Natural Product: NPC988

Natural Product IDNPC988
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Dihydrotanshinone I
IUPAC Name (1R)-1,6-dimethyl-1,2-dihydronaphtho[1,2-g][1]benzofuran-10,11-dione
Synonyms Dihydrotanshinone; Dihydrotanshinone I
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL227075
PubChem CID 11425923
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0002548] Tanshinones, isotanshinones, and derivatives

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 HARGZZNYNSYSGJ-JTQLQIEISA-N
Standard InCHI InChI=1S/C18H14O3/c1-9-4-3-5-12-11(9)6-7-13-15(12)17(20)16(19)14-10(2)8-21-18(13)14/h3-7,10H,8H2,1-2H3/t10-/m0/s1
SMILES C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1cccc2C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   278.09 Volume:   290.937
?
Van der Waals volume.
Dense:   0.956 LogP:   3.139
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.063
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.83
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   22.0
TPSA:   43.37
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   0.0 Rings:   4.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.694 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.186 Fsp3:   0.222
MCE-18:   70.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   1
Colloidal aggregators:   0.751 Fluc inhibitor:   0.958
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.615
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.443
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.432 Promiscuous compounds:   0.175

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.455 MDCK Permeability:   -4.481
Pgp-inhibitor:   0.998 Pgp-substrate:   0.033
PAMPA:   0.195
?
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):   0.01
20% Bioavailability (F20%):   0.186 30% Bioavailability (F30%):   0.905
50% Bioavailability (F50%):   0.856

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.76
Plasma Protein Binding (PPB):   98.164% Volume Distribution (VD):   0.294
Fu: 1.699%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.011
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.988 CYP1A2-substrate:   0.999
CYP2C19-inhibitor:   0.064 CYP2C19-substrate:   0.997
CYP2C9-inhibitor:   0.01 CYP2C9-substrate:   0.963
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.92
CYP3A4-inhibitor:   0.006 CYP3A4-substrate:   0.98
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.995
HLM stability:   0.953
?
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):  4.637 Half-life (T1/2):  0.835

