Rubiadin-1-methyl ether 3-O-beta-primeveroside - Compound Card

Rubiadin-1-methyl ether 3-O-beta-primeveroside

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Rubiadin-1-methyl ether 3-O-beta-primeveroside

Structure
Zoomed Structure
  • Family: Plantae - Rubiaceae
  • Kingdom: Plantae
  • Class: Quinone
    • Subclass: Anthraquinone Glycoside
Canonical Smiles COc1c(C)c(OC2O[C@H](COC3OC[C@H]([C@@H]([C@H]3O)O)O)[C@H]([C@@H]([C@H]2O)O)O)cc2c1C(=O)c1ccccc1C2=O
InChI InChI=1S/C27H30O13/c1-10-15(7-13-17(25(10)36-2)19(30)12-6-4-3-5-11(12)18(13)29)39-27-24(35)22(33)21(32)16(40-27)9-38-26-23(34)20(31)14(28)8-37-26/h3-7,14,16,20-24,26-28,31-35H,8-9H2,1-2H3/t14-,16-,20+,21-,22+,23-,24-,26?,27?/m1/s1
InChIKey HPTOQSCKOYXXPI-HJKUWBGBSA-N
Formula C27H30O13
HBA 13
HBD 6
MW 562.52
Rotatable Bonds 6
TPSA 201.67
LogP -1.58
Number Rings 5
Number Aromatic Rings 2
Heavy Atom Count 40
Formal Charge 0
Fraction CSP3 0.48
Exact Mass 562.17
Number of Lipinski Rule Violations 3
# Species Family Kingdom NCBI Taxonomy ID
1 Pentas bussei Rubiaceae Plantae 387051
2 Pentas lanceolata Rubiaceae Plantae 25385

Showing of synonyms

  • Bukuru J, De Kimpe N, et al. (2003). Isolation and structural elucidation of natural products from Pentas bussei K. Krause, Pentas lanceolata (Forsk.) Deflers and Pentas parvifolia Hiern (Rubiaceae). Ph.D. Thesis, University of Ghent, Faculty of Bioscience Engineering, Belgium,2003. [View] [PubMed]

No compound-protein relationship available.

Structure

SMILES: O1CCCCC1OCC2CCCC(O2)Oc(c3)ccc(c34)C(=O)c5c(C4=O)cccc5

Level: 2

Mol. Weight: 562.52 g/mol

Structure

SMILES: c1cccc(C2=O)c1C(=O)c(c23)ccc(c3)OC4CCCCO4

Level: 1

Mol. Weight: 562.52 g/mol

Structure

SMILES: O1CCCCC1COC2CCCCO2

Level: 1

Mol. Weight: 562.52 g/mol

Structure

SMILES: c1cccc(c12)C(=O)c3c(C2=O)cccc3

Level: 0

Mol. Weight: 562.52 g/mol

Structure

SMILES: C1CCOCC1

Level: 0

Mol. Weight: 562.52 g/mol

No bioactivities available.

Absorption

Caco-2 (logPapp)
-6.41
Human Oral Bioavailability 20%
Non-Bioavailable
Human Intestinal Absorption
Non-Absorbed
Madin-Darby Canine Kidney
-4.890
Human Oral Bioavailability 50%
Non-Bioavailable
P-Glycoprotein Inhibitor
Non-Inhibitor
P-Glycoprotein Substrate
Substrate
Skin Permeability
1.47

Distribution

Blood-Brain Barrier (CNS)
-
Blood-Brain Barrier
Non-Penetrable
Fraction Unbound (Human)
0.920
Plasma Protein Binding
79.5
Steady State Volume of Distribution
-

Metabolism

Breast Cancer Resistance Protein
Non-Inhibitor
CYP 1A2 Inhibitor
Non-Inhibitor
CYP 1A2 Substrate
Non-Substrate
CYP 2C19 Inhibitor
Non-Inhibitor
CYP 2C19 Substrate
Non-Substrate
CYP 2C9 Inhibitor
Non-Inhibitor
CYP 2C9 Substrate
Non-Substrate
CYP 2D6 Inhibitor
Non-Inhibitor
CYP 2D6 Substrate
Non-Substrate
CYP 3A4 Inhibitor
Non-Inhibitor
CYP 3A4 Substrate
Substrate
OATP1B1
Non-Inhibitor
OATP1B3
Non-Inhibitor

