacophore Points	Probability (0.7 ≤ Tversky Score ≤ 1.0)
Ribosyldihydronicotinamide dehydrogenase [quinone]	P16083	NQO2_HUMAN	Homo sapiens	3	0.9072
rRNA N-glycosylase	D9J2T9	D9J2T9_MOMBA	Momordica balsamina	3	0.9001
Cathepsin S	P25774	CATS_HUMAN	Homo sapiens	3	0.8983
Norsolorinic acid synthase	Q12053	AFLC_ASPPU	Aspergillus parasiticus	3	0.8977
Flavoredoxin	Q72HI0	Q72HI0_THET2	Thermus thermophilus	3	0.8962
Uracil phosphoribosyltransferase	Q26998	UPP_TOXGO	Toxoplasma gondii	3	0.8787
D-aminoacyl-tRNA deacylase	Q8IIS0	DTD_PLAF7	Plasmodium falciparum	3	0.8714
Mycocyclosin synthase	P9WPP7	CP121_MYCTU	Mycobacterium tuberculosis	4	0.8657
HTH-type transcriptional repressor PurR	P0ACP7	PURR_ECOLI	Escherichia coli	3	0.8646
Serine/threonine-protein kinase 24	Q9Y6E0	STK24_HUMAN	Homo sapiens	3	0.8624
Uracil phosphoribosyltransferase	Q26998	UPP_TOXGO	Toxoplasma gondii	3	0.8523
Apoptosis regulator Bcl-2	P10415	BCL2_HUMAN	Homo sapiens	3	0.8481
Thymidine phosphorylase	Q7CP66	TYPH_SALTY	Salmonella typhimurium	3	0.8426
Beta-secretase 1	P56817	BACE1_HUMAN	Homo sapiens	3	0.8387
Serine/threonine-protein kinase 10	O94804	STK10_HUMAN	Homo sapiens	3	0.8380
Proliferating cell nuclear antigen	P12004	PCNA_HUMAN	Homo sapiens	3	0.8224
Photosynthetic reaction center cytochrome c subunit	P07173	CYCR_BLAVI	Blastochloris viridis	3	0.8184
Ribosyldihydronicotinamide dehydrogenase [quinone]	P16083	NQO2_HUMAN	Homo sapiens	3	0.8183
HTH-type transcriptional repressor PurR	P0ACP7	PURR_ECOLI	Escherichia coli	3	0.8172
Phenylalanine-4-hydroxylase	P00439	PH4H_HUMAN	Homo sapiens	3	0.8046
Queuine tRNA-ribosyltransferase	P28720	TGT_ZYMMO	Zymomonas mobilis subsp. mobilis	3	0.8042
Carbonic anhydrase 2	P00918	CAH2_HUMAN	Homo sapiens	3	0.7906
Soluble acetylcholine receptor	Q8WSF8	Q8WSF8_APLCA	Aplysia californica	3	0.7882
Chitinase A	Q9AMP1	Q9AMP1_VIBHA	Vibrio harveyi	3	0.7882
Epidermal growth factor receptor	P00533	EGFR_HUMAN	Homo sapiens	3	0.7870
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7838
Nodulin-13	P93330	NOD13_MEDTR	Medicago truncatula	3	0.7833
Methionine aminopeptidase 2	P50579	MAP2_HUMAN	Homo sapiens	3	0.7781
Stromelysin-1	P08254	MMP3_HUMAN	Homo sapiens	3	0.7774
Cytochrome P450	Q93H81	Q93H81_STRAX	Streptomyces avermitilis	3	0.7740
HTH-type transcriptional repressor PurR	P0ACP7	PURR_ECOLI	Escherichia coli	3	0.7721
HTH-type transcriptional repressor PurR	P0ACP7	PURR_ECOLI	Escherichia coli	3	0.7667
Ribosyldihydronicotinamide dehydrogenase [quinone]	P16083	NQO2_HUMAN	Homo sapiens	3	0.7662
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase	Q8DNV6	Q8DNV6_STRR6	Streptococcus pneumoniae	3	0.7621
Ribosyldihydronicotinamide dehydrogenase [quinone]	P16083	NQO2_HUMAN	Homo sapiens	3	0.7570
Soluble cytochrome b562	P0ABE7	C562_ECOLX	Escherichia coli	3	0.7563
Tetracycline repressor protein class D	P0ACT4	TETR4_ECOLX	Escherichia coli	3	0.7547
Ribosyldihydronicotinamide dehydrogenase [quinone]	P16083	NQO2_HUMAN	Homo sapiens	3	0.7502
Ribosyldihydronicotinamide dehydrogenase [quinone]	P16083	NQO2_HUMAN	Homo sapiens	3	0.7497
Lethal(3)malignant brain tumor-like protein 1	Q9Y468	LMBL1_HUMAN	Homo sapiens	3	0.7490
