Gardenifolin D - Compound Card

Gardenifolin D

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Gardenifolin D

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+/m1/s1
InChIKey FULHECCATAOIBE-PGLKTIABSA-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]
CPRiL: 158228
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%
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
77.76
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
1.080
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
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
-10.260
Rat (Acute)
2.180
Rat (Chronic Oral)
2.730
Fathead Minnow
4.940
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
452.430
Hydration Free Energy
-6.750
Log(D) at pH=7.4
3.420
Log(P)
2.14
Log S
-4.26
Log(Vapor Pressure)
-8.25
Melting Point
155.39
pKa Acid
8.55
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 0.9380
Thymidine phosphorylase Q7CP66 TYPH_SALTY Salmonella typhimurium 3 0.9136
Serine/threonine-protein kinase 10 O94804 STK10_HUMAN Homo sapiens 3 0.9084
rRNA N-glycosylase D9J2T9 D9J2T9_MOMBA Momordica balsamina 3 0.9068
Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase Q9TQS6 DHDH_MACFA Macaca fascicularis 3 0.9021
Serine/threonine-protein kinase 24 Q9Y6E0 STK24_HUMAN Homo sapiens 3 0.8917
Heat shock protein HSP 90-alpha P07900 HS90A_HUMAN Homo sapiens 3 0.8909
NAD-capped RNA hydrolase NudC P32664 NUDC_ECOLI Escherichia coli 3 0.8843
Uracil phosphoribosyltransferase Q26998 UPP_TOXGO Toxoplasma gondii 3 0.8836
Cathepsin S P25774 CATS_HUMAN Homo sapiens 3 0.8803
Epidermal growth factor receptor P00533 EGFR_HUMAN Homo sapiens 3 0.8736
Uracil phosphoribosyltransferase Q26998 UPP_TOXGO Toxoplasma gondii 3 0.8695
NAD(P)H-hydrate epimerase Q8K4Z3 NNRE_MOUSE Mus musculus 3 0.8639
Chitinase A Q9AMP1 Q9AMP1_VIBHA Vibrio harveyi 3 0.8567
Epidermal growth factor receptor P00533 EGFR_HUMAN Homo sapiens 3 0.8544
HTH-type transcriptional repressor PurR P0ACP7 PURR_ECOLI Escherichia coli 3 0.8479
Pyridoxal kinase P82197 PDXK_SHEEP Ovis aries 3 0.8409
Genome polyprotein P26663 POLG_HCVBK Hepatitis C virus genotype 1b 3 0.8369
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A Q9Y233 PDE10_HUMAN Homo sapiens 3 0.8324
Adenylate cyclase 2 A0A2U2H3Y1 A0A384LKY8_YERPE Yersinia pestis 3 0.8305
HTH-type transcriptional repressor PurR P0ACP7 PURR_ECOLI Escherichia coli 3 0.8291
Queuine tRNA-ribosyltransferase P28720 TGT_ZYMMO Zymomonas mobilis subsp. mobilis 3 0.8263
MAP kinase-activated protein kinase 2 P49137 MAPK2_HUMAN Homo sapiens 3 0.8249
Mitogen-activated protein kinase 1 P28482 MK01_HUMAN Homo sapiens 3 0.8245
DNA gyrase subunit A P0AES5 GYRA_SHIFL Shigella flexneri 3 0.8244
Karilysin D0EM77 KLY_TANFA Tannerella forsythia 3 0.8237
Pancreatic alpha-amylase P04746 AMYP_HUMAN Homo sapiens 3 0.8186
Chitinase Q54276 Q54276_SERMA Serratia marcescens 3 0.8140
Protein mono-ADP-ribosyltransferase PARP3 Q9Y6F1 PARP3_HUMAN Homo sapiens 3 0.8087
Norsolorinic acid synthase Q12053 AFLC_ASPPU Aspergillus parasiticus 3 0.8085
Queuine tRNA-ribosyltransferase P28720 TGT_ZYMMO Zymomonas mobilis subsp. mobilis 3 0.8067
Rhodopsin kinase GRK1 P28327 GRK1_BOVIN Bos taurus 3 0.8039
Hypoxanthine phosphoribosyltransferase Q4DRC4 Q4DRC4_TRYCC Trypanosoma cruzi 3 0.7941
Activin receptor type-1 Q04771 ACVR1_HUMAN Homo sapiens 3 0.7792
Abscisic acid receptor PYL2 O80992 PYL2_ARATH Arabidopsis thaliana 3 0.7782
HTH-type transcriptional repressor PurR P0ACP7 PURR_ECOLI Escherichia coli 3 0.7697
Mycocyclosin synthase P9WPP7 CP121_MYCTU Mycobacterium tuberculosis 3 0.7678
Endothiapepsin P11838 CARP_CRYPA Cryphonectria parasitica 3 0.7622
Beta-secretase 1 P56817 BACE1_HUMAN Homo sapiens 3 0.7583
Methylketone synthase I E0YCS2 E0YCS2_SOLHA Solanum habrochaites 3 0.7579
Stromelysin-1 P08254 MMP3_HUMAN Homo sapiens 3 0.7575
2-aminohexano-6-lactam racemase Q7M181 ACLR_ACHOB Achromobacter obae 3 0.7563