Excretion

Clearance
5.040
Organic Cation Transporter 2
Non-Inhibitor
Half-Life of Drug
-

Toxicity

AMES Mutagenesis
Safe
Avian
Safe
Bee
Toxic
Bioconcentration Factor
-2.740
Biodegradation
Toxic
Carcinogenesis
Safe
Crustacean
Safe
Liver Injury I (DILI)
Safe
Eye Corrosion
Safe
Eye Irritation
Safe
Maximum Tolerated Dose
0.780
Liver Injury II
Toxic
hERG Blockers
Safe
Daphnia Maga
5.170
Micronucleos
Toxic
NR-AhR
Safe
NR-AR
Safe
NR-AR-LBD
Safe
NR-Aromatase
Safe
NR-ER
Safe
NR-ER-LBD
Safe
NR-GR
Safe
NR-PPAR-gamma
Safe
NR-TR
Safe
T. Pyriformis
-4328.970
Rat (Acute)
2.830
Rat (Chronic Oral)
4.060
Fathead Minnow
11.380
Respiratory Disease
Safe
Skin Sensitisation
Safe
SR-ARE
Safe
SR-ATAD5
Safe
SR-HSE
Safe
SR-MMP
Safe
SR-p53
Safe

General Properties

Boiling Point
512.940
Hydration Free Energy
-2.920
Log(D) at pH=7.4
0.240
Log(P)
0.31
Log S
-3.38
Log(Vapor Pressure)
-11.4
Melting Point
198.17
pKa Acid
3.65
pKa Basic
4.07
Protein Name UniProt ID Entry Name Species #Pharmacophore Points Probability (0.7 ≤ Tversky Score ≤ 1.0)
Alpha-ketoglutarate-dependent dioxygenase FTO Q9C0B1 FTO_HUMAN Homo sapiens 3 0.9605
Alpha-ketoglutarate-dependent dioxygenase FTO Q9C0B1 FTO_HUMAN Homo sapiens 3 0.9605
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.9401
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.9401
Fibroblast growth factor receptor 1 P11362 FGFR1_HUMAN Homo sapiens 3 0.9349
Fibroblast growth factor receptor 1 P11362 FGFR1_HUMAN Homo sapiens 3 0.9349
Flavin reductase (NADPH) P30043 BLVRB_HUMAN Homo sapiens 3 0.9302
Flavin reductase (NADPH) P30043 BLVRB_HUMAN Homo sapiens 3 0.9302
Cathepsin S P25774 CATS_HUMAN Homo sapiens 3 0.9122
Cathepsin S P25774 CATS_HUMAN Homo sapiens 3 0.9122
Fatty acid-binding protein, intestinal P12104 FABPI_HUMAN Homo sapiens 3 0.8418
Fatty acid-binding protein, intestinal P12104 FABPI_HUMAN Homo sapiens 3 0.8418
Nitric oxide synthase, inducible P29477 NOS2_MOUSE Mus musculus 4 0.8230
Nitric oxide synthase, inducible P29477 NOS2_MOUSE Mus musculus 4 0.8230
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.8087
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.8087
Cholinesterase P06276 CHLE_HUMAN Homo sapiens 3 0.8019
Cholinesterase P06276 CHLE_HUMAN Homo sapiens 3 0.8019
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A Q9Y233 PDE10_HUMAN Homo sapiens 3 0.7988
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A Q9Y233 PDE10_HUMAN Homo sapiens 3 0.7988
Lactotransferrin P24627 TRFL_BOVIN Bos taurus 2 0.7961
Lactotransferrin P24627 TRFL_BOVIN Bos taurus 2 0.7961
Ribosyldihydronicotinamide dehydrogenase [quinone] P16083 NQO2_HUMAN Homo sapiens 3 0.7957
Ribosyldihydronicotinamide dehydrogenase [quinone] P16083 NQO2_HUMAN Homo sapiens 3 0.7957
Calmodulin P62157 CALM_BOVIN Bos taurus 3 0.7922
Calmodulin P62157 CALM_BOVIN Bos taurus 3 0.7922
Aldo-keto reductase family 1 member B1 P15121 ALDR_HUMAN Homo sapiens 2 0.7877
Aldo-keto reductase family 1 member B1 P15121 ALDR_HUMAN Homo sapiens 2 0.7877
Casein kinase II subunit alpha P28523 CSK2A_MAIZE Zea mays 3 0.7854
Casein kinase II subunit alpha P28523 CSK2A_MAIZE Zea mays 3 0.7854
