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Gardenifolin C

Family: Plantae - 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
InChI	InChI=1S/C21H22O7/c1-25-17-10-13(5-6-16(17)23)20-15(11-22)14-8-12(4-7-19(24)27-3)9-18(26-2)21(14)28-20/h4-10,15,20,22-23H,11H2,1-3H3/b7-4+/t15-,20+/m0/s1
InChIKey	DPDJZJNYBSGDHT-ZTLSKPKQSA-N
Formula	C₂₁H₂₂O₇
HBA	7
HBD	2
MW	386.4
Rotatable Bonds	6
TPSA	94.45
LogP	2.81
Number Rings	3
Number Aromatic Rings	2
Heavy Atom Count	28
Formal Charge	0
Fraction CSP3	0.29
Exact Mass	386.14
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]

Pubchem: 92852582

Cas: 107296-48-0

Zinc: ZINC000028862507

Chembl: CHEMBL4128624

No compound-protein relationship available.

SMILES: c1cccc(c12)OC(C2)c3ccccc3

Level: 1

Mol. Weight: 386.4 g/mol

SMILES: C1COc(c12)cccc2

Level: 0

Mol. Weight: 386.4 g/mol

SMILES: c1ccccc1

Level: 0

Mol. Weight: 386.4 g/mol

Cytotoxic

Absorption

Caco-2 (logPapp): -4.54
Human Oral Bioavailability 20%: Non-Bioavailable
Human Intestinal Absorption: Absorbed
Madin-Darby Canine Kidney: -4.700
Human Oral Bioavailability 50%: Non-Bioavailable
P-Glycoprotein Inhibitor: Inhibitor
P-Glycoprotein Substrate: Non-Substrate
Skin Permeability: -2.7

Distribution

Blood-Brain Barrier (CNS): -
Blood-Brain Barrier: Penetrable
Fraction Unbound (Human): 1.120
Plasma Protein Binding: 73.95
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: 10.940
Organic Cation Transporter 2: Non-Inhibitor
Half-Life of Drug: -

Toxicity

AMES Mutagenesis: Safe
Avian: Safe
Bee: Toxic
Bioconcentration Factor: 1.250
Biodegradation: Safe
Carcinogenesis: Safe
Crustacean: Toxic
Liver Injury I (DILI): Safe
Eye Corrosion: Safe
Eye Irritation: Safe
Maximum Tolerated Dose: 0.700
Liver Injury II: Toxic
hERG Blockers: Safe
Daphnia Maga: 5.540
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: -10.110
Rat (Acute): 2.180
Rat (Chronic Oral): 2.780
Fathead Minnow: 4.960
Respiratory Disease: Toxic
Skin Sensitisation: Safe
SR-ARE: Toxic
SR-ATAD5: Toxic
SR-HSE: Safe
SR-MMP: Toxic
SR-p53: Safe

General Properties

Boiling Point: 452.660
Hydration Free Energy: -6.460
Log(D) at pH=7.4: 3.200
Log(P): 2.0
Log S: -4.21
Log(Vapor Pressure): -8.41
Melting Point: 153.41
pKa Acid: 8.43
pKa Basic: 2.75

