Gardenifolin F - Compound Card

Gardenifolin F

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Gardenifolin F

Structure
Zoomed Structure
  • 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)O)OC
InChI InChI=1S/C21H22O7/c1-25-17-6-5-13(10-16(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 FULHECCATAOIBE-UOPUXJMHSA-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]

No compound-protein relationship available.

Structure

SMILES: c1cccc(c12)OC(C2)c3ccccc3

Level: 1

Mol. Weight: 386.4 g/mol

Structure

SMILES: C1COc(c12)cccc2

Level: 0

Mol. Weight: 386.4 g/mol

Structure

SMILES: c1ccccc1

Level: 0

Mol. Weight: 386.4 g/mol

Cytotoxic

Absorption

Caco-2 (logPapp)
-4.51
Human Oral Bioavailability 20%
Non-Bioavailable
Human Intestinal Absorption
Absorbed
Madin-Darby Canine Kidney
-4.710
Human Oral Bioavailability 50%
Non-Bioavailable
P-Glycoprotein Inhibitor
Inhibitor
P-Glycoprotein Substrate
Non-Substrate
Skin Permeability
-2.53

Distribution

Blood-Brain Barrier (CNS)
-
Blood-Brain Barrier
Penetrable
Fraction Unbound (Human)
1.140
Plasma Protein Binding
77.71
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
10.010
Organic Cation Transporter 2
Non-Inhibitor
Half-Life of Drug
-

Toxicity

AMES Mutagenesis
Safe
Avian
Safe
Bee
Toxic
Bioconcentration Factor
1.070
Biodegradation
Safe
Carcinogenesis
Safe
Crustacean
Toxic
Liver Injury I (DILI)
Safe
Eye Corrosion
Safe
Eye Irritation
Safe
Maximum Tolerated Dose
0.740
Liver Injury II
Toxic
hERG Blockers
Safe
Daphnia Maga
5.480
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
-12.110
Rat (Acute)
2.190
Rat (Chronic Oral)
2.730
Fathead Minnow
4.790
Respiratory Disease
Safe
Skin Sensitisation
Safe
SR-ARE
Toxic
SR-ATAD5
Safe
SR-HSE
Safe
SR-MMP
Toxic
SR-p53
Safe

