Natural Product: NPC288669

Natural Product IDNPC288669
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 5,7-Dihydroxy-2-(4-Hydroxy-3-Methoxyphenyl)-3,6,8-Trimethoxychromen-4-One
IUPAC Name 5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-3,6,8-trimethoxychromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL77156
PubChem CID 5386959
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002593] 8-O-methylated flavonoids

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 DEQJJTUOVGHXHW-UHFFFAOYSA-N
Standard InCHI InChI=1S/C19H18O9/c1-24-10-7-8(5-6-9(10)20)15-18(26-3)13(22)11-12(21)17(25-2)14(23)19(27-4)16(11)28-15/h5-7,20-21,23H,1-4H3
SMILES COc1cc(ccc1O)c1c(c(=O)c2c(c(c(c(c2o1)OC)O)OC)O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   390.1 Volume:   369.531
?
Van der Waals volume.
Dense:   1.056 LogP:   2.028
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.145
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.786
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   18.0
TPSA:   127.82
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.602 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.676 Fsp3:   0.211
MCE-18:   21.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.279 Fluc inhibitor:   0.358
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.815
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.43
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.33 Promiscuous compounds:   0.779

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.221 MDCK Permeability:   -4.805
Pgp-inhibitor:   0.838 Pgp-substrate:   0.128
PAMPA:   0.097
?
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):   0.017
20% Bioavailability (F20%):   0.055 30% Bioavailability (F30%):   0.21
50% Bioavailability (F50%):   0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.021 MRP1:   0.973
Plasma Protein Binding (PPB):   95.276% Volume Distribution (VD):   -0.547
Fu: 4.91%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.521
OATP1B3 inhibitor:   0.962 BCRP inhibitor:   0.977
BSEP inhibitor:   0.991

ADMET: Metabolism

CYP1A2-inhibitor:   0.994 CYP1A2-substrate:   0.063
CYP2C19-inhibitor:   0.182 CYP2C19-substrate:   0.214
CYP2C9-inhibitor:   0.243 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.747 CYP2D6-substrate:   0.933
CYP3A4-inhibitor:   0.09 CYP3A4-substrate:   0.026
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.992
HLM stability:   0.655
?
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):  3.256 Half-life (T1/2):  1.684