Protein Name	UniProt ID	Entry Name	Species	#Pharmacophore Points	Probability (0.7 ≤ Tversky Score ≤ 1.0)
Mycocyclosin synthase	P9WPP7	CP121_MYCTU	Mycobacterium tuberculosis	3	0.9211
D-aminoacyl-tRNA deacylase	Q8IIS0	DTD_PLAF7	Plasmodium falciparum	3	0.9189
Flavoredoxin	Q72HI0	Q72HI0_THET2	Thermus thermophilus	3	0.8902
Mycocyclosin synthase	P9WPP7	CP121_MYCTU	Mycobacterium tuberculosis	4	0.8890
Thymidine phosphorylase	Q7CP66	TYPH_SALTY	Salmonella typhimurium	3	0.8810
Uracil phosphoribosyltransferase	Q26998	UPP_TOXGO	Toxoplasma gondii	3	0.8789
Xylose isomerase	P24300	XYLA_STRRU	Streptomyces rubiginosus	3	0.8541
Proliferating cell nuclear antigen	P12004	PCNA_HUMAN	Homo sapiens	3	0.8539
Uracil phosphoribosyltransferase	Q26998	UPP_TOXGO	Toxoplasma gondii	3	0.8527
Histone deacetylase 8	Q9BY41	HDAC8_HUMAN	Homo sapiens	3	0.8446
Stromelysin-1	P08254	MMP3_HUMAN	Homo sapiens	3	0.8435
Protein ppBat	Q8A8A4	Q8A8A4_BACTN	Bacteroides thetaiotaomicron VPI-5482	3	0.8231
rRNA N-glycosylase	D9J2T9	D9J2T9_MOMBA	Momordica balsamina	3	0.8231
Purine nucleoside phosphorylase	P00491	PNPH_HUMAN	Homo sapiens	3	0.8178
Pantothenate synthetase	P9WIL5	PANC_MYCTU	Mycobacterium tuberculosis	3	0.8175
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.8167
Steroid Delta-isomerase	P00947	SDIS_COMTE	Comamonas testosteroni	3	0.8135
Chitinase A	Q9AMP1	Q9AMP1_VIBHA	Vibrio harveyi	3	0.8097
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	Q9Y233	PDE10_HUMAN	Homo sapiens	3	0.8020
Serine/threonine-protein kinase 24	Q9Y6E0	STK24_HUMAN	Homo sapiens	3	0.7987
3',5'-cyclic-AMP phosphodiesterase 4D	Q08499	PDE4D_HUMAN	Homo sapiens	3	0.7968
Hypoxanthine phosphoribosyltransferase	Q4DRC4	Q4DRC4_TRYCC	Trypanosoma cruzi	3	0.7966
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	Q9Y233	PDE10_HUMAN	Homo sapiens	3	0.7961
Carbonic anhydrase 2	P00918	CAH2_HUMAN	Homo sapiens	3	0.7957
Abscisic acid receptor PYL2	O80992	PYL2_ARATH	Arabidopsis thaliana	3	0.7955
Basic phospholipase A2 VRV-PL-VIIIa	P59071	PA2B8_DABRR	Daboia russelii	3	0.7937
Mitogen-activated protein kinase 1	P28482	MK01_HUMAN	Homo sapiens	3	0.7904
Histone deacetylase 8	Q9BY41	HDAC8_HUMAN	Homo sapiens	3	0.7854
Soluble acetylcholine receptor	Q8WSF8	Q8WSF8_APLCA	Aplysia californica	3	0.7803
GCN5-related N-acetyltransferase	B1YEL6	B1YEL6_EXIS2	Exiguobacterium sibiricum	3	0.7748
Streptogramin A acetyltransferase	P50870	VATD_ENTFC	Enterococcus faecium	3	0.7738
GCN5-related N-acetyltransferase	B1YEL6	B1YEL6_EXIS2	Exiguobacterium sibiricum	3	0.7718
Tetracycline repressor protein class D	P0ACT4	TETR4_ECOLX	Escherichia coli	3	0.7671
Streptavidin	P22629	SAV_STRAV	Streptomyces avidinii	3	0.7653
Serine/threonine-protein kinase Chk1	O14757	CHK1_HUMAN	Homo sapiens	3	0.7534
cGMP-dependent 3',5'-cyclic phosphodiesterase	O00408	PDE2A_HUMAN	Homo sapiens	3	0.7522
Tau-tubulin kinase 1	Q5TCY1	TTBK1_HUMAN	Homo sapiens	4	0.7496
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7412
Pyruvate kinase PKM	P14618	KPYM_HUMAN	Homo sapiens	3	0.7385
Oxygenase	Q194P4	Q194P4_STRAA	Streptomyces argillaceus	3	0.7335