Basic phospholipase A2 VRV-PL-VIIIa	P59071	PA2B8_DABRR	Daboia russelii	2	0.7481
Carbonic anhydrase 2	P00918	CAH2_HUMAN	Homo sapiens	3	0.7470
Mitogen-activated protein kinase 1	P28482	MK01_HUMAN	Homo sapiens	3	0.7458
Aldo-keto reductase family 1 member C3	P42330	AK1C3_HUMAN	Homo sapiens	2	0.7448
Gag-Pol polyprotein	P12497	POL_HV1N5	Human immunodeficiency virus type 1 group M subtype B	3	0.7431
Thymidylate synthase	P00469	TYSY_LACCA	Lacticaseibacillus casei	3	0.7406
Gag-Pol polyprotein	P05896	POL_SIVM1	Simian immunodeficiency virus	3	0.7397
Na(+):neurotransmitter symporter (Snf family)	O67854	O67854_AQUAE	Aquifex aeolicus	3	0.7364
Ribosyldihydronicotinamide dehydrogenase [quinone]	P16083	NQO2_HUMAN	Homo sapiens	3	0.7353
Purine nucleoside phosphorylase	P00491	PNPH_HUMAN	Homo sapiens	3	0.7349
Calmodulin	P62157	CALM_BOVIN	Bos taurus	3	0.7334
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	Q9Y233	PDE10_HUMAN	Homo sapiens	3	0.7318
MAP kinase-activated protein kinase 2	P49137	MAPK2_HUMAN	Homo sapiens	3	0.7311
Glycogen synthase kinase-3 beta	P49841	GSK3B_HUMAN	Homo sapiens	3	0.7298
Polymerase acidic protein	C3W5S0	C3W5S0_I09A0	Influenza A virus	2	0.7292
Tyrosine-protein kinase Lck	P06239	LCK_HUMAN	Homo sapiens	3	0.7279
Epidermal growth factor receptor	P00533	EGFR_HUMAN	Homo sapiens	3	0.7262
Gag-Pol polyprotein	P03367	POL_HV1BR	Human immunodeficiency virus type 1 group M subtype B	3	0.7229
UDP-galactopyranose mutase	Q48485	GLF1_KLEPN	Klebsiella pneumoniae	3	0.7222
Queuine tRNA-ribosyltransferase	P28720	TGT_ZYMMO	Zymomonas mobilis subsp. mobilis	3	0.7221
F420-dependent NADP reductase	O29370	FNO_ARCFU	Archaeoglobus fulgidus	4	0.7215
Carbonic anhydrase 2	P00918	CAH2_HUMAN	Homo sapiens	3	0.7212
Peptidyl-prolyl cis-trans isomerase FKBP1A	P62942	FKB1A_HUMAN	Homo sapiens	3	0.7201
Genome polyprotein	P26663	POLG_HCVBK	Hepatitis C virus genotype 1b	3	0.7159
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7144
Nitric oxide synthase oxygenase	O34453	NOSO_BACSU	Bacillus subtilis	3	0.7125
Nitric oxide synthase, inducible	P29477	NOS2_MOUSE	Mus musculus	3	0.7104
CmeR	Q7B8P6	Q7B8P6_CAMJU	Campylobacter jejuni	2	0.7095
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7091
Mycocyclosin synthase	P9WPP7	CP121_MYCTU	Mycobacterium tuberculosis	2	0.7070
Aldo-keto reductase family 1 member C3	P42330	AK1C3_HUMAN	Homo sapiens	3	0.7057
cGMP-dependent 3',5'-cyclic phosphodiesterase	O00408	PDE2A_HUMAN	Homo sapiens	3	0.7053
Thymidylate synthase	P00469	TYSY_LACCA	Lacticaseibacillus casei	2	0.7047
4-hydroxyphenylacetate 3-monooxygenase	Q8YHT7	Q8YHT7_BRUME	Brucella melitensis biotype 1	2	0.7041
Pantothenate synthetase	P9WIL5	PANC_MYCTU	Mycobacterium tuberculosis	3	0.7039
Aldo-keto reductase family 1 member C2	P52895	AK1C2_HUMAN	Homo sapiens	2	0.7026
GCN5-related N-acetyltransferase	B1YEL6	B1YEL6_EXIS2	Exiguobacterium sibiricum	3	0.7025
Protein ppBat	Q8A8A4	Q8A8A4_BACTN	Bacteroides thetaiotaomicron VPI-5482	3	0.7020
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7019

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