Gardenifolin B - Compound Card

Gardenifolin B

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Gardenifolin B

Structure
Zoomed Structure
  • 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)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+/m1/s1
InChIKey FULHECCATAOIBE-CMYGLUHGSA-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: 196.25 g/mol

Structure

SMILES: C1COc(c12)cccc2

Level: 0

Mol. Weight: 120.15 g/mol

Structure

SMILES: c1ccccc1

Level: 0

Mol. Weight: 78.11 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%
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)
1.140
Plasma Protein Binding
77.4
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
10.030
Organic Cation Transporter 2
Non-Inhibitor
Half-Life of Drug
-

Toxicity

AMES Mutagenesis
Safe
Avian
Safe
Bee
Toxic
Bioconcentration Factor
1.040
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
5.460
Micronucleos
Toxic
NR-AhR
Toxic
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
-12.200
Rat (Acute)
2.180
Rat (Chronic Oral)
2.730
Fathead Minnow
4.770
Respiratory Disease
Safe
Skin Sensitisation
Safe
SR-ARE
Toxic
SR-ATAD5
Toxic
SR-HSE
Safe
SR-MMP
Toxic
SR-p53
Safe

General Properties

Boiling Point
451.860
Hydration Free Energy
-6.760
Log(D) at pH=7.4
3.370
Log(P)
2.18
Log S
-4.21
Log(Vapor Pressure)
-8.37
Melting Point
148.2
pKa Acid
8.51
pKa Basic
2.32
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 0.9374
Serine/threonine-protein kinase 10 O94804 STK10_HUMAN Homo sapiens 3 0.9270
rRNA N-glycosylase D9J2T9 D9J2T9_MOMBA Momordica balsamina 3 0.9217
Serine/threonine-protein kinase 24 Q9Y6E0 STK24_HUMAN Homo sapiens 3 0.9184
Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase Q9TQS6 DHDH_MACFA Macaca fascicularis 3 0.9132
Thymidine phosphorylase Q7CP66 TYPH_SALTY Salmonella typhimurium 3 0.9113
Tetracycline repressor protein class D P0ACT4 TETR4_ECOLX Escherichia coli 3 0.9030
Pyridoxal kinase P82197 PDXK_SHEEP Ovis aries 3 0.8967
Tetracycline repressor protein class D P0ACT4 TETR4_ECOLX Escherichia coli 3 0.8958
Chitinase A Q9AMP1 Q9AMP1_VIBHA Vibrio harveyi 3 0.8934
NAD(P)H-hydrate epimerase Q8K4Z3 NNRE_MOUSE Mus musculus 3 0.8898
Uracil phosphoribosyltransferase Q26998 UPP_TOXGO Toxoplasma gondii 3 0.8842
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.8774
Epidermal growth factor receptor P00533 EGFR_HUMAN Homo sapiens 3 0.8756
Thymidylate synthase P00469 TYSY_LACCA Lacticaseibacillus casei 3 0.8716
HTH-type transcriptional repressor PurR P0ACP7 PURR_ECOLI Escherichia coli 3 0.8710
Uracil phosphoribosyltransferase Q26998 UPP_TOXGO Toxoplasma gondii 3 0.8697
Tetracycline repressor protein class D P0ACT4 TETR4_ECOLX Escherichia coli 3 0.8696
Epidermal growth factor receptor P00533 EGFR_HUMAN Homo sapiens 3 0.8684
Heat shock protein HSP 90-alpha P07900 HS90A_HUMAN Homo sapiens 3 0.8567
Serine/threonine-protein kinase PLK1 P53350 PLK1_HUMAN Homo sapiens 4 0.8451
Phospholipase A2, major isoenzyme P00592 PA21B_PIG Sus scrofa 3 0.8410
Serine/threonine-protein kinase 24 Q9Y6E0 STK24_HUMAN Homo sapiens 3 0.8383
Pancreatic alpha-amylase P04746 AMYP_HUMAN Homo sapiens 3 0.8371