General Properties

Boiling Point
451.330
Hydration Free Energy
-6.730
Log(D) at pH=7.4
3.370
Log(P)
2.22
Log S
-4.21
Log(Vapor Pressure)
-8.37
Melting Point
148.95
pKa Acid
8.51
pKa Basic
2.34
Protein Name UniProt ID Entry Name Species #Pharmacophore Points Probability (0.7 ≤ Tversky Score ≤ 1.0)
Serine/threonine-protein kinase 24 Q9Y6E0 STK24_HUMAN Homo sapiens 3 0.9231
Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase Q9TQS6 DHDH_MACFA Macaca fascicularis 3 0.9183
Thymidine phosphorylase Q7CP66 TYPH_SALTY Salmonella typhimurium 3 0.9134
Norsolorinic acid synthase Q12053 AFLC_ASPPU Aspergillus parasiticus 3 0.9092
Serine/threonine-protein kinase 10 O94804 STK10_HUMAN Homo sapiens 3 0.9009
Cytohesin-2 Q99418 CYH2_HUMAN Homo sapiens 3 0.8967
Epidermal growth factor receptor P00533 EGFR_HUMAN Homo sapiens 3 0.8915
Stromelysin-1 P08254 MMP3_HUMAN Homo sapiens 3 0.8904
3',5'-cyclic-AMP phosphodiesterase 4D Q08499 PDE4D_HUMAN Homo sapiens 3 0.8841
Uracil phosphoribosyltransferase Q26998 UPP_TOXGO Toxoplasma gondii 3 0.8836
Gag-Pol polyprotein P03367 POL_HV1BR Human immunodeficiency virus type 1 group M subtype B 4 0.8708
Thymidylate synthase P00469 TYSY_LACCA Lacticaseibacillus casei 3 0.8676
Proliferating cell nuclear antigen P12004 PCNA_HUMAN Homo sapiens 3 0.8661
Tetracycline repressor protein class D P0ACT4 TETR4_ECOLX Escherichia coli 3 0.8652
Cathepsin S P25774 CATS_HUMAN Homo sapiens 3 0.8502
Epidermal growth factor receptor P00533 EGFR_HUMAN Homo sapiens 3 0.8500
RNA polymerase sigma factor SigA Q5SKW1 Q5SKW1_THET8 Thermus thermophilus 3 0.8449
Uracil phosphoribosyltransferase Q26998 UPP_TOXGO Toxoplasma gondii 3 0.8439
Phospholipase A2, major isoenzyme P00592 PA21B_PIG Sus scrofa 3 0.8403
Beta-secretase 1 P56817 BACE1_HUMAN Homo sapiens 3 0.8396
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase Q8DNV6 Q8DNV6_STRR6 Streptococcus pneumoniae 3 0.8385
MAP kinase-activated protein kinase 2 P49137 MAPK2_HUMAN Homo sapiens 3 0.8346
NAD(P)H-hydrate epimerase Q8K4Z3 NNRE_MOUSE Mus musculus 3 0.8287
Steroid Delta-isomerase P00947 SDIS_COMTE Comamonas testosteroni 3 0.8275
Fibroblast growth factor receptor 1 P11362 FGFR1_HUMAN Homo sapiens 3 0.8138
Cytochrome P450 Q93H81 Q93H81_STRAX Streptomyces avermitilis 3 0.8119
Endothiapepsin P11838 CARP_CRYPA Cryphonectria parasitica 3 0.8100
Serine/threonine-protein kinase 24 Q9Y6E0 STK24_HUMAN Homo sapiens 3 0.8087
Protein mono-ADP-ribosyltransferase PARP3 Q9Y6F1 PARP3_HUMAN Homo sapiens 3 0.8065
Rhodopsin kinase GRK1 P28327 GRK1_BOVIN Bos taurus 3 0.8016
Chitinase A Q9AMP1 Q9AMP1_VIBHA Vibrio harveyi 3 0.8011
Cyclin-dependent kinase 2 P24941 CDK2_HUMAN Homo sapiens 3 0.8011
D-aminoacyl-tRNA deacylase Q8IIS0 DTD_PLAF7 Plasmodium falciparum 3 0.8009
Soluble acetylcholine receptor Q8WSF8 Q8WSF8_APLCA Aplysia californica 3 0.7976
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 3 0.7926
Chitinase Q54276 Q54276_SERMA Serratia marcescens 3 0.7891
Gag-Pol polyprotein P12497 POL_HV1N5 Human immunodeficiency virus type 1 group M subtype B 3 0.7866
2-phospho-L-lactate transferase Q8PVT6 COFD_METMA Methanosarcina mazei 3 0.7821
Tetracycline repressor protein class D P0ACT4 TETR4_ECOLX Escherichia coli 3 0.7754
Sulfide-quinone reductase B7JBP8 SQRD_ACIF2 Acidithiobacillus ferrooxidans) 3 0.7753
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.7746
Peroxisome proliferator-activated receptor gamma P37231 PPARG_HUMAN Homo sapiens 3 0.7722
Ribonuclease J H9CZL7 H9CZL7_DEIRD Deinococcus radiodurans 3 0.7692
Tetracycline repressor protein class H P51561 TETR8_PASMD Pasteurella multocida 3 0.7680
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 2 0.7662