Tryptophan--tRNA ligase Q9PIB4 SYW_CAMJE Campylobacter jejuni subsp. jejuni serotype O:2 4 0.7523
Beta-secretase 1 P56817 BACE1_HUMAN Homo sapiens 3 0.7512
Gag-Pol polyprotein P03367 POL_HV1BR Human immunodeficiency virus type 1 group M subtype B 3 0.7511
Ribonuclease J H9CZL7 H9CZL7_DEIRD Deinococcus radiodurans 3 0.7506
Serine/threonine-protein kinase 24 Q9Y6E0 STK24_HUMAN Homo sapiens 3 0.7476
Phenylalanine-4-hydroxylase P00439 PH4H_HUMAN Homo sapiens 4 0.7458
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic Q43088 RBCMT_PEA Pisum sativum 3 0.7436
Thymidylate synthase P0A884 TYSY_ECOLI Escherichia coli 4 0.7430
NADPH dehydrogenase 1 Q02899 OYE1_SACPS Saccharomyces pastorianus 3 0.7385
Nodulin-13 P93330 NOD13_MEDTR Medicago truncatula 3 0.7360
UDP-galactopyranose mutase Q48485 GLF1_KLEPN Klebsiella pneumoniae 4 0.7351
Beta-secretase 1 P56817 BACE1_HUMAN Homo sapiens 2 0.7347
Type II methyltransferase M.TaqI P14385 MTTA_THEAQ Thermus aquaticus 3 0.7336
Gag-Pol polyprotein P03367 POL_HV1BR Human immunodeficiency virus type 1 group M subtype B 3 0.7326
2',3'-cyclic-nucleotide 3'-phosphodiesterase P16330 CN37_MOUSE Mus musculus 2 0.7302
Tetracycline repressor protein class D P0ACT4 TETR4_ECOLX Escherichia coli 2 0.7294
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic Q43088 RBCMT_PEA Pisum sativum 3 0.7287
Geranyl diphosphate 2-C-methyltransferase D3KYU3 GPPMT_STRLS Streptomyces lasalocidi 3 0.7285
Pheromone-binding protein ASP1 Q9U9J6 Q9U9J6_APIME Apis mellifera 3 0.7276
Serine/threonine-protein kinase SKY1 Q03656 SKY1_YEAST Saccharomyces cerevisiae 2 0.7273
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic Q43088 RBCMT_PEA Pisum sativum 3 0.7265
Dual specificity mitogen-activated protein kinase kinase 1 Q02750 MP2K1_HUMAN Homo sapiens 3 0.7259
2',3'-cyclic-nucleotide 3'-phosphodiesterase P16330 CN37_MOUSE Mus musculus 2 0.7230
Phosphatidylinositol 5-phosphate 4-kinase type-2 beta P78356 PI42B_HUMAN Homo sapiens 3 0.7225
Gag-Pol polyprotein P04584 POL_HV2RO Human immunodeficiency virus type 2 subtype A 3 0.7205
Enoyl-ACP reductase Q9BJJ9 Q9BJJ9_PLAFA Plasmodium falciparum 3 0.7178
Mitogen-activated protein kinase 1 P63086 MK01_RAT Rattus norvegicus 3 0.7162
2',3'-cyclic-nucleotide 3'-phosphodiesterase P16330 CN37_MOUSE Mus musculus 2 0.7133
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A Q9Y233 PDE10_HUMAN Homo sapiens 3 0.7116
Bifunctional epoxide hydrolase 2 P34913 HYES_HUMAN Homo sapiens 2 0.7106
WxcM-like protein Q12KT8 Q12KT8_SHEDO Shewanella denitrificans 3 0.7104
Tetracycline repressor protein class D P0ACT4 TETR4_ECOLX Escherichia coli 3 0.7102
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 2 0.7097
Gag-Pol polyprotein P03367 POL_HV1BR Human immunodeficiency virus type 1 group M subtype B 3 0.7091
Rho family GTPase C4M4W4 C4M4W4_ENTHI Entamoeba histolytica 4 0.7076
Calmodulin-like domain protein kinase Q3HNM4 Q3HNM4_EIMTE Eimeria tenella 4 0.7071
Cytosolic purine 5'-nucleotidase P49902 5NTC_HUMAN Homo sapiens 2 0.7070
N-terminal acetyltransferase A complex subunit NAT1 P12945 NAT1_YEAST Saccharomyces cerevisiae 2 0.7069
Hypoxanthine-guanine phosphoribosyltransferase P00492 HPRT_HUMAN Homo sapiens 3 0.7061
Genome polyprotein Q2YHF0 POLG_DEN4T Dengue virus type 4 3 0.7049
Orotidine 5'-phosphate decarboxylase O26232 PYRF_METTH Methanothermobacter thermautotrophicus 3 0.7042
Ribosomal small subunit pseudouridine synthase A P0AA43 RSUA_ECOLI Escherichia coli 3 0.7040
Protocatechuate 3,4-dioxygenase beta chain P00437 PCXB_PSEPU Pseudomonas putida 2 0.7040
Mycinamicin III 3''-O-methyltransferase Q49492 MYCF_MICGR Micromonospora griseorubida 2 0.7035
Carbonyl reductase [NADPH] 1 P16152 CBR1_HUMAN Homo sapiens 3 0.7030
Serpin domain-containing protein H0ZQY2 H0ZQY2_TAEGU Taeniopygia guttata 3 0.7023
Mycocyclosin synthase P9WPP7 CP121_MYCTU Mycobacterium tuberculosis 4 0.7020

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