Beta-secretase 1 P56817 BACE1_HUMAN Homo sapiens 3 0.8338
Protein mono-ADP-ribosyltransferase PARP3 Q9Y6F1 PARP3_HUMAN Homo sapiens 3 0.8325
Tetracycline repressor protein class D P0ACT4 TETR4_ECOLX Escherichia coli 3 0.8324
Biflaviolin synthase CYP158A1 Q9KZF5 C1581_STRCO Streptomyces coelicolor / M145) 3 0.8310
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.8295
DNA gyrase subunit A P0AES5 GYRA_SHIFL Shigella flexneri 3 0.8292
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 3 0.8275
MAP kinase-activated protein kinase 2 P49137 MAPK2_HUMAN Homo sapiens 3 0.8268
Cathepsin S P25774 CATS_HUMAN Homo sapiens 3 0.8249
Queuine tRNA-ribosyltransferase P28720 TGT_ZYMMO Zymomonas mobilis subsp. mobilis 3 0.8249
HTH-type transcriptional repressor PurR P0ACP7 PURR_ECOLI Escherichia coli 3 0.8238
3',5'-cyclic-AMP phosphodiesterase 4D Q08499 PDE4D_HUMAN Homo sapiens 3 0.8222
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform P48736 PK3CG_HUMAN Homo sapiens 3 0.8222
Endothiapepsin P11838 CARP_CRYPA Cryphonectria parasitica 3 0.8208
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A Q9Y233 PDE10_HUMAN Homo sapiens 3 0.8196
RNA polymerase sigma factor SigA Q5SKW1 Q5SKW1_THET8 Thermus thermophilus 3 0.8106
HTH-type transcriptional repressor PurR P0ACP7 PURR_ECOLI Escherichia coli 3 0.8092
Rhodopsin kinase GRK1 P28327 GRK1_BOVIN Bos taurus 3 0.8069
Queuine tRNA-ribosyltransferase P28720 TGT_ZYMMO Zymomonas mobilis subsp. mobilis 3 0.8048
Hypoxanthine phosphoribosyltransferase Q4DRC4 Q4DRC4_TRYCC Trypanosoma cruzi 3 0.8037
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A Q9Y233 PDE10_HUMAN Homo sapiens 3 0.8034
Cytochrome P450 Q93H81 Q93H81_STRAX Streptomyces avermitilis 3 0.8011
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase Q8DNV6 Q8DNV6_STRR6 Streptococcus pneumoniae 3 0.7973
Chitinase Q54276 Q54276_SERMA Serratia marcescens 3 0.7920
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial Q0QF01 SDHA_PIG Sus scrofa 3 0.7915
Mycocyclosin synthase P9WPP7 CP121_MYCTU Mycobacterium tuberculosis 4 0.7819
histidine kinase O32393 O32393_ARTPT Arthrospira platensis 3 0.7763
Steroid Delta-isomerase P00947 SDIS_COMTE Comamonas testosteroni 3 0.7740
Ribonuclease J H9CZL7 H9CZL7_DEIRD Deinococcus radiodurans 3 0.7739
Tyrosine-protein kinase JAK2 O60674 JAK2_HUMAN Homo sapiens 3 0.7696
Norsolorinic acid synthase Q12053 AFLC_ASPPU Aspergillus parasiticus 3 0.7681
HTH-type transcriptional regulator TtgR Q9AIU0 TTGR_PSEPT Pseudomonas putida 3 0.7670
Gag-Pol polyprotein P03367 POL_HV1BR Human immunodeficiency virus type 1 group M subtype B 3 0.7630
Activin receptor type-1 Q04771 ACVR1_HUMAN Homo sapiens 3 0.7619
Soluble cytochrome b562 P0ABE7 C562_ECOLX Escherichia coli 3 0.7608
Thymidylate synthase P0A886 TYSY_ECO57 Escherichia coli O157:H7 3 0.7594
3',5'-cyclic-AMP phosphodiesterase 4D Q08499 PDE4D_HUMAN Homo sapiens 3 0.7577
Stromelysin-1 P08254 MMP3_HUMAN Homo sapiens 3 0.7574
Phenylalanine-4-hydroxylase P00439 PH4H_HUMAN Homo sapiens 4 0.7523
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 2 0.7500
Adenylate cyclase 2 A0A2U2H3Y1 A0A384LKY8_YERPE Yersinia pestis 3 0.7476