ADMET: Toxicity

hERG Blockers:  0.066 hERG Blockers (10um):  0.487
Human Hepatotoxicity (H-HT):  0.444 Drug-induced Liver Injury (DILI):  0.7
AMES Toxicity:  0.432 Rat Oral Acute Toxicity:  0.339
Maximum Recommended Daily Dose:  0.334 Skin Sensitization:  0.789
Carcinogencity:  0.703 Eye Corrosion:  0.189
Eye Irritation:  0.929 Respiratory Toxicity:  0.568
Drug-induced Neurotoxicity:  0.188 Ototoxicity:  0.236
Hematotoxicity:  0.309 Drug-induced Nephrotoxicity:  0.198
Genotoxicity:  0.281 RPMI-8226 Immunitoxicity:  0.107
A549 Cytotoxicity:  0.249 Hek293 Cytotoxicity:  0.34
BCF:   0.945
?
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:   3.534
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.349
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.867
?
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
NPO24630 Sophora exigua Species Fabaceae Eukaryota n.a. root n.a. DOI[10.1016/0031-9422(92)80056-K]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.procbio.2005.03.071]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. DOI[10.1023/A:1011684619614]
NPO11199 Agelas nakamurai Species Agelasidae Eukaryota n.a. at a depth of 14 m near the island of Ambon (Seram Seilale), Indonesia 1997-AUG PMID[10514317]
NPO24630 Sophora exigua Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10839220]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[12357398]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[12483566]
NPO11199 Agelas nakamurai Species Agelasidae Eukaryota n.a. n.a. n.a. PMID[14677933]
NPO25324 Phorbas amaranthus Species Hymedesmiidae Eukaryota n.a. n.a. n.a. PMID[15104518]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[15497948]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[15921417]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[16209910]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[16499339]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[16872138]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[16904330]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[17125234]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[17827664]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[19246197]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota Ginkgo biloba n.a. n.a. PMID[19246197]
NPO23546 Clausena lansium Species Rutaceae Eukaryota leaves n.a. n.a. PMID[19327990]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[19427327]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[20225834]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[20814854]
NPO25772 Lippia mexicana Species Verbenaceae Eukaryota n.a. flower n.a. PMID[20942442]
NPO25772 Lippia mexicana Species Verbenaceae Eukaryota n.a. leaf n.a. PMID[20942442]
NPO25772 Lippia mexicana Species Verbenaceae Eukaryota n.a. stem n.a. PMID[20942442]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[21548578]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota isolated from the leaves of Viguiera robusta n.a. n.a. PMID[21548578]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. mycelium n.a. PMID[21548578]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[21640594]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[21854043]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[22112725]
NPO23546 Clausena lansium Species Rutaceae Eukaryota Stems n.a. n.a. PMID[22372931]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[22593034]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[23072467]
NPO26819 Xanthium pungens Species Asteraceae Eukaryota burrs n.a. n.a. PMID[2380717]
NPO26819 Xanthium pungens Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[2380717]
NPO23546 Clausena lansium Species Rutaceae Eukaryota Roots n.a. n.a. PMID[24798144]
NPO24324 Halobacterium salinarum Species Halobacteriaceae Archaea n.a. n.a. n.a. PMID[24823651]
NPO11199 Agelas nakamurai Species Agelasidae Eukaryota n.a. Okinawan n.a. PMID[26083682]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. Xichang of Sichuan Province, China n.a. PMID[26125976]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[26343828]
NPO23546 Clausena lansium Species Rutaceae Eukaryota Leaves n.a. n.a. PMID[26523463]
NPO25474 Ocotea pulchella Species Lauraceae Eukaryota n.a. stem n.a. PMID[27482860]
NPO25474 Ocotea pulchella Species Lauraceae Eukaryota n.a. leaf n.a. PMID[27482860]
NPO25474 Ocotea pulchella Species Lauraceae Eukaryota n.a. root n.a. PMID[27482860]
NPO8912 Daphne giraldii Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[27627130]
NPO8912 Daphne giraldii Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[28371676]
NPO24447 Thalictrum cultratum Species Ranunculaceae Eukaryota Roots n.a. n.a. PMID[29131616]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[30970599]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[33118348]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[36432211]
NPO28927 Gutierrezia microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[3655803]
NPO26001 Carlina acaulis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37630400]
NPO26889 Chaetomium subaffine Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[436014]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[5066072]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. PMID[7116505]
NPO11199 Agelas nakamurai Species Agelasidae Eukaryota n.a. papua new guinean n.a. PMID[9784179]
NPO26889 Chaetomium subaffine Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[CiteXplore Id]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[CiteXplore Id]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25474 Ocotea pulchella Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24510 Turricula parryi Species Namaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20052 Flemingia chappar Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26889 Chaetomium subaffine Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22785 Nicotiana debneyi Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11199 Agelas nakamurai Species Agelasidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24630 Sophora exigua Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25324 Phorbas amaranthus Species Hymedesmiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26819 Xanthium pungens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26677 Garcinia pseudoguttifera Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25643 Streptomyces chattanoogensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO26483 Chrysosplenium echinus Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28927 Gutierrezia microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26853 Baccharis magellanica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18359 Canella winterana Species Canellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24736 Acacia pycnantha Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25093 Ericameria diffusa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25910 Trichoderma polysporum Species Hypocreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8912 Daphne giraldii Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25520 Uncaria laevigata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26916 Thermopsis alpina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26744 Heliotropium eichwaldii Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26001 Carlina acaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26457 Alpinia allughas Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26916 Thermopsis alpina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24447 Thalictrum cultratum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25520 Uncaria laevigata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26744 Heliotropium eichwaldii Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21594 Sporobolus cynosuroides Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26677 Garcinia pseudoguttifera Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28927 Gutierrezia microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26916 Thermopsis alpina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28927 Gutierrezia microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[Title]
NPO28927 Gutierrezia microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21594 Sporobolus cynosuroides Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25474 Ocotea pulchella Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26786 Berkheya zeyheri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26916 Thermopsis alpina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26312 Cirsium tanakae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10241 Afrocarpus falcatus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20052 Flemingia chappar Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18359 Canella winterana Species Canellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26853 Baccharis magellanica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26645 Beilschmiedia volckii Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26525 Eriostemon thryptomenoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25643 Streptomyces chattanoogensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11199 Agelas nakamurai Species Agelasidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24447 Thalictrum cultratum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26457 Alpinia allughas Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26083 Eumorphia sericea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24653 Calonectria cylindrospora Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26483 Chrysosplenium echinus Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24171 Chaetomium globosum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26677 Garcinia pseudoguttifera Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25520 Uncaria laevigata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26848 Ligularia lamarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25772 Lippia mexicana Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24630 Sophora exigua Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25402 Kuehneromyces mutabilis Species Strophariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24510 Turricula parryi Species Namaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23684 Narcissus obesus Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25324 Phorbas amaranthus Species Hymedesmiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8912 Daphne giraldii Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24324 Halobacterium salinarum Species Halobacteriaceae Archaea n.a. n.a. n.a. Database[UNPD]
NPO22785 Nicotiana debneyi Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24736 Acacia pycnantha Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25910 Trichoderma polysporum Species Hypocreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26709 Phyllanthus discoideus Species Leiothrichidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25093 Ericameria diffusa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26744 Heliotropium eichwaldii Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24834 Cystoseira jabukae Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26210 Eupatorium birmanicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26115 Asterogyne martiana Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26889 Chaetomium subaffine Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26001 Carlina acaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26819 Xanthium pungens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21702 Decachaeta thieleana n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26975 Aloe vulgaris Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26945 Crangon vulgaris Species Crangonidae 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

