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Gardenifolin A

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-CXANYAOZSA-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: 145960886

Zinc: ZINC000015152995

Chembl: CHEMBL4127638

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: 73.61
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: Non-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: 1.200
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: 5.520
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: -12.040
Rat (Acute): 2.180
Rat (Chronic Oral): 2.780
Fathead Minnow: 4.820
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: 452.110
Hydration Free Energy: -6.460
Log(D) at pH=7.4: 3.160
Log(P): 2.04
Log S: -4.16
Log(Vapor Pressure): -8.51
Melting Point: 146.14
pKa Acid: 8.4
pKa Basic: 2.74

Protein Name	UniProt ID	Entry Name	Species	#Pharmacophore Points	Probability (0.7 ≤ Tversky Score ≤ 1.0)
D-aminoacyl-tRNA deacylase	Q8IIS0	DTD_PLAF7	Plasmodium falciparum	3	0.9240
Chitinase A	Q9AMP1	Q9AMP1_VIBHA	Vibrio harveyi	3	0.9197
Flavoredoxin	Q72HI0	Q72HI0_THET2	Thermus thermophilus	3	0.8934
Mycocyclosin synthase	P9WPP7	CP121_MYCTU	Mycobacterium tuberculosis	4	0.8914
Thymidine phosphorylase	Q7CP66	TYPH_SALTY	Salmonella typhimurium	3	0.8859
Uracil phosphoribosyltransferase	Q26998	UPP_TOXGO	Toxoplasma gondii	3	0.8799
Probable NDP-rhamnosyltransferase	Q9ALM8	Q9ALM8_SACSN	Saccharopolyspora spinosa	3	0.8610
Uracil phosphoribosyltransferase	Q26998	UPP_TOXGO	Toxoplasma gondii	3	0.8583
Peroxisome proliferator-activated receptor gamma	P37231	PPARG_HUMAN	Homo sapiens	3	0.8563
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	Q9Y233	PDE10_HUMAN	Homo sapiens	3	0.8488
Cathepsin S	P25774	CATS_HUMAN	Homo sapiens	3	0.8470
Proliferating cell nuclear antigen	P12004	PCNA_HUMAN	Homo sapiens	3	0.8390
Nuclear receptor subfamily 4immunitygroup A member 1	P22736	NR4A1_HUMAN	Homo sapiens	3	0.8383
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.8329
Rhodopsin kinase GRK1	P28327	GRK1_BOVIN	Bos taurus	3	0.8311
Pantothenate synthetase	P9WIL5	PANC_MYCTU	Mycobacterium tuberculosis	3	0.8242
rRNA N-glycosylase	D9J2T9	D9J2T9_MOMBA	Momordica balsamina	3	0.8234
Phospholipase A2, major isoenzyme	P00592	PA21B_PIG	Sus scrofa	3	0.8224
Carbonic anhydrase 2	P00918	CAH2_HUMAN	Homo sapiens	3	0.8219
Purine nucleoside phosphorylase	P00491	PNPH_HUMAN	Homo sapiens	3	0.8219
Phytohormone-binding protein CSBP	A0A1S3THR8	PHBP_VIGRR	Vigna radiata var. radiata	3	0.8190
Soluble acetylcholine receptor	Q8WSF8	Q8WSF8_APLCA	Aplysia californica	3	0.8182
Serine/threonine-protein kinase 24	Q9Y6E0	STK24_HUMAN	Homo sapiens	3	0.8172
Xylose isomerase	P24300	XYLA_STRRU	Streptomyces rubiginosus	3	0.8153
Focal adhesion kinase 1	Q05397	FAK1_HUMAN	Homo sapiens	4	0.8123