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic Q43088 RBCMT_PEA Pisum sativum 3 0.7440
Phosphodiesterase Q8WQX9 Q8WQX9_9TRYP Trypanosoma brucei 3 0.7436
Deoxycytidine kinase P27707 DCK_HUMAN Homo sapiens 5 0.7432
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic Q43088 RBCMT_PEA Pisum sativum 3 0.7403
Type II methyltransferase M.TaqI P14385 MTTA_THEAQ Thermus aquaticus 3 0.7389
CCA-adding enzyme O28126 CCA_ARCFU Archaeoglobus fulgidus 2 0.7380
Tyrosine-protein kinase Lck P06239 LCK_HUMAN Homo sapiens 3 0.7366
Acetylcholinesterase P04058 ACES_TETCF Tetronarce californica 3 0.7357
Ephrin type-B receptor 4 P54760 EPHB4_HUMAN Homo sapiens 3 0.7350
Dipeptidyl peptidase 4 P27487 DPP4_HUMAN Homo sapiens 3 0.7334
NADPH-dependent 7-cyano-7-deazaguanine reductase Q9KTK0 QUEF_VIBCH Vibrio cholerae serotype O1 3 0.7328
Alpha-ketoglutarate-dependent dioxygenase FTO Q9C0B1 FTO_HUMAN Homo sapiens 4 0.7327
Soluble acetylcholine receptor Q8WSF8 Q8WSF8_APLCA Aplysia californica 3 0.7311
Cyclin-dependent kinase 9 P50750 CDK9_HUMAN Homo sapiens 3 0.7309
Abscisic acid receptor PYL2 O80992 PYL2_ARATH Arabidopsis thaliana 3 0.7305
HTH-type transcriptional regulator TtgR Q9AIU0 TTGR_PSEPT Pseudomonas putida 3 0.7302
Ribosomal RNA small subunit methyltransferase NEP1 Q06287 NEP1_YEAST Saccharomyces cerevisiae 4 0.7287
Nodulin-13 P93330 NOD13_MEDTR Medicago truncatula 3 0.7281
Oxygenase Q194P4 Q194P4_STRAA Streptomyces argillaceus 3 0.7277
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic Q43088 RBCMT_PEA Pisum sativum 3 0.7266
DNA-directed DNA polymerase Q38087 DPOL_BPR69 Escherichia phage RB69 2 0.7265
Cytosolic purine 5'-nucleotidase P49902 5NTC_HUMAN Homo sapiens 2 0.7259
Histone deacetylase 4 P56524 HDAC4_HUMAN Homo sapiens 2 0.7257
Tetracycline repressor protein class D P0ACT4 TETR4_ECOLX Escherichia coli 3 0.7250
Gag-Pol polyprotein P03369 POL_HV1A2 Human immunodeficiency virus type 1 group M subtype B 3 0.7238
Non-receptor tyrosine-protein kinase TYK2 P29597 TYK2_HUMAN Homo sapiens 4 0.7235
Pyridoxal kinase O00764 PDXK_HUMAN Homo sapiens 2 0.7220
Bifunctional epoxide hydrolase 2 P34913 HYES_HUMAN Homo sapiens 2 0.7216
17beta-hydroxysteroid dehydrogenase O93874 O93874_COCLU Cochliobolus lunatus 3 0.7215
Methylketone synthase I E0YCS2 E0YCS2_SOLHA Solanum habrochaites 3 0.7209
Orotidine 5'-phosphate decarboxylase Q5L0U0 PYRF_GEOKA Geobacillus kaustophilus 3 0.7204
N-terminal acetyltransferase A complex subunit NAT1 P12945 NAT1_YEAST Saccharomyces cerevisiae 2 0.7198
Beta-secretase 1 P56817 BACE1_HUMAN Homo sapiens 3 0.7189
DNA polymerase III subunit epsilon P03007 DPO3E_ECOLI Escherichia coli 3 0.7188
1-deoxy-D-xylulose 5-phosphate reductoisomerase P45568 DXR_ECOLI Escherichia coli 2 0.7179
Casein kinase I isoform gamma-3 Q9Y6M4 KC1G3_HUMAN Homo sapiens 3 0.7174
WxcM-like protein Q12KT8 Q12KT8_SHEDO Shewanella denitrificans 3 0.7171
Mitogen-activated protein kinase 1 P63086 MK01_RAT Rattus norvegicus 3 0.7169
Dual specificity mitogen-activated protein kinase kinase 1 Q02750 MP2K1_HUMAN Homo sapiens 3 0.7161
3'-5' exoribonuclease Rv2179c P9WJ73 EXRBN_MYCTU Mycobacterium tuberculosis 2 0.7154
