Natural Product: NPC282169

Natural Product IDNPC282169
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Apigenin-7-O-Beta-D-Glucuronide
IUPAC Name (2S,3S,4S,5R,6S)-3,4,5-trihydroxy-6-[5-hydroxy-2-(4-hydroxyphenyl)-4-oxochromen-7-yl]oxyoxane-2-carboxylic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL254213
PubChem CID 5319484
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0002934] Flavonoid O-glucuronides
              • [CHEMONTID:0003534] Flavonoid-7-O-glucuronides

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey JBFOLLJCGUCDQP-ZFORQUDYSA-N
Standard InCHI InChI=1S/C21H18O11/c22-9-3-1-8(2-4-9)13-7-12(24)15-11(23)5-10(6-14(15)31-13)30-21-18(27)16(25)17(26)19(32-21)20(28)29/h1-7,16-19,21-23,25-27H,(H,28,29)/t16-,17-,18+,19-,21+/m0/s1
SMILES OC(=O)[C@H]1O[C@@H](Oc2cc(O)c3c(c2)oc(cc3=O)c2ccc(cc2)O)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   446.08 Volume:   410.511
?
Van der Waals volume.
Dense:   1.087 LogP:   1.126
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.401
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.291
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   25.0
TPSA:   187.12
?
Topological Polar Surface Area.
 H-Bond Acceptor:   11.0
H-Bond Donor:   6.0 Rings:   4.0
Heavy Atoms:   11.0

MedChem Properties

QED Drug-Likeness Score:   0.32 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.874 Fsp3:   0.238
MCE-18:   88.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.469 Fluc inhibitor:   0.459
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.965
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.885
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.283 Promiscuous compounds:   0.392

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.541 MDCK Permeability:   -5.106
Pgp-inhibitor:   0.0 Pgp-substrate:   0.511
PAMPA:   1.0
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.091
20% Bioavailability (F20%):   0.187 30% Bioavailability (F30%):   0.597
50% Bioavailability (F50%):   0.953

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.863
Plasma Protein Binding (PPB):   83.829% Volume Distribution (VD):   -0.031
Fu: 13.557%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.161
OATP1B3 inhibitor:   0.664 BCRP inhibitor:   0.034
BSEP inhibitor:   0.004

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.171 CYP2C9-substrate:   0.005
CYP2D6-inhibitor:   0.009 CYP2D6-substrate:   0.284
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.097
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.853
HLM stability:   0.007
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  1.776 Half-life (T1/2):  3.441