Mycocyclosin synthase	P9WPP7	CP121_MYCTU	Mycobacterium tuberculosis	3	0.8122
Hypoxanthine phosphoribosyltransferase	Q4DRC4	Q4DRC4_TRYCC	Trypanosoma cruzi	3	0.8086
Methylketone synthase I	E0YCS2	E0YCS2_SOLHA	Solanum habrochaites	3	0.8049
histidine kinase	O32393	O32393_ARTPT	Arthrospira platensis	3	0.8037
Mitogen-activated protein kinase 1	P28482	MK01_HUMAN	Homo sapiens	3	0.7976
3',5'-cyclic-AMP phosphodiesterase 4D	Q08499	PDE4D_HUMAN	Homo sapiens	3	0.7942
GCN5-related N-acetyltransferase	B1YEL6	B1YEL6_EXIS2	Exiguobacterium sibiricum	3	0.7928
GCN5-related N-acetyltransferase	B1YEL6	B1YEL6_EXIS2	Exiguobacterium sibiricum	3	0.7878
Tetracycline repressor protein class D	P0ACT4	TETR4_ECOLX	Escherichia coli	3	0.7803
Protein ppBat	Q8A8A4	Q8A8A4_BACTN	Bacteroides thetaiotaomicron VPI-5482	3	0.7799
Gag-Pol polyprotein	P03367	POL_HV1BR	Human immunodeficiency virus type 1 group M subtype B	3	0.7794
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4	Q9Y3Q4	HCN4_HUMAN	Homo sapiens	4	0.7752
Riboflavin synthase	P0AFU8	RISA_ECOLI	Escherichia coli	3	0.7721
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7720
Tetracycline repressor protein class D	P0ACT4	TETR4_ECOLX	Escherichia coli	3	0.7693
Tyrosine-protein kinase JAK2	O60674	JAK2_HUMAN	Homo sapiens	3	0.7680
NAD-capped RNA hydrolase NudC	P32664	NUDC_ECOLI	Escherichia coli	3	0.7676
Stromelysin-1	P08254	MMP3_HUMAN	Homo sapiens	3	0.7653
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial	Q15119	PDK2_HUMAN	Homo sapiens	3	0.7630
Dual specificity mitogen-activated protein kinase kinase 1	Q02750	MP2K1_HUMAN	Homo sapiens	3	0.7607
Streptogramin A acetyltransferase	P50870	VATD_ENTFC	Enterococcus faecium	3	0.7602
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7597
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7592
Basic phospholipase A2 VRV-PL-VIIIa	P59071	PA2B8_DABRR	Daboia russelii	3	0.7585
Serine/threonine-protein kinase Chk1	O14757	CHK1_HUMAN	Homo sapiens	3	0.7554
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7541
cAMP-dependent protein kinase catalytic subunit alpha	P00517	KAPCA_BOVIN	Bos taurus	4	0.7535
Heat shock protein HSP 90-alpha	P07900	HS90A_HUMAN	Homo sapiens	3	0.7497
HTH-type transcriptional repressor PurR	P0ACP7	PURR_ECOLI	Escherichia coli	3	0.7491
Gag-Pol polyprotein	P03367	POL_HV1BR	Human immunodeficiency virus type 1 group M subtype B	3	0.7490
Basic phospholipase A2 VRV-PL-VIIIa	P59071	PA2B8_DABRR	Daboia russelii	2	0.7483
Beta-secretase 1	P56817	BACE1_HUMAN	Homo sapiens	3	0.7479
cGMP-dependent 3',5'-cyclic phosphodiesterase	O00408	PDE2A_HUMAN	Homo sapiens	3	0.7477
cAMP-dependent protein kinase type I-alpha regulatory subunit	P00514	KAP0_BOVIN	Bos taurus	2	0.7477
Abscisic acid receptor PYL2	O80992	PYL2_ARATH	Arabidopsis thaliana	3	0.7470