Lethal factor	P15917	LEF_BACAN	Bacillus anthracis	3	0.7315
Methylmalonyl-CoA decarboxylase	P52045	SCPB_ECOLI	Escherichia coli	3	0.7293
Bromodomain-containing protein 2	P25440	BRD2_HUMAN	Homo sapiens	3	0.7275
CCA-adding enzyme	O28126	CCA_ARCFU	Archaeoglobus fulgidus	2	0.7274
WxcM-like protein	Q12KT8	Q12KT8_SHEDO	Shewanella denitrificans	3	0.7257
Catechol O-methyltransferase	P22734	COMT_RAT	Rattus norvegicus	3	0.7249
Beta-secretase 1	P56817	BACE1_HUMAN	Homo sapiens	2	0.7226
Histone-lysine N-methyltransferase EHMT1	Q9H9B1	EHMT1_HUMAN	Homo sapiens	3	0.7220
Lactotransferrin	P24627	TRFL_BOVIN	Bos taurus	2	0.7216
Bifunctional epoxide hydrolase 2	P34913	HYES_HUMAN	Homo sapiens	2	0.7216
Polymerase acidic protein	C3W5S0	C3W5S0_I09A0	Influenza A virus	2	0.7192
2',3'-cyclic-nucleotide 3'-phosphodiesterase	P16330	CN37_MOUSE	Mus musculus	2	0.7191
N-terminal acetyltransferase A complex subunit NAT1	P12945	NAT1_YEAST	Saccharomyces cerevisiae	2	0.7180
Mitogen-activated protein kinase 14	Q16539	MK14_HUMAN	Homo sapiens	3	0.7169
Tyrosine-protein kinase JAK2	O60674	JAK2_HUMAN	Homo sapiens	3	0.7163
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic	Q43088	RBCMT_PEA	Pisum sativum	3	0.7154
Pheromone-binding protein ASP1	Q9U9J6	Q9U9J6_APIME	Apis mellifera	3	0.7147
Basic phospholipase A2 VRV-PL-VIIIa	P59071	PA2B8_DABRR	Daboia russelii	2	0.7140
Tetracycline repressor protein class D	P0ACT4	TETR4_ECOLX	Escherichia coli	2	0.7127
2',3'-cyclic-nucleotide 3'-phosphodiesterase	P16330	CN37_MOUSE	Mus musculus	2	0.7127
2',3'-cyclic-nucleotide 3'-phosphodiesterase	P16330	CN37_MOUSE	Mus musculus	2	0.7119
Casein kinase I isoform gamma-3	Q9Y6M4	KC1G3_HUMAN	Homo sapiens	3	0.7117
Non-receptor tyrosine-protein kinase TYK2	P29597	TYK2_HUMAN	Homo sapiens	3	0.7111
Beta-glucuronidase	P05804	BGLR_ECOLI	Escherichia coli	3	0.7097
Nitric oxide synthase oxygenase	O34453	NOSO_BACSU	Bacillus subtilis	3	0.7097
Thymidylate synthase	P00469	TYSY_LACCA	Lacticaseibacillus casei	2	0.7094
Nitric oxide synthase, inducible	P29477	NOS2_MOUSE	Mus musculus	3	0.7090
Ethylene receptor 1	P49333	ETR1_ARATH	Arabidopsis thaliana	3	0.7078
Cyclic AMP receptor protein	Q5SID7	CRP_THET8	Thermus thermophilus	2	0.7066
dTDP-4-dehydrorhamnose 3,5-epimerase	A0A6L7H6N0	A0A1S0QLH9_BACAN	Bacillus anthracis	3	0.7061
Peroxisome proliferator-activated receptor gamma	P37231	PPARG_HUMAN	Homo sapiens	3	0.7047
L-lactate dehydrogenase A chain	P13491	LDHA_RABIT	Oryctolagus cuniculus	2	0.7042
Tyrosine-protein kinase JAK2	O60674	JAK2_HUMAN	Homo sapiens	3	0.7038
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4	Q8GZB6	SUVH4_ARATH	Arabidopsis thaliana	3	0.7037
Catechol O-methyltransferase	P22734	COMT_RAT	Rattus norvegicus	3	0.7032
HTH-type transcriptional repressor PurR	P0ACP7	PURR_ECOLI	Escherichia coli	3	0.7020
HTH-type transcriptional repressor PurR	P0ACP7	PURR_ECOLI	Escherichia coli	3	0.7015
Homoserine dehydrogenase	P31116	DHOM_YEAST	Saccharomyces cerevisiae	3	0.7007

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