Streptogramin A acetyltransferase P50870 VATD_ENTFC Enterococcus faecium 3 0.7153
Glycogen synthase kinase-3 beta P49841 GSK3B_HUMAN Homo sapiens 3 0.7152
L-lactate dehydrogenase A chain P13491 LDHA_RABIT Oryctolagus cuniculus 2 0.7151
Homoserine dehydrogenase P31116 DHOM_YEAST Saccharomyces cerevisiae 3 0.7147
Xylose isomerase P24300 XYLA_STRRU Streptomyces rubiginosus 3 0.7139
cAMP-dependent protein kinase type I-alpha regulatory subunit P00514 KAP0_BOVIN Bos taurus 2 0.7137
Chalcone--flavanone isomerase 1 P28012 CFI1_MEDSA Medicago sativa 3 0.7123
Cytohesin-2 Q99418 CYH2_HUMAN Homo sapiens 3 0.7120
NAD-capped RNA hydrolase NudC P32664 NUDC_ECOLI Escherichia coli 3 0.7120
Albumin P02768 ALBU_HUMAN Homo sapiens 3 0.7119
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.7119
Gag-Pol polyprotein P03367 POL_HV1BR Human immunodeficiency virus type 1 group M subtype B 3 0.7113
UDP-galactopyranose mutase Q48485 GLF1_KLEPN Klebsiella pneumoniae 4 0.7111
2',3'-cyclic-nucleotide 3'-phosphodiesterase P16330 CN37_MOUSE Mus musculus 2 0.7108
Polymerase acidic protein C3W5S0 C3W5S0_I09A0 Influenza A virus 2 0.7104
Nucleoside diphosphate kinase A 2 P52175 NDKA2_BOVIN Bos taurus 3 0.7101
Genome polyprotein Q2YHF0 POLG_DEN4T Dengue virus type 4 3 0.7097
Glycogen synthase Q9V2J8 Q9V2J8_PYRAB Pyrococcus abyssi 3 0.7095
Serpin domain-containing protein H0ZQY2 H0ZQY2_TAEGU Taeniopygia guttata 3 0.7094
Beta-secretase 1 P56817 BACE1_HUMAN Homo sapiens 2 0.7090
Protein ppBat Q8A8A4 Q8A8A4_BACTN Bacteroides thetaiotaomicron VPI-5482 3 0.7085
Cobalt-precorrin-4 C(11)-methyltransferase O87696 CBIF_BACME Priestia megaterium 3 0.7082
Beta-glucuronidase P05804 BGLR_ECOLI Escherichia coli 3 0.7076
dTDP-4-dehydrorhamnose 3,5-epimerase A0A6L7H6N0 A0A1S0QLH9_BACAN Bacillus anthracis 3 0.7076
Rho family GTPase C4M4W4 C4M4W4_ENTHI Entamoeba histolytica 4 0.7070
Serine/threonine-protein kinase Chk1 O14757 CHK1_HUMAN Homo sapiens 3 0.7069
Ribonuclease 4 P15468 RNAS4_PIG Sus scrofa 2 0.7066
Lactotransferrin P24627 TRFL_BOVIN Bos taurus 2 0.7065
Hypoxanthine-guanine phosphoribosyltransferase P00492 HPRT_HUMAN Homo sapiens 3 0.7061
CCA-adding enzyme O28126 CCA_ARCFU Archaeoglobus fulgidus 2 0.7056
Tyrosine-protein kinase JAK2 O60674 JAK2_HUMAN Homo sapiens 3 0.7053
Gag-Pol polyprotein P04584 POL_HV2RO Human immunodeficiency virus type 2 subtype A 3 0.7051
Protocatechuate 3,4-dioxygenase beta chain P00437 PCXB_PSEPU Pseudomonas putida 2 0.7042
Ribosomal small subunit pseudouridine synthase A P0AA43 RSUA_ECOLI Escherichia coli 3 0.7039
cGMP-dependent protein kinase 1 Q13976 KGP1_HUMAN Homo sapiens 2 0.7033
Catechol O-methyltransferase P22734 COMT_RAT Rattus norvegicus 3 0.7022
Cyclic nucleotide-gated potassium channel mll3241 Q98GN8 CNGK1_RHILO Mesorhizobium japonicum) 4 0.7017
Mitochondrial poly(A) polymerase F1NBW0 F1NBW0_CHICK Gallus gallus 2 0.7014
Tetracycline repressor protein class D P0ACT4 TETR4_ECOLX Escherichia coli 3 0.7010
4-hydroxyphenylacetate 3-monooxygenase Q8YHT7 Q8YHT7_BRUME Brucella melitensis biotype 1 2 0.7002
Decapping and exoribonuclease protein O70348 DXO_MOUSE Mus musculus 3 0.7000

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