Mycocyclosin synthase	P9WPP7	CP121_MYCTU	Mycobacterium tuberculosis	3	0.7465
DNA-directed DNA polymerase	Q38087	DPOL_BPR69	Escherichia phage RB69	3	0.7460
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7450
3'-5' exoribonuclease Rv2179c	P9WJ73	EXRBN_MYCTU	Mycobacterium tuberculosis	2	0.7421
Thymidylate synthase	P0A886	TYSY_ECO57	Escherichia coli O157:H7	3	0.7409
Orotidine 5'-phosphate decarboxylase	Q5L0U0	PYRF_GEOKA	Geobacillus kaustophilus	3	0.7405
Dipeptidyl peptidase 4	P27487	DPP4_HUMAN	Homo sapiens	3	0.7400
Catechol O-methyltransferase	P22734	COMT_RAT	Rattus norvegicus	3	0.7394
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic	Q43088	RBCMT_PEA	Pisum sativum	3	0.7390
Endothiapepsin	P11838	CARP_CRYPA	Cryphonectria parasitica	3	0.7389
Dual specificity mitogen-activated protein kinase kinase 1	Q02750	MP2K1_HUMAN	Homo sapiens	3	0.7377
Streptavidin	P22629	SAV_STRAV	Streptomyces avidinii	3	0.7373
Tau-tubulin kinase 1	Q5TCY1	TTBK1_HUMAN	Homo sapiens	4	0.7349
Heat shock protein HSP 90-alpha	P07900	HS90A_HUMAN	Homo sapiens	3	0.7348
Mitochondrial poly(A) polymerase	F1NBW0	F1NBW0_CHICK	Gallus gallus	2	0.7347
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	P48736	PK3CG_HUMAN	Homo sapiens	3	0.7335
Methylmalonyl-CoA decarboxylase	P52045	SCPB_ECOLI	Escherichia coli	3	0.7321
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic	Q43088	RBCMT_PEA	Pisum sativum	3	0.7303
Histone-lysine N-methyltransferase EHMT2	Q96KQ7	EHMT2_HUMAN	Homo sapiens	3	0.7301
Tyrosine-protein kinase JAK2	O60674	JAK2_HUMAN	Homo sapiens	3	0.7297
Tetracycline repressor protein class D	P0ACT4	TETR4_ECOLX	Escherichia coli	2	0.7281
Polymerase acidic protein	C3W5S0	C3W5S0_I09A0	Influenza A virus	2	0.7270
CREB-binding protein	Q92793	CBP_HUMAN	Homo sapiens	3	0.7258
DNA-directed DNA polymerase	Q38087	DPOL_BPR69	Escherichia phage RB69	2	0.7253
Bromodomain-containing protein 2	P25440	BRD2_HUMAN	Homo sapiens	3	0.7250
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7227
Bifunctional epoxide hydrolase 2	P34913	HYES_HUMAN	Homo sapiens	2	0.7221
CCA-adding enzyme	O28126	CCA_ARCFU	Archaeoglobus fulgidus	2	0.7206
Beta-glucuronidase	P05804	BGLR_ECOLI	Escherichia coli	3	0.7204
WxcM-like protein	Q12KT8	Q12KT8_SHEDO	Shewanella denitrificans	3	0.7201
CCA-adding enzyme	O28126	CCA_ARCFU	Archaeoglobus fulgidus	2	0.7192
Cyclin-dependent kinase 2	P24941	CDK2_HUMAN	Homo sapiens	3	0.7182
Beta-lactamase	Q9L5C8	Q9L5C8_ECOLX	Escherichia coli	3	0.7177
Pancreatic alpha-amylase	P04746	AMYP_HUMAN	Homo sapiens	2	0.7175
Phosphatidylinositol 5-phosphate 4-kinase type-2 beta	P78356	PI42B_HUMAN	Homo sapiens	3	0.7168
Histone-lysine N-methyltransferase EHMT1	Q9H9B1	EHMT1_HUMAN	Homo sapiens	3	0.7158
2',3'-cyclic-nucleotide 3'-phosphodiesterase	P16330	CN37_MOUSE	Mus musculus	3	0.7147