ADMET: Toxicity

hERG Blockers:  0.013 hERG Blockers (10um):  0.069
Human Hepatotoxicity (H-HT):  0.385 Drug-induced Liver Injury (DILI):  0.971
AMES Toxicity:  0.595 Rat Oral Acute Toxicity:  0.092
Maximum Recommended Daily Dose:  0.139 Skin Sensitization:  0.959
Carcinogencity:  0.058 Eye Corrosion:  0.0
Eye Irritation:  0.856 Respiratory Toxicity:  0.095
Drug-induced Neurotoxicity:  0.002 Ototoxicity:  0.455
Hematotoxicity:  0.051 Drug-induced Nephrotoxicity:  0.379
Genotoxicity:  0.89 RPMI-8226 Immunitoxicity:  0.113
A549 Cytotoxicity:  0.199 Hek293 Cytotoxicity:  0.334
BCF:   0.25
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   2.888
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.225
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.385
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO4986 Eschscholzia californica Species Papaveraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)98060-9]
NPO6987 Tolypothrix byssoidea Species Tolypothrichaceae Bacteria n.a. n.a. n.a. PMID[11429991]
NPO8374 Allium siculum Species Amaryllidaceae Eukaryota bulb n.a. n.a. PMID[12141853]
NPO4986 Eschscholzia californica Species Papaveraceae Eukaryota n.a. Oakham, MA, US n.a. PMID[16562853]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[16755060]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. leaf n.a. PMID[16926516]
NPO23838 Kitasatospora kifunensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[17191679]
NPO4986 Eschscholzia californica Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[17250743]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. fruit n.a. PMID[17262892]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17616609]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[17666848]
NPO32975 ocimum sanctum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17850106]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17929896]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[18239311]
NPO4380 Erigeron annuus Species Asteraceae Eukaryota flowers n.a. n.a. PMID[18298080]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19113967]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19159274]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19256529]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19785430]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19962306]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20078074]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. isolated from sediment collected using a hand held deep water sampling device at >33 m depth in Vanuatu 2003 PMID[20303767]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. fruit n.a. PMID[21163339]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21667925]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21954885]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22106303]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota stem bark of Melia azedarach n.a. n.a. PMID[22409377]
NPO23380 Camellia japonica Species Theaceae Eukaryota flower buds n.a. n.a. PMID[22834923]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23557488]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23563483]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. leaf n.a. PMID[24066589]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota whole plants Nanning District, Guangxi Province, China 2012-Sep PMID[25647077]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota aerial parts Seoul, Korea n.a. PMID[26331882]
NPO27467 Anigozanthos rufus Species Haemodoraceae Eukaryota n.a. n.a. n.a. PMID[28682615]
NPO40019 Anigozanthos pulcherrimus Species Haemodoraceae Eukaryota n.a. n.a. n.a. PMID[28682615]
NPO23380 Camellia japonica Species Theaceae Eukaryota Roots n.a. n.a. PMID[30395460]
NPO41592 Bacillus licheniformis DW2â–³lrp::BrnQ [BrnQ Lrp] Strain Bacillaceae Bacteria n.a. n.a. n.a. PMID[30417137]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. PMID[32569471]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. PMID[3430163]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37446759]
NPO52675 Lactuca saligna Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38338341]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. PMID[39065796]
NPO53552 Verbascum gimgimense Genus Scrophulariaceae Eukaryota n.a. n.a. n.a. PMID[39632482]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[7622436]
NPO14757 Acacia acuminata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7656 Pachyrhizus tuberosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4986 Eschscholzia californica Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14730 Bonnetia dinizii Species Bonnetiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8231 Jaspis digonoxea Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4380 Erigeron annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10412 Aglaia erythrosperma Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8374 Allium siculum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7295 Arabis hirsuta Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11112 Inulanthera nuda Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4319 Rubia lanceolata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24439 Tristagma uniflorum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11437 Alluaudia ascendens Species Didiereaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11798 Anthemis pseudocotula Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6987 Tolypothrix byssoidea Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO6284 Frasera caroliniensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2090 Baccharis thesioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12534 Gastrophysa cyanea Species Chrysomelidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40019 Anigozanthos pulcherrimus Species Haemodoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27467 Anigozanthos rufus Species Haemodoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO52675 Lactuca saligna Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4986 Eschscholzia californica Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO228 Physostigma venenosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4380 Erigeron annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO228 Physostigma venenosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4380 Erigeron annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4986 Eschscholzia californica Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO228 Physostigma venenosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4986 Eschscholzia californica Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23838 Kitasatospora kifunensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13295 Teucrium nuchense Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7295 Arabis hirsuta Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5406 Veronica chamaedrys Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13653 Sorbus domestica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4214 Centaurea collina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8231 Jaspis digonoxea Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9385 Glycosmis ovoidea Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14084 Roccella fucoides Species Roccellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2509 Strombus gigas Species Strombidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14730 Bonnetia dinizii Species Bonnetiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11112 Inulanthera nuda Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10196 Echinocereus blanckii Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4489 Achillea serbica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12739 Pseudoscleropodium purum Species Brachytheciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11189 Anabaena sphaerica Species Nostocaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2090 Baccharis thesioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8719 Fusarium vasinfectum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10826 Rabdosia weisiensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO368 Dendroaspis angusticeps Species Elapidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO228 Physostigma venenosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6284 Frasera caroliniensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4986 Eschscholzia californica Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14757 Acacia acuminata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18458 Raukaua simplex Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10412 Aglaia erythrosperma Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24439 Tristagma uniflorum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6710 Sinapis nigra Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5445 Euonymus nanus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4380 Erigeron annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6987 Tolypothrix byssoidea Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11437 Alluaudia ascendens Species Didiereaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15620 Kingiella taenialis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11798 Anthemis pseudocotula Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4319 Rubia lanceolata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1689 Epimedium pubescens Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7656 Pachyrhizus tuberosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12059 Triticum estivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3342 Kniphofia pumila Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8374 Allium siculum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11546 Ledebouria floribunda Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12534 Gastrophysa cyanea Species Chrysomelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10889 Heterochordaria abietina n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO27467 Anigozanthos rufus Species Haemodoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9497 Myrtopsis novae-caledoniae Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference
NPO23380 Camellia japonica n.a. Flowers 0.230 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 0.219 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 1.044 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 0.214 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 0.224 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 0.215 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 0.222 n.a. n.a. μg/100g PMID[39065796]
NPO4031.1 Cynara cardunculus var. scolymus Raw n.a. 7.400000215 n.a. n.a. mg/100g Database [PHENOL EXPLORER]
NPO4031.1 Cynara cardunculus var. scolymus n.a. n.a. 7.4 n.a. n.a. mg/100g of FW Database [Phenol-Explorer]
NPO52675 Lactuca saligna n.a. Aerial parts 8.89 n.a. n.a. mg/kg PMID[38338341]
NPO53552 Verbascum gimgimense n.a. n.a. 0.465 n.a. n.a. mg/g PMID[39632482]

