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Palicoside
- Family: Plantae - Loganiaceae
- Kingdom: Plantae
-
Class: Alkaloid
- Subclass: Indole Alkaloid Glycoside
| Canonical Smiles | OC[C@H]1O[C@@H](O[C@@H]2OC=C([C@H]([C@H]2C=C)C[C@@H]2N(C)CCc3c2[nH]c2c3cccc2)C(=O)O)[C@@H]([C@H]([C@@H]1O)O)O |
|---|---|
| InChI | InChI=1S/C27H34N2O9/c1-3-13-16(10-19-21-15(8-9-29(19)2)14-6-4-5-7-18(14)28-21)17(25(34)35)12-36-26(13)38-27-24(33)23(32)22(31)20(11-30)37-27/h3-7,12-13,16,19-20,22-24,26-28,30-33H,1,8-11H2,2H3,(H,34,35)/t13-,16+,19+,20-,22-,23+,24-,26+,27+/m1/s1 |
| InChIKey | AZBVCHVFXBXKII-NTXHKPOFSA-N |
| Formula | C27H34N2O9 |
| HBA | 9 |
| HBD | 6 |
| MW | 530.57 |
| Rotatable Bonds | 7 |
| TPSA | 164.94 |
| LogP | 0.65 |
| Number Rings | 5 |
| Number Aromatic Rings | 2 |
| Heavy Atom Count | 38 |
| Formal Charge | 0 |
| Fraction CSP3 | 0.52 |
| Exact Mass | 530.23 |
| Number of Lipinski Rule Violations | 2 |
| # | Species | Family | Kingdom | NCBI Taxonomy ID |
|---|---|---|---|---|
| 1 | Strychnos usambarensis | Loganiaceae | Plantae | 992791 |
Showing of synonyms
Palicoside
(2S,3R,4S)-3-ethenyl-4-[[(1S)-2-methyl-1,3,4,9-tetrahydropyrido[3,4-b]indol-1-yl]methyl]-2-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-3,4-dihydro-2H-pyran-5-carboxylic acid
- Cao M, Muganga R, et al. (2012). LC-SPE-NMR-MS analysis of Strychnos usambarensis fruits from Rwanda.. Phytochemistry Letters, 2012, 5(1), 170-173. [View]
No compound-protein relationship available.
SMILES: c1cccc2[nH]c(c3c12)C(NCC3)CC4C=COC(C4)OC5CCCCO5
Level: 2
Mol. Weight: 530.57 g/mol
SMILES: C1COC=CC1CC(NCC2)c(c2c34)[nH]c3cccc4
Level: 1
Mol. Weight: 530.57 g/mol
SMILES: O1C=CCCC1OC2CCCCO2
Level: 1
Mol. Weight: 530.57 g/mol
SMILES: C1CNCc(c1c23)[nH]c2cccc3
Level: 0
Mol. Weight: 530.57 g/mol
SMILES: C1CCOCC1
Level: 0
Mol. Weight: 530.57 g/mol
SMILES: C1=COCCC1
Level: 0
Mol. Weight: 530.57 g/mol
No bioactivities available.
Absorption
- Caco-2 (logPapp)
- -6.49
- Human Oral Bioavailability 20%
- Non-Bioavailable
- Human Intestinal Absorption
- Non-Absorbed
- Madin-Darby Canine Kidney
- -5.540
- Human Oral Bioavailability 50%
- Non-Bioavailable
- P-Glycoprotein Inhibitor
- Non-Inhibitor
- P-Glycoprotein Substrate
- Substrate
- Skin Permeability
- -1.35
Distribution
- Blood-Brain Barrier (CNS)
- -
- Blood-Brain Barrier
- Non-Penetrable
- Fraction Unbound (Human)
- 0.810
- Plasma Protein Binding
- 60.16
- 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
- Non-Substrate
- OATP1B1
- Non-Inhibitor
- OATP1B3
- Inhibitor
Excretion
- Clearance
- 3.070
- Organic Cation Transporter 2
- Non-Inhibitor
- Half-Life of Drug
- -
Toxicity
- AMES Mutagenesis
- Safe
- Avian
- Safe
- Bee
- Safe
- Bioconcentration Factor
- -1.740
- Biodegradation
- Safe
- Carcinogenesis
- Safe
- Crustacean
- Safe
- Liver Injury I (DILI)
- Toxic
- Eye Corrosion
- Safe
- Eye Irritation
- Safe
- Maximum Tolerated Dose
- 0.080
- Liver Injury II
- Toxic
- hERG Blockers
- Safe
- Daphnia Maga
- 8.530
- 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
- -2283.730
- Rat (Acute)
- 2.600
- Rat (Chronic Oral)
- 3.130
- Fathead Minnow
- 4.340
- Respiratory Disease
- Toxic
- Skin Sensitisation
- Safe
- SR-ARE
- Safe
- SR-ATAD5
- Safe
- SR-HSE
- Safe
- SR-MMP
- Safe
- SR-p53
- Safe
General Properties
- Boiling Point
- 495.660
- Hydration Free Energy