Steroid C26-monooxygenase	P9WPP1	CP125_MYCTU	Mycobacterium tuberculosis	3	0.7142
1-deoxy-D-xylulose 5-phosphate reductoisomerase	P45568	DXR_ECOLI	Escherichia coli	2	0.7142
histone deacetylase	A5H660	A5H660_SCHMA	Schistosoma mansoni	3	0.7140
Vascular endothelial growth factor receptor 2	P35968	VGFR2_HUMAN	Homo sapiens	3	0.7135
Pheromone-binding protein ASP1	Q9U9J6	Q9U9J6_APIME	Apis mellifera	2	0.7135
Nitric oxide synthase oxygenase	O34453	NOSO_BACSU	Bacillus subtilis	3	0.7127
3',5'-cyclic-AMP phosphodiesterase 4D	Q08499	PDE4D_HUMAN	Homo sapiens	3	0.7125
2',3'-cyclic-nucleotide 3'-phosphodiesterase	P16330	CN37_MOUSE	Mus musculus	2	0.7114
ATP-dependent protease subunit HslV	P0A7B8	HSLV_ECOLI	Escherichia coli	3	0.7112
Bromodomain-containing protein 2	P25440	BRD2_HUMAN	Homo sapiens	3	0.7111
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic	Q43088	RBCMT_PEA	Pisum sativum	3	0.7109
Serine/threonine-protein kinase Chk1	O14757	CHK1_HUMAN	Homo sapiens	3	0.7102
Gag-Pol polyprotein	P03367	POL_HV1BR	Human immunodeficiency virus type 1 group M subtype B	3	0.7097
Fibroblast growth factor receptor 1	P11362	FGFR1_HUMAN	Homo sapiens	3	0.7091
Nitric oxide synthase, inducible	P29477	NOS2_MOUSE	Mus musculus	3	0.7086
Transthyretin	P02767	TTHY_RAT	Rattus norvegicus	3	0.7086
Serine/threonine-protein kinase 24	Q9Y6E0	STK24_HUMAN	Homo sapiens	3	0.7085
Histone-lysine N-methyltransferase SETD7	Q8WTS6	SETD7_HUMAN	Homo sapiens	3	0.7085
HTH-type transcriptional regulator TtgR	Q9AIU0	TTGR_PSEPT	Pseudomonas putida	4	0.7080
dTDP-4-dehydrorhamnose 3,5-epimerase	A0A6L7H6N0	A0A1S0QLH9_BACAN	Bacillus anthracis	3	0.7075
Biflaviolin synthase CYP158A1	Q9KZF5	C1581_STRCO	Streptomyces coelicolor / M145)	3	0.7060
Histone deacetylase 7	Q8WUI4	HDAC7_HUMAN	Homo sapiens	3	0.7056
Basic phospholipase A2 VRV-PL-VIIIa	P59071	PA2B8_DABRR	Daboia russelii	2	0.7054
Lethal factor	P15917	LEF_BACAN	Bacillus anthracis	3	0.7050
Lactotransferrin	P24627	TRFL_BOVIN	Bos taurus	2	0.7049
Hypoxanthine-guanine phosphoribosyltransferase	P00492	HPRT_HUMAN	Homo sapiens	3	0.7044
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4	Q8GZB6	SUVH4_ARATH	Arabidopsis thaliana	3	0.7031
14-3-3 protein gamma	P61981	1433G_HUMAN	Homo sapiens	3	0.7029
3',5'-cyclic-AMP phosphodiesterase 4D	Q08499	PDE4D_HUMAN	Homo sapiens	3	0.7023
Glycoside Hydrolase Family 13	Q65MI2	Q65MI2_BACLD	Bacillus licheniformis	2	0.7021
Cytosolic purine 5'-nucleotidase	P49902	5NTC_HUMAN	Homo sapiens	2	0.7015
Dual specificity mitogen-activated protein kinase kinase 1	Q02750	MP2K1_HUMAN	Homo sapiens	3	0.7013
Homoserine dehydrogenase	P31116	DHOM_YEAST	Saccharomyces cerevisiae	3	0.7012
Steroid Delta-isomerase	P00947	SDIS_COMTE	Comamonas testosteroni	3	0.7008

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