Protein ppBat Q8A8A4 Q8A8A4_BACTN Bacteroides thetaiotaomicron VPI-5482 3 0.7657
Calmodulin-domain protein kinase 1, putative A3FQ16 A3FQ16_CRYPI Cryptosporidium parvum 3 0.7652
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.7611
Queuine tRNA-ribosyltransferase P28720 TGT_ZYMMO Zymomonas mobilis subsp. mobilis 3 0.7589
Serpin domain-containing protein H0ZQY2 H0ZQY2_TAEGU Taeniopygia guttata 3 0.7570
Anthocyanidin 3-O-glucosyltransferase UFGT P51094 UFOG_VITVI Vitis vinifera 3 0.7561
Putative HMP/thiamine-binding protein YkoF O34911 YKOF_BACSU Bacillus subtilis 3 0.7552
Mitogen-activated protein kinase 10 P53779 MK10_HUMAN Homo sapiens 3 0.7543
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.7541
Death-associated protein kinase 1 P53355 DAPK1_HUMAN Homo sapiens 4 0.7516
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 2 0.7504
Dual specificity mitogen-activated protein kinase kinase 1 Q02750 MP2K1_HUMAN Homo sapiens 3 0.7491
cAMP-dependent protein kinase type I-alpha regulatory subunit P00514 KAP0_BOVIN Bos taurus 2 0.7480
NAD-capped RNA hydrolase NudC P32664 NUDC_ECOLI Escherichia coli 3 0.7476
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase Q81LL4 MTNN_BACAN Bacillus anthracis 3 0.7469
Glycogen synthase kinase-3 beta P49841 GSK3B_HUMAN Homo sapiens 3 0.7466
Carbonyl reductase [NADPH] 1 P16152 CBR1_HUMAN Homo sapiens 3 0.7461
3'-5' exoribonuclease Rv2179c P9WJ73 EXRBN_MYCTU Mycobacterium tuberculosis 2 0.7461
F420-dependent NADP reductase O29370 FNO_ARCFU Archaeoglobus fulgidus 4 0.7456
Cyclin-dependent kinase 2 P24941 CDK2_HUMAN Homo sapiens 3 0.7440
Queuine tRNA-ribosyltransferase P28720 TGT_ZYMMO Zymomonas mobilis subsp. mobilis 3 0.7434
Cyclin-dependent kinase 2 P24941 CDK2_HUMAN Homo sapiens 3 0.7433
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic Q43088 RBCMT_PEA Pisum sativum 3 0.7423
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.7420
Casein kinase I isoform gamma-3 Q9Y6M4 KC1G3_HUMAN Homo sapiens 3 0.7413
HTH-type transcriptional repressor PurR P0ACP7 PURR_ECOLI Escherichia coli 3 0.7406
Phytohormone-binding protein CSBP A0A1S3THR8 PHBP_VIGRR Vigna radiata var. radiata 3 0.7382
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic Q43088 RBCMT_PEA Pisum sativum 3 0.7367
Purine nucleoside phosphorylase P00491 PNPH_HUMAN Homo sapiens 3 0.7364
HTH-type transcriptional regulator TtgR Q9AIU0 TTGR_PSEPT Pseudomonas putida 4 0.7361
Abscisic acid receptor PYL2 O80992 PYL2_ARATH Arabidopsis thaliana 3 0.7358
Pheromone-binding protein ASP1 Q9U9J6 Q9U9J6_APIME Apis mellifera 3 0.7353
Xylose isomerase P24300 XYLA_STRRU Streptomyces rubiginosus 3 0.7340
Mitochondrial poly(A) polymerase F1NBW0 F1NBW0_CHICK Gallus gallus 2 0.7339
Adenosine 5'-monophosphoramidase HINT1 P80912 HINT1_RABIT Oryctolagus cuniculus 3 0.7339
Alpha-ketoglutarate-dependent dioxygenase FTO Q9C0B1 FTO_HUMAN Homo sapiens 3 0.7323
NADPH-dependent oxidoreductase 2-alkenal reductase Q39172 AER_ARATH Arabidopsis thaliana 3 0.7323
Tyrosine-protein kinase Lck P06239 LCK_HUMAN Homo sapiens 3 0.7305
Nucleoside diphosphate kinase P15266 NDK_MYXXA Myxococcus xanthus 3 0.7292
Kinesin-like protein KIF11 P52732 KIF11_HUMAN Homo sapiens 3 0.7289
Kinesin-like protein KIF11 P52732 KIF11_HUMAN Homo sapiens 3 0.7285
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A Q9Y233 PDE10_HUMAN Homo sapiens 3 0.7273
14-3-3 protein gamma P61981 1433G_HUMAN Homo sapiens 3 0.7256
Beta-1 adrenergic receptor P07700 ADRB1_MELGA Meleagris gallopavo 2 0.7251
DNA-directed DNA polymerase Q38087 DPOL_BPR69 Escherichia phage RB69 2 0.7248