Mitogen-activated protein kinase 1 P28482 MK01_HUMAN Homo sapiens 3 0.7780
Mitogen-activated protein kinase 1 P28482 MK01_HUMAN Homo sapiens 3 0.7780
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 2 0.7758
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 2 0.7758
Carbonyl reductase [NADPH] 1 P16152 CBR1_HUMAN Homo sapiens 2 0.7749
Carbonyl reductase [NADPH] 1 P16152 CBR1_HUMAN Homo sapiens 2 0.7749
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 2 0.7718
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 2 0.7718
Carbonyl reductase [NADPH] 1 P16152 CBR1_HUMAN Homo sapiens 2 0.7709
Carbonyl reductase [NADPH] 1 P16152 CBR1_HUMAN Homo sapiens 2 0.7709
Beta-secretase 1 P56817 BACE1_HUMAN Homo sapiens 2 0.7700
Beta-secretase 1 P56817 BACE1_HUMAN Homo sapiens 2 0.7700
TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase Q6T1W8 FDTA_ANETH Aneurinibacillus thermoaerophilus 4 0.7687
TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase Q6T1W8 FDTA_ANETH Aneurinibacillus thermoaerophilus 4 0.7687
Carbonyl reductase [NADPH] 1 P16152 CBR1_HUMAN Homo sapiens 2 0.7680
Carbonyl reductase [NADPH] 1 P16152 CBR1_HUMAN Homo sapiens 2 0.7680
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 2 0.7667
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 2 0.7667
Tyrosine-protein kinase Lck P06239 LCK_HUMAN Homo sapiens 3 0.7664
Tyrosine-protein kinase Lck P06239 LCK_HUMAN Homo sapiens 3 0.7664
Prothrombin P00734 THRB_HUMAN Homo sapiens 3 0.7629
Prothrombin P00734 THRB_HUMAN Homo sapiens 3 0.7629
Cyclin-dependent kinase 2 P24941 CDK2_HUMAN Homo sapiens 3 0.7536
Cyclin-dependent kinase 2 P24941 CDK2_HUMAN Homo sapiens 3 0.7536
Dipeptidyl peptidase 4 P27487 DPP4_HUMAN Homo sapiens 3 0.7513
Dipeptidyl peptidase 4 P27487 DPP4_HUMAN Homo sapiens 3 0.7513
Protein S100-A13 Q99584 S10AD_HUMAN Homo sapiens 3 0.7504
Protein S100-A13 Q99584 S10AD_HUMAN Homo sapiens 3 0.7504
DNA ligase P43813 DNLJ_HAEIN Haemophilus influenzae 2 0.7498
DNA ligase P43813 DNLJ_HAEIN Haemophilus influenzae 2 0.7498
Casein kinase I isoform gamma-3 Q9Y6M4 KC1G3_HUMAN Homo sapiens 3 0.7473
Casein kinase I isoform gamma-3 Q9Y6M4 KC1G3_HUMAN Homo sapiens 3 0.7473
Endothiapepsin P11838 CARP_CRYPA Cryphonectria parasitica 3 0.7465
Endothiapepsin P11838 CARP_CRYPA Cryphonectria parasitica 3 0.7465
Genome polyprotein O92972 POLG_HCVJ4 Hepatitis C virus genotype 1b 3 0.7454
Genome polyprotein O92972 POLG_HCVJ4 Hepatitis C virus genotype 1b 3 0.7454
Lactotransferrin P24627 TRFL_BOVIN Bos taurus 2 0.7449
Lactotransferrin P24627 TRFL_BOVIN Bos taurus 2 0.7449
Gag-Pol polyprotein P12497 POL_HV1N5 Human immunodeficiency virus type 1 group M subtype B 2 0.7444
Gag-Pol polyprotein P12497 POL_HV1N5 Human immunodeficiency virus type 1 group M subtype B 2 0.7444
Serine/threonine-protein kinase Chk1 O14757 CHK1_HUMAN Homo sapiens 3 0.7429
Serine/threonine-protein kinase Chk1 O14757 CHK1_HUMAN Homo sapiens 3 0.7429
Mitogen-activated protein kinase 10 P53779 MK10_HUMAN Homo sapiens 3 0.7426
Mitogen-activated protein kinase 10 P53779 MK10_HUMAN Homo sapiens 3 0.7426