- -3.270
- Log(D) at pH=7.4
- 0.080
- Log(P)
- 0.09
- Log S
- -2.78
- Log(Vapor Pressure)
- -13.96
- Melting Point
- 136.7
- pKa Acid
- 2.38
- pKa Basic
- 7.82
| Protein Name | UniProt ID | Entry Name | Species | #Pharmacophore Points | Probability (0.7 ≤ Tversky Score ≤ 1.0) |
|---|---|---|---|---|---|
| Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | Q05603 | COBT_SALTY | Salmonella typhimurium | 3 | 0.9511 |
| Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | F6MZ55 | F6MZ55_9FIRM | Sporomusa ovata | 3 | 0.9335 |
| Serine/threonine-protein kinase Chk2 | O96017 | CHK2_HUMAN | Homo sapiens | 3 | 0.9282 |
| Endothiapepsin | P11838 | CARP_CRYPA | Cryphonectria parasitica | 3 | 0.9247 |
| 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | Q84HC8 | NCSB1_STRCZ | Streptomyces carzinostaticus | 3 | 0.9087 |
| Glycogen phosphorylase, muscle form | P00489 | PYGM_RABIT | Oryctolagus cuniculus | 4 | 0.8790 |
| Disks large homolog 1 | Q12959 | DLG1_HUMAN | Homo sapiens | 4 | 0.8773 |
| clade A/E 93TH057 HIV-1 gp120 core | A0A0M3KKW9 | A0A0M3KKW9_9HIV1 | Human immunodeficiency virus 1 | 3 | 0.8716 |
| Carbonic anhydrase 12 | O43570 | CAH12_HUMAN | Homo sapiens | 3 | 0.8528 |
| Nitric oxide synthase, inducible | P35228 | NOS2_HUMAN | Homo sapiens | 3 | 0.8528 |
| Kynurenine--oxoglutarate transaminase 1 | Q16773 | KAT1_HUMAN | Homo sapiens | 3 | 0.8478 |
| Thiamine-phosphate synthase | P39594 | THIE_BACSU | Bacillus subtilis | 3 | 0.8388 |
| Methionine aminopeptidase | P0AE18 | MAP1_ECOLI | Escherichia coli | 4 | 0.8323 |
| 4-chlorobenzoyl CoA ligase | Q8GN86 | Q8GN86_9BURK | Alcaligenes sp. AL3007 | 3 | 0.8079 |
| Steroid Delta-isomerase | P07445 | SDIS_PSEPU | Pseudomonas putida | 3 | 0.8039 |
| Pteridine reductase, putative | Q581W1 | Q581W1_TRYB2 | Trypanosoma brucei brucei | 3 | 0.8025 |
| Carminomycin 4-O-methyltransferase DnrK | Q06528 | DNRK_STRPE | Streptomyces peucetius | 3 | 0.8014 |
| Gamma-aminobutyric acid type B receptor subunit 1 | Q9UBS5 | GABR1_HUMAN | Homo sapiens | 3 | 0.7970 |
| Liver carboxylesterase 1 | P23141 | EST1_HUMAN | Homo sapiens | 3 | 0.7928 |
| Heat shock protein HSP 90-alpha | P07900 | HS90A_HUMAN | Homo sapiens | 3 | 0.7926 |
| M17 leucyl aminopeptidase | Q8IL11 | Q8IL11_PLAF7 | Plasmodium falciparum | 3 | 0.7919 |
| Nucleoside diphosphate kinase | O58429 | NDK_PYRHO | Pyrococcus horikoshii | 3 | 0.7894 |
| Glutathione S-transferase A1 | P08263 | GSTA1_HUMAN | Homo sapiens | 3 | 0.7893 |
| Purine nucleoside phosphorylase | P00491 | PNPH_HUMAN | Homo sapiens | 3 | 0.7858 |
| Endothiapepsin | P11838 | CARP_CRYPA | Cryphonectria parasitica | 3 | 0.7788 |
| Gag-Pol polyprotein | P04585 | POL_HV1H2 | Human immunodeficiency virus type 1 group M subtype B | 3 | 0.7778 |
| beta-glucosidase | Q92AS9 | Q92AS9_LISIN | Listeria innocua serovar 6a | 3 | 0.7778 |
| Aldo-keto reductase family 1 member B1 | P15121 | ALDR_HUMAN | Homo sapiens | 3 | 0.7767 |
| Succinyl-CoA:acetate CoA-transferase | B3EY95 | SCACT_ACEAC | Acetobacter aceti | 3 | 0.7767 |
| Polymerase basic protein 2 | P31345 | PB2_I75A3 | Influenza A virus | 3 | 0.7741 |
| Rhodopsin kinase GRK1 | P28327 | GRK1_BOVIN | Bos taurus | 3 | 0.7701 |
| Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | F6MZ55 | F6MZ55_9FIRM | Sporomusa ovata | 3 | 0.7651 |