Gag-Pol polyprotein O12158 POL_HV192 Human immunodeficiency virus type 1 group M subtype C 3 0.7247
Polymerase acidic protein C3W5S0 C3W5S0_I09A0 Influenza A virus 2 0.7247
Beta-hexosaminidase Q9KU37 NAGZ_VIBCH Vibrio cholerae serotype O1 3 0.7242
Mycocyclosin synthase P9WPP7 CP121_MYCTU Mycobacterium tuberculosis 4 0.7240
Putative S-adenosyl-L-methionine-dependent methyltransferase ML2640 Q9CCZ4 Y2640_MYCLE Mycobacterium leprae 3 0.7239
Tyrosine-protein kinase Lck P06239 LCK_HUMAN Homo sapiens 3 0.7227
2',3'-cyclic-nucleotide 3'-phosphodiesterase P16330 CN37_MOUSE Mus musculus 2 0.7223
Kinesin-like protein KIF11 P52732 KIF11_HUMAN Homo sapiens 3 0.7223
Gag-Pol polyprotein P04584 POL_HV2RO Human immunodeficiency virus type 2 subtype A 3 0.7213
Cyclin-dependent kinase 2 P24941 CDK2_HUMAN Homo sapiens 3 0.7210
RNA-dependent RNA polymerase Q6A562 Q6A562_9VIRU Thosea asigna virus 2 0.7201
Bifunctional epoxide hydrolase 2 P34913 HYES_HUMAN Homo sapiens 2 0.7195
Purine nucleoside phosphorylase 2 P45563 XAPA_ECOLI Escherichia coli 3 0.7191
Orotidine 5'-phosphate decarboxylase Q5L0U0 PYRF_GEOKA Geobacillus kaustophilus 3 0.7190
Matrix metalloproteinase-9 P14780 MMP9_HUMAN Homo sapiens 3 0.7184
1-deoxy-D-xylulose 5-phosphate reductoisomerase P45568 DXR_ECOLI Escherichia coli 2 0.7181
CCA-adding enzyme O28126 CCA_ARCFU Archaeoglobus fulgidus 2 0.7179
Metallo-beta-lactamase type 2 P52699 BLAB_SERMA Serratia marcescens 3 0.7178
Cytosolic purine 5'-nucleotidase P49902 5NTC_HUMAN Homo sapiens 2 0.7176
Estrogen receptor P03372 ESR1_HUMAN Homo sapiens 3 0.7163
CCA-adding enzyme O28126 CCA_ARCFU Archaeoglobus fulgidus 2 0.7160
Pancreatic alpha-amylase P04746 AMYP_HUMAN Homo sapiens 2 0.7159
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 2 0.7153
Dipeptidyl peptidase 4 P27487 DPP4_HUMAN Homo sapiens 3 0.7145
Biflaviolin synthase CYP158A1 Q9KZF5 C1581_STRCO Streptomyces coelicolor / M145) 3 0.7142
Metallo-beta-lactamase type 2 C7C422 BLAN1_KLEPN Klebsiella pneumoniae 2 0.7142
Tyrosine-protein kinase HCK P08631 HCK_HUMAN Homo sapiens 3 0.7134
DNA polymerase III subunit epsilon P03007 DPO3E_ECOLI Escherichia coli 2 0.7133
WxcM-like protein Q12KT8 Q12KT8_SHEDO Shewanella denitrificans 3 0.7130
cAMP-dependent protein kinase type I-alpha regulatory subunit P00514 KAP0_BOVIN Bos taurus 3 0.7119
Glycogen synthase Q9V2J8 Q9V2J8_PYRAB Pyrococcus abyssi 3 0.7118
Liver carboxylesterase 1 P23141 EST1_HUMAN Homo sapiens 3 0.7116
Oxygenase Q194P4 Q194P4_STRAA Streptomyces argillaceus 3 0.7092
Glycogen synthase Q9V2J8 Q9V2J8_PYRAB Pyrococcus abyssi 3 0.7091
Albumin P02768 ALBU_HUMAN Homo sapiens 3 0.7083
Flavoredoxin Q72HI0 Q72HI0_THET2 Thermus thermophilus 2 0.7077
N-terminal acetyltransferase A complex subunit NAT1 P12945 NAT1_YEAST Saccharomyces cerevisiae 2 0.7070
HTH-type transcriptional repressor PurR P0ACP7 PURR_ECOLI Escherichia coli 3 0.7070
L-lactate dehydrogenase A chain P13491 LDHA_RABIT Oryctolagus cuniculus 2 0.7069
3-hydroxyanthranilate 3,4-dioxygenase Q1LCS4 3HAO_CUPMC Cupriavidus metallidurans 2 0.7068
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic Q43088 RBCMT_PEA Pisum sativum 3 0.7055
Dihydropteroate synthase Q81VW8 Q81VW8_BACAN Bacillus anthracis 2 0.7033
Bromodomain-containing protein 2 P25440 BRD2_HUMAN Homo sapiens 3 0.7021
[LysW]-aminoadipate kinase O50147 LYSZ_THET2 Thermus thermophilus 3 0.7015
NTPase P4 Q94M05 Q94M05_9VIRU Pseudomonas phage phi12 3 0.7014
Activin receptor type-1 Q04771 ACVR1_HUMAN Homo sapiens 3 0.7007
Hypoxanthine-guanine phosphoribosyltransferase P00492 HPRT_HUMAN Homo sapiens 3 0.7005
Nodulin-13 P93330 NOD13_MEDTR Medicago truncatula 3 0.7004

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