Gag-Pol polyprotein P05896 POL_SIVM1 Simian immunodeficiency virus 3 0.7406
Gag-Pol polyprotein P05896 POL_SIVM1 Simian immunodeficiency virus 3 0.7406
Flavoredoxin Q72HI0 Q72HI0_THET2 Thermus thermophilus 2 0.7387
Flavoredoxin Q72HI0 Q72HI0_THET2 Thermus thermophilus 2 0.7387
Chymotrypsinogen A P00766 CTRA_BOVIN Bos taurus 3 0.7365
Chymotrypsinogen A P00766 CTRA_BOVIN Bos taurus 3 0.7365
Glycogen synthase kinase-3 beta P49841 GSK3B_HUMAN Homo sapiens 2 0.7361
Glycogen synthase kinase-3 beta P49841 GSK3B_HUMAN Homo sapiens 2 0.7361
Aldo-keto reductase family 1 member B10 O60218 AK1BA_HUMAN Homo sapiens 3 0.7353
Aldo-keto reductase family 1 member B10 O60218 AK1BA_HUMAN Homo sapiens 3 0.7353
Fibroblast growth factor receptor 1 P11362 FGFR1_HUMAN Homo sapiens 3 0.7326
Fibroblast growth factor receptor 1 P11362 FGFR1_HUMAN Homo sapiens 3 0.7326
Beta-secretase 1 P56817 BACE1_HUMAN Homo sapiens 2 0.7310
Beta-secretase 1 P56817 BACE1_HUMAN Homo sapiens 2 0.7310
Chitinase A Q9AMP1 Q9AMP1_VIBHA Vibrio harveyi 2 0.7293
Chitinase A Q9AMP1 Q9AMP1_VIBHA Vibrio harveyi 2 0.7293
TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase Q6T1W8 FDTA_ANETH Aneurinibacillus thermoaerophilus 3 0.7288
TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase Q6T1W8 FDTA_ANETH Aneurinibacillus thermoaerophilus 3 0.7288
TetR family transcriptional regulator Q58L87 Q58L87_MYCSM Mycolicibacterium smegmatis 2 0.7286
TetR family transcriptional regulator Q58L87 Q58L87_MYCSM Mycolicibacterium smegmatis 2 0.7286
Oxygenase Q194P4 Q194P4_STRAA Streptomyces argillaceus 3 0.7268
Oxygenase Q194P4 Q194P4_STRAA Streptomyces argillaceus 3 0.7268
Prostaglandin F2a synthase Q8I6L9 Q8I6L9_TRYCR Trypanosoma cruzi 2 0.7254
Prostaglandin F2a synthase Q8I6L9 Q8I6L9_TRYCR Trypanosoma cruzi 2 0.7254
Disks large homolog 1 Q12959 DLG1_HUMAN Homo sapiens 3 0.7241
Disks large homolog 1 Q12959 DLG1_HUMAN Homo sapiens 3 0.7241
Lethal(3)malignant brain tumor-like protein 1 Q9Y468 LMBL1_HUMAN Homo sapiens 3 0.7234
Lethal(3)malignant brain tumor-like protein 1 Q9Y468 LMBL1_HUMAN Homo sapiens 3 0.7234
Cytosolic purine 5'-nucleotidase P49902 5NTC_HUMAN Homo sapiens 2 0.7220
Cytosolic purine 5'-nucleotidase P49902 5NTC_HUMAN Homo sapiens 2 0.7220
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.7218
Carbonic anhydrase 2 P00918 CAH2_HUMAN Homo sapiens 3 0.7218
Lactoperoxidase A0A452E9Y6 PERL_CAPHI Capra hircus 2 0.7213
Lactoperoxidase A0A452E9Y6 PERL_CAPHI Capra hircus 2 0.7213
F420-dependent methylenetetrahydromethanopterin dehydrogenase P94951 MTD_METKA Methanopyrus kandleri 2 0.7206
F420-dependent methylenetetrahydromethanopterin dehydrogenase P94951 MTD_METKA Methanopyrus kandleri 2 0.7206
Protein ppBat Q8A8A4 Q8A8A4_BACTN Bacteroides thetaiotaomicron VPI-5482 2 0.7186
Protein ppBat Q8A8A4 Q8A8A4_BACTN Bacteroides thetaiotaomicron VPI-5482 2 0.7186
Cytohesin-2 Q99418 CYH2_HUMAN Homo sapiens 3 0.7170
Cytohesin-2 Q99418 CYH2_HUMAN Homo sapiens 3 0.7170
Tyrosine-protein kinase JAK3 P52333 JAK3_HUMAN Homo sapiens 2 0.7157
Tyrosine-protein kinase JAK3 P52333 JAK3_HUMAN Homo sapiens 2 0.7157
Plasma membrane ATPase Q42932 Q42932_NICPL Nicotiana plumbaginifolia 2 0.7146