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
NPT518 Protein complex Tubulin Homo sapiens IC50 > 40000.0 nM PMID[9632366]
NPT518 Protein complex Tubulin Homo sapiens Inhibition = 6.0 % PMID[9632366]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT517 Cell line Panel NCI-60 (60 carcinoma cell lines) Homo sapiens GI50 = 27000.0 nM PMID[9632366]
NPT367 Cell line MDA-N Homo sapiens GI50 n.a. 48083.93 nM PubChem BioAssay data set
NPT368 Cell line SN12C Homo sapiens GI50 n.a. 59841.16 nM PubChem BioAssay data set
NPT369 Cell line ACHN Homo sapiens GI50 n.a. 41879.36 nM PubChem BioAssay data set
NPT370 Cell line NCI-H23 Homo sapiens GI50 n.a. 52360.04 nM PubChem BioAssay data set
NPT371 Cell line UO-31 Homo sapiens GI50 n.a. 31622.78 nM PubChem BioAssay data set
NPT116 Cell line HL-60 Homo sapiens GI50 n.a. 33496.54 nM PubChem BioAssay data set
NPT373 Cell line SK-MEL-5 Homo sapiens GI50 n.a. 29785.16 nM PubChem BioAssay data set
NPT374 Cell line SF-539 Homo sapiens GI50 n.a. 40364.54 nM PubChem BioAssay data set
NPT90 Cell line DU-145 Homo sapiens GI50 n.a. 31988.95 nM PubChem BioAssay data set
NPT375 Cell line Malme-3M Homo sapiens GI50 n.a. 34673.69 nM PubChem BioAssay data set
NPT111 Cell line K562 Homo sapiens GI50 n.a. 58613.82 nM PubChem BioAssay data set
NPT376 Cell line A498 Homo sapiens GI50 n.a. 37325.02 nM PubChem BioAssay data set
NPT377 Cell line OVCAR-3 Homo sapiens GI50 n.a. 24322.04 nM PubChem BioAssay data set
NPT112 Cell line MOLT-4 Homo sapiens GI50 n.a. 95499.26 nM PubChem BioAssay data set
NPT379 Cell line HOP-62 Homo sapiens GI50 n.a. 23067.47 nM PubChem BioAssay data set
NPT378 Cell line NCI/ADR-RES Homo sapiens GI50 n.a. 50815.94 nM PubChem BioAssay data set
NPT380 Cell line U-251 Homo sapiens GI50 n.a. 26424.09 nM PubChem BioAssay data set
NPT381 Cell line OVCAR-8 Homo sapiens GI50 n.a. 68548.82 nM PubChem BioAssay data set
NPT382 Cell line OVCAR-5 Homo sapiens GI50 n.a. 100000.0 nM PubChem BioAssay data set
NPT383 Cell line SNB-19 Homo sapiens GI50 n.a. 100000.0 nM PubChem BioAssay data set
NPT82 Cell line MDA-MB-231 Homo sapiens GI50 n.a. 44157.04 nM PubChem BioAssay data set
NPT385 Cell line SR Homo sapiens GI50 n.a. 41495.4 nM PubChem BioAssay data set
NPT384 Cell line TK-10 Homo sapiens GI50 n.a. 31332.86 nM PubChem BioAssay data set
NPT323 Cell line SW-620 Homo sapiens GI50 n.a. 94406.09 nM PubChem BioAssay data set
NPT386 Cell line KM12 Homo sapiens GI50 n.a. 100000.0 nM PubChem BioAssay data set
NPT455 Cell line NCI-H522 Homo sapiens GI50 n.a. 29107.17 nM PubChem BioAssay data set
NPT387 Cell line M14 Homo sapiens GI50 n.a. 10375.28 nM PubChem BioAssay data set
NPT388 Cell line NCI-H322M Homo sapiens GI50 n.a. 65765.78 nM PubChem BioAssay data set
NPT389 Cell line RPMI-8226 Homo sapiens GI50 n.a. 26121.61 nM PubChem BioAssay data set
NPT456 Cell line OVCAR-4 Homo sapiens GI50 n.a. 74131.02 nM PubChem BioAssay data set
NPT390 Cell line LOX IMVI Homo sapiens GI50 n.a. 26915.35 nM PubChem BioAssay data set
NPT457 Cell line BT-549 Homo sapiens GI50 n.a. 37931.5 nM PubChem BioAssay data set
NPT147 Cell line SK-MEL-2 Homo sapiens GI50 n.a. 24774.22 nM PubChem BioAssay data set
NPT391 Cell line HCC 2998 Homo sapiens GI50 n.a. 45289.76 nM PubChem BioAssay data set
NPT81 Cell line A549 Homo sapiens GI50 n.a. 65313.06 nM PubChem BioAssay data set
NPT393 Cell line HCT-116 Homo sapiens GI50 n.a. 50582.47 nM PubChem BioAssay data set
NPT148 Cell line HCT-15 Homo sapiens GI50 n.a. 28840.32 nM PubChem BioAssay data set
NPT394 Cell line EKVX Homo sapiens GI50 n.a. 78704.58 nM PubChem BioAssay data set
NPT306 Cell line PC-3 Homo sapiens GI50 n.a. 48865.24 nM PubChem BioAssay data set
NPT83 Cell line MCF7 Homo sapiens GI50 n.a. 28906.8 nM PubChem BioAssay data set
NPT146 Cell line SK-OV-3 Homo sapiens GI50 n.a. 17947.34 nM PubChem BioAssay data set
NPT397 Cell line NCI-H460 Homo sapiens GI50 n.a. 46131.76 nM PubChem BioAssay data set
NPT396 Cell line T47D Homo sapiens GI50 n.a. 20276.83 nM PubChem BioAssay data set
NPT398 Cell line UACC-62 Homo sapiens GI50 n.a. 20749.14 nM PubChem BioAssay data set
NPT308 Cell line CAKI-1 Homo sapiens GI50 n.a. 24774.22 nM PubChem BioAssay data set
NPT400 Cell line MDA-MB-435 Homo sapiens GI50 n.a. 17782.79 nM PubChem BioAssay data set
NPT458 Cell line IGROV-1 Homo sapiens GI50 n.a. 25351.29 nM PubChem BioAssay data set
NPT399 Cell line SF-295 Homo sapiens GI50 n.a. 44874.54 nM PubChem BioAssay data set
NPT402 Cell line Hs-578T Homo sapiens GI50 n.a. 14859.36 nM PubChem BioAssay data set
NPT401 Cell line 786-0 Homo sapiens GI50 n.a. 38106.58 nM PubChem BioAssay data set
NPT403 Cell line UACC-257 Homo sapiens GI50 n.a. 60534.09 nM PubChem BioAssay data set
NPT404 Cell line CCRF-CEM Homo sapiens GI50 n.a. 35237.09 nM PubChem BioAssay data set
NPT139 Cell line HT-29 Homo sapiens GI50 n.a. 68076.94 nM PubChem BioAssay data set
NPT405 Cell line NCI-H226 Homo sapiens GI50 n.a. 34914.03 nM PubChem BioAssay data set
NPT170 Cell line SK-MEL-28 Homo sapiens GI50 n.a. 56754.46 nM PubChem BioAssay data set
NPT407 Cell line COLO 205 Homo sapiens GI50 n.a. 100000.0 nM PubChem BioAssay data set