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT68 Individual protein Aldose reductase Rattus norvegicus IC50 = 1280.0 nM PMID[18298080]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT113 Cell line RAW264.7 Mus musculus IC50 > 100000.0 nM PMID[33667099]
NPT2257 Cell line MCF-10A Homo sapiens IC50 = 42000.0 nM PMID[33257172]
NPT784 Cell line MDA-MB-468 Homo sapiens IC50 = 13000.0 nM PMID[33257172]
NPT113 Cell line RAW264.7 Mus musculus CC50 > 100000.0 nM PMID[33667099]
NPT188 Organism Candida parapsilosis Candida parapsilosis MIC = 64.0 ug.mL-1 PMID[31427220]
NPT20 Organism Candida albicans Candida albicans MIC > 256.0 ug.mL-1 PMID[31427220]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC282169 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8889 High Similarity NPC20505
0.8514 High Similarity NPC608742
0.7792 Intermediate Similarity NPC43211
0.7215 Intermediate Similarity NPC210094
0.6795 Remote Similarity NPC331652
0.679 Remote Similarity NPC237435
0.6782 Remote Similarity NPC64051
0.6709 Remote Similarity NPC39360
0.6709 Remote Similarity NPC29763
0.6709 Remote Similarity NPC210003
0.6707 Remote Similarity NPC610187
0.6522 Remote Similarity NPC253685
0.6471 Remote Similarity NPC600989
0.6463 Remote Similarity NPC27942
0.6386 Remote Similarity NPC135277
0.631 Remote Similarity NPC115760
0.6265 Remote Similarity NPC101191
0.6264 Remote Similarity NPC229409
0.6098 Remote Similarity NPC19709
0.6056 Remote Similarity NPC234133
0.6024 Remote Similarity NPC189142
0.6024 Remote Similarity NPC77660
0.5889 Remote Similarity NPC44931
0.587 Remote Similarity NPC46202
0.5814 Remote Similarity NPC235260
0.5814 Remote Similarity NPC155763
0.5747 Remote Similarity NPC601144
0.5684 Remote Similarity NPC270675
0.5684 Remote Similarity NPC195685
0.5647 Remote Similarity NPC95090
0.5647 Remote Similarity NPC27408
0.5618 Remote Similarity NPC190003
0.5595 Remote Similarity NPC473043
0.5581 Remote Similarity NPC181712
0.5529 Remote Similarity NPC261866
0.551 Remote Similarity NPC472994
0.5506 Remote Similarity NPC311830
0.5495 Remote Similarity NPC606546
0.5484 Remote Similarity NPC65003
0.5455 Remote Similarity NPC49344
0.5408 Remote Similarity NPC101636
0.5408 Remote Similarity NPC298171
0.5385 Remote Similarity NPC222674
0.5341 Remote Similarity NPC138927
0.5333 Remote Similarity NPC108406
0.5319 Remote Similarity NPC210073
0.5294 Remote Similarity NPC472993
0.5222 Remote Similarity NPC22832
0.5222 Remote Similarity NPC243930
0.5222 Remote Similarity NPC264735
0.5172 Remote Similarity NPC249281
0.5172 Remote Similarity NPC108831
0.5172 Remote Similarity NPC182634
0.5161 Remote Similarity NPC8856
0.5155 Remote Similarity NPC65711
0.5152 Remote Similarity NPC479765
0.5114 Remote Similarity NPC93337
0.5114 Remote Similarity NPC297987
0.5114 Remote Similarity NPC146792
0.5114 Remote Similarity NPC323593
0.5114 Remote Similarity NPC203500
0.5104 Remote Similarity NPC122809
0.5102 Remote Similarity NPC210961
0.5067 Remote Similarity NPC127447
0.5067 Remote Similarity NPC29353
0.5056 Remote Similarity NPC105025
0.5056 Remote Similarity NPC610763
0.5051 Remote Similarity NPC479766
0.505 Remote Similarity NPC179862

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC282169 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.679 Remote Similarity NPD4338 Clinical (unspecified phase)

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data