Plasma membrane ATPase Q42932 Q42932_NICPL Nicotiana plumbaginifolia 2 0.7146
Lactoperoxidase P80025 PERL_BOVIN Bos taurus 2 0.7140
Lactoperoxidase P80025 PERL_BOVIN Bos taurus 2 0.7140
4-hydroxyphenylacetate 3-monooxygenase Q8YHT7 Q8YHT7_BRUME Brucella melitensis biotype 1 2 0.7138
4-hydroxyphenylacetate 3-monooxygenase Q8YHT7 Q8YHT7_BRUME Brucella melitensis biotype 1 2 0.7138
Serine/threonine-protein kinase 24 Q9Y6E0 STK24_HUMAN Homo sapiens 3 0.7113
Serine/threonine-protein kinase 24 Q9Y6E0 STK24_HUMAN Homo sapiens 3 0.7113
Glycogen phosphorylase, muscle form P00489 PYGM_RABIT Oryctolagus cuniculus 3 0.7090
Glycogen phosphorylase, muscle form P00489 PYGM_RABIT Oryctolagus cuniculus 3 0.7090
D-alanyl-D-alanine carboxypeptidase P15555 DAC_STRSR Streptomyces sp 2 0.7076
D-alanyl-D-alanine carboxypeptidase P15555 DAC_STRSR Streptomyces sp 2 0.7076
Glutathione S-transferase P P09211 GSTP1_HUMAN Homo sapiens 2 0.7071
Glutathione S-transferase P P09211 GSTP1_HUMAN Homo sapiens 2 0.7071
Aurora kinase A O14965 AURKA_HUMAN Homo sapiens 2 0.7069
Aurora kinase A O14965 AURKA_HUMAN Homo sapiens 2 0.7069
Transcriptional regulator, PadR-like family A2RI36 A2RI36_LACLM Lactococcus lactis subsp. cremoris 2 0.7063
Transcriptional regulator, PadR-like family A2RI36 A2RI36_LACLM Lactococcus lactis subsp. cremoris 2 0.7063
Tyrosine-protein kinase Lck P06239 LCK_HUMAN Homo sapiens 3 0.7059
Tyrosine-protein kinase Lck P06239 LCK_HUMAN Homo sapiens 3 0.7059
Serine/threonine-protein kinase pim-1 P11309 PIM1_HUMAN Homo sapiens 4 0.7054
Serine/threonine-protein kinase pim-1 P11309 PIM1_HUMAN Homo sapiens 4 0.7054
Stromelysin-1 P08254 MMP3_HUMAN Homo sapiens 2 0.7054
Stromelysin-1 P08254 MMP3_HUMAN Homo sapiens 2 0.7054
Cytidine deaminase P19079 CDD_BACSU Bacillus subtilis 4 0.7053
Cytidine deaminase P19079 CDD_BACSU Bacillus subtilis 4 0.7053
Tyrosine-protein kinase Lck P06239 LCK_HUMAN Homo sapiens 3 0.7052
Tyrosine-protein kinase Lck P06239 LCK_HUMAN Homo sapiens 3 0.7052
2-phospho-L-lactate transferase Q8PVT6 COFD_METMA Methanosarcina mazei 2 0.7042
2-phospho-L-lactate transferase Q8PVT6 COFD_METMA Methanosarcina mazei 2 0.7042
Gag-Pol polyprotein P0C6F2 POL_HV1LW Human immunodeficiency virus type 1 group M subtype B 3 0.7037
Gag-Pol polyprotein P0C6F2 POL_HV1LW Human immunodeficiency virus type 1 group M subtype B 3 0.7037
Polyprotein Q80J95 Q80J95_9CALI Murine norovirus 1 2 0.7016
Polyprotein Q80J95 Q80J95_9CALI Murine norovirus 1 2 0.7016
2-Hydroxyacid oxidase 1 Q9UJM8 HAOX1_HUMAN Homo sapiens 3 0.7015
2-Hydroxyacid oxidase 1 Q9UJM8 HAOX1_HUMAN Homo sapiens 3 0.7015
Coagulation factor X P00742 FA10_HUMAN Homo sapiens 2 0.7009
Coagulation factor X P00742 FA10_HUMAN Homo sapiens 2 0.7009
S-adenosylmethionine decarboxylase proenzyme P17707 DCAM_HUMAN Homo sapiens 3 0.7006
S-adenosylmethionine decarboxylase proenzyme P17707 DCAM_HUMAN Homo sapiens 3 0.7006
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 2 0.7003
Basic phospholipase A2 VRV-PL-VIIIa P59071 PA2B8_DABRR Daboia russelii 2 0.7003

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