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 NPC288669 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
0.7736 Intermediate Similarity NPC191459
0.7636 Intermediate Similarity NPC253634
0.7593 Intermediate Similarity NPC130894
0.7368 Intermediate Similarity NPC19687
0.7321 Intermediate Similarity NPC204854
0.7222 Intermediate Similarity NPC7973
0.7193 Intermediate Similarity NPC4455
0.6897 Remote Similarity NPC78302
0.678 Remote Similarity NPC152166
0.65 Remote Similarity NPC261004
0.6333 Remote Similarity NPC18607
0.623 Remote Similarity NPC279989
0.623 Remote Similarity NPC78326
0.6066 Remote Similarity NPC179126
0.6066 Remote Similarity NPC236223
0.5833 Remote Similarity NPC176665
0.5667 Remote Similarity NPC275836
0.5574 Remote Similarity NPC105242
0.5556 Remote Similarity NPC610401
0.55 Remote Similarity NPC245546
0.5484 Remote Similarity NPC22472
0.541 Remote Similarity NPC266960
0.5397 Remote Similarity NPC146165
0.5397 Remote Similarity NPC83508
0.5323 Remote Similarity NPC163524
0.5312 Remote Similarity NPC7846
0.5312 Remote Similarity NPC4481
0.5246 Remote Similarity NPC602963
0.5238 Remote Similarity NPC600155
0.5231 Remote Similarity NPC227325
0.5161 Remote Similarity NPC274327
0.5161 Remote Similarity NPC292107
0.5156 Remote Similarity NPC115798
0.5156 Remote Similarity NPC280339
0.5156 Remote Similarity NPC183597
0.5079 Remote Similarity NPC143828
0.5079 Remote Similarity NPC605144
0.5079 Remote Similarity NPC606763
0.5077 Remote Similarity NPC235215
0.5077 Remote Similarity NPC128863

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC288669 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
NPD

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