| Aspartate-semialdehyde dehydrogenase | Q51344 | DHAS_PSEAE | Pseudomonas aeruginosa | 3 | 0.7607 |
| Bromodomain-containing protein 4 | O60885 | BRD4_HUMAN | Homo sapiens | 2 | 0.7597 |
| L-lactate dehydrogenase A chain | P04642 | LDHA_RAT | Rattus norvegicus | 3 | 0.7582 |
| Benzoylformate decarboxylase | P20906 | MDLC_PSEPU | Pseudomonas putida | 3 | 0.7537 |
| 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase | O33877 | FABA_PSEAE | Pseudomonas aeruginosa | 3 | 0.7477 |
| ATP synthase subunit alpha, mitochondrial | P19483 | ATPA_BOVIN | Bos taurus | 3 | 0.7446 |
| Genome polyprotein | P26663 | POLG_HCVBK | Hepatitis C virus genotype 1b | 3 | 0.7439 |
| 4-chlorobenzoyl CoA ligase | Q8GN86 | Q8GN86_9BURK | Alcaligenes sp. AL3007 | 3 | 0.7364 |
| 5-formyltetrahydrofolate cyclo-ligase | P75430 | MTHFS_MYCPN | Mycoplasma pneumoniae | 2 | 0.7363 |
| Beta-secretase 1 | P56817 | BACE1_HUMAN | Homo sapiens | 2 | 0.7352 |
| Ribonuclease 4 | P15468 | RNAS4_PIG | Sus scrofa | 3 | 0.7323 |
| Histidinol dehydrogenase | P06988 | HISX_ECOLI | Escherichia coli | 2 | 0.7299 |
| 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | Q84HC8 | NCSB1_STRCZ | Streptomyces carzinostaticus | 3 | 0.7294 |
| Glycoside Hydrolase Family 13 | Q65MI2 | Q65MI2_BACLD | Bacillus licheniformis | 2 | 0.7256 |
| 4-chlorobenzoyl CoA ligase | Q8GN86 | Q8GN86_9BURK | Alcaligenes sp. AL3007 | 2 | 0.7244 |
| rRNA N-glycosylase | D9J2T9 | D9J2T9_MOMBA | Momordica balsamina | 2 | 0.7218 |
| Serpin domain-containing protein | H0ZQY2 | H0ZQY2_TAEGU | Taeniopygia guttata | 3 | 0.7207 |
| Steroid Delta-isomerase | P07445 | SDIS_PSEPU | Pseudomonas putida | 2 | 0.7194 |
| CREB-binding protein | Q92793 | CBP_HUMAN | Homo sapiens | 2 | 0.7194 |
| Pentaerythritol tetranitrate reductase | P71278 | P71278_ENTCL | Enterobacter cloacae | 2 | 0.7187 |
| Large structural protein | Q91L20 | Q91L20_9MONO | Human metapneumovirus | 3 | 0.7181 |
| 2'-5'-oligoadenylate synthase 1 | P00973 | OAS1_HUMAN | Homo sapiens | 2 | 0.7180 |
| Carbonic anhydrase 2 | P00918 | CAH2_HUMAN | Homo sapiens | 2 | 0.7177 |
| Polymerase acidic protein | C3W5S0 | C3W5S0_I09A0 | Influenza A virus | 2 | 0.7163 |
| ADP-ribosyl-[dinitrogen reductase] hydrolase | A7XNI2 | A7XNI2_AZOBR | Azospirillum brasilense | 2 | 0.7152 |
| Class 10 plant pathogenesis-related protein 2B | Q9LLQ2 | P102B_LUPLU | Lupinus luteus | 2 | 0.7138 |
| Gentisate 1,2-dioxygenase | Q67FT0 | Q67FT0_PSESE | Pseudaminobacter salicylatoxidans | 2 | 0.7122 |
| Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | Q05603 | COBT_SALTY | Salmonella typhimurium | 2 | 0.7121 |
| Small heat shock protein StHsp14.0 | Q970D9 | Q970D9_SULTO | Sulfurisphaera tokodaii | 3 | 0.7107 |
| Gag-Pol polyprotein | P0C6F2 | POL_HV1LW | Human immunodeficiency virus type 1 group M subtype B | 3 | 0.7098 |
| Histone H3 | P61830 | H3_YEAST | Saccharomyces cerevisiae | 2 | 0.7084 |
| Albumin | P02768 | ALBU_HUMAN | Homo sapiens | 3 | 0.7082 |
| Carbonic anhydrase 4 | Q64444 | CAH4_MOUSE | Mus musculus | 2 | 0.7047 |
| D-alanine--D-alanine ligase | Q5HEB7 | DDL_STAAC | Staphylococcus aureus | 3 | 0.7045 |
| Acidic mammalian chitinase | Q9BZP6 | CHIA_HUMAN | Homo sapiens | 2 | 0.7043 |
| Chalcone synthase 2 | P30074 | CHS2_MEDSA | Medicago sativa | 2 | 0.7031 |
| Carbonic anhydrase 1 | P00915 | CAH1_HUMAN | Homo sapiens | 2 | 0.7012 |