ADMET: Toxicity

hERG Blockers:  0.057 hERG Blockers (10um):  0.362
Human Hepatotoxicity (H-HT):  0.932 Drug-induced Liver Injury (DILI):  0.989
AMES Toxicity:  0.965 Rat Oral Acute Toxicity:  0.539
Maximum Recommended Daily Dose:  0.711 Skin Sensitization:  0.994
Carcinogencity:  0.986 Eye Corrosion:  0.006
Eye Irritation:  0.88 Respiratory Toxicity:  0.405
Drug-induced Neurotoxicity:  0.872 Ototoxicity:  0.537
Hematotoxicity:  0.928 Drug-induced Nephrotoxicity:  0.975
Genotoxicity:  0.983 RPMI-8226 Immunitoxicity:  0.303
A549 Cytotoxicity:  0.344 Hek293 Cytotoxicity:  0.65
BCF:   1.768
?
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:   5.032
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.454
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.201
?
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
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[ 17014425]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/bab.1236]
NPO16750 Salvia castanea Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s00709-015-0790-9]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.indcrop.2010.09.006]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[11374966]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[11473439]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[12141863]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[12880325]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[1567426]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[16038550]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[17217287]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17583950]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18855446]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20455578]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20515057]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21775156]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23286284]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24108414]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27569393]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29185738]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30351923]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[3655791]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[37570961]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota roots n.a. n.a. PMID[9834151]
NPO28257 Dioscorea communis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO415 Deguelia hatschbachii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25212 Ritterella rubra n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22016 Notholaena dealbata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4009 Allochromatium minutissimum Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO23960 Artemisia siversiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27437 Camptothecium lutescens Species Brachytheciaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26223 Cladonia bellidiflora Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25868 Decachaeta ovatifolia n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO12476 Delphinium cyphoplectrum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26087 Euphorbia retusa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10497 Hydrolithon reinboldii Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26054 Palmaria palmata Species Palmariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6346 Phallusia fumigata Species Ascidiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26316 Pleurophycus gardneri Species Alariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23417 Rhabdia lycioides n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO10155 Stauntonia obovatifoliola Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25974 Streptomyces lateritius Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO24740 Uvaria klaineana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24988 Viburnum sieboldi Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11487 Senecio madagascariensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18449 Salvia yunnanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16750 Salvia castanea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6321 Agathosma thymifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12800 Glycine falcata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22758 Picradeniopsis pringlei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14213 Salvia bulleyana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25813.1 Salvia przewalskii var. mandarinorum Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18449 Salvia yunnanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27947 Salvia flava Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16750 Salvia castanea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19925 Salvia sinica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2385 Salvia bowleyana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28397 Wisteria sinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14213 Salvia bulleyana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28397 Wisteria sinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19925 Salvia sinica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27947 Salvia flava Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28257 Dioscorea communis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18449 Salvia yunnanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25813.1 Salvia przewalskii var. mandarinorum Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2385 Salvia bowleyana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16750 Salvia castanea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24740 Uvaria klaineana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28397 Wisteria sinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26223 Cladonia bellidiflora Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23417 Rhabdia lycioides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6346 Phallusia fumigata Species Ascidiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25974 Streptomyces lateritius Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO415 Deguelia hatschbachii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24988 Viburnum sieboldi Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28189 Metzgeria pubescens Species Metzgeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4009 Allochromatium minutissimum Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14253 Bothriocline longipes Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22016 Notholaena dealbata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26054 Palmaria palmata Species Palmariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24740 Uvaria klaineana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25868 Decachaeta ovatifolia n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26087 Euphorbia retusa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11003 Euphorbia sancta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28257 Dioscorea communis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12476 Delphinium cyphoplectrum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6321 Agathosma thymifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO191 Amaranthus hybr Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10497 Hydrolithon reinboldii Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16750 Salvia castanea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12800 Glycine falcata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23960 Artemisia siversiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11814 Asphodeline tenuior Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11985 Glycyrrhiza triphylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11487 Senecio madagascariensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27437 Camptothecium lutescens Species Brachytheciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25212 Ritterella rubra n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10155 Stauntonia obovatifoliola Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26316 Pleurophycus gardneri Species Alariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13164 Iris hoogiana Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22758 Picradeniopsis pringlei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18449 Salvia yunnanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27947 Salvia flava Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28397 Wisteria sinensis Species Fabaceae 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
NPT198 Individual protein Vitamin D receptor Homo sapiens Potency n.a. 19952.6 nM PubChem BioAssay data set
NPT199 Individual protein DNA polymerase kappa Homo sapiens Potency n.a. 33587.5 nM PubChem BioAssay data set
NPT200 Individual protein SARS coronavirus 3C-like proteinase SARS coronavirus IC50 = 14400.0 nM PMID[22884354]
NPT200 Individual protein SARS coronavirus 3C-like proteinase SARS coronavirus IC50 = 4900.0 nM PMID[22884354]
NPT200 Individual protein SARS coronavirus 3C-like proteinase SARS coronavirus Ki = 11200.0 nM PMID[22884354]
NPT200 Individual protein SARS coronavirus 3C-like proteinase SARS coronavirus IC50 = 1200.0 nM PMID[22884354]
NPT202 Individual protein Protease Human immunodeficiency virus 1 IC50 = 50600.0 nM PMID[22884354]
NPT200 Individual protein SARS coronavirus 3C-like proteinase SARS coronavirus IC50 = 10700.0 nM PMID[22884354]
NPT203 Individual protein Carboxylesterase 2 Homo sapiens Inhibition = 80.8 % PMID[23286284]
NPT204 Individual protein Acetylcholinesterase Homo sapiens Ki > 100000.0 nM PMID[23286284]
NPT204 Individual protein Acetylcholinesterase Homo sapiens Ki = 1950.0 nM PMID[23286284]
NPT203 Individual protein Carboxylesterase 2 Homo sapiens Ki = 1830.0 nM PMID[23286284]
NPT203 Individual protein Carboxylesterase 2 Homo sapiens Ki = 118.0 nM PMID[23286284]
NPT166 Individual protein Acyl coenzyme A:cholesterol acyltransferase Homo sapiens Ki = 398.0 nM PMID[23286284]
NPT205 Individual protein Protein-tyrosine phosphatase 1C Homo sapiens IC50 = 3670.0 nM PMID[23957426]
NPT206 Individual protein Protein-tyrosine phosphatase 2C Homo sapiens IC50 = 3940.0 nM PMID[23957426]
NPT204 Individual protein Acetylcholinesterase Homo sapiens IC50 = 1000.0 nM PMID[24900610]
NPT204 Individual protein Acetylcholinesterase Homo sapiens Ki = 600.0 nM PMID[24900610]
NPT50 Individual protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency = 10000.0 nM PubChem BioAssay data set
NPT55 Individual protein Putative fructose-1,6-bisphosphate aldolase Giardia intestinalis Potency = 7062.7 nM PubChem BioAssay data set
NPT72 Individual protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 129.07 % PMID[23571415]
NPT5886 Individual protein ELAV-like protein 1 Homo sapiens IC50 = 68.0 nM PMID[28587461]
NPT5886 Individual protein ELAV-like protein 1 Homo sapiens IC50 = 149.0 nM PMID[28587461]
NPT5886 Individual protein ELAV-like protein 1 Homo sapiens Ki = 50.0 nM PMID[29313684]
NPT67 Individual protein Cholinesterase Equus caballus Inhibition = -3.19 % PMID[23062825]
NPT68 Individual protein Aldose reductase Rattus norvegicus IC50 = 1202.26 nM DOI[10.1007/s00044-011-9681-6]
NPT73 Individual protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 111.45 % PMID[23571415]
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = -14.12 % DOI[10.6019/CHEMBL4495564]
NPT21762 Single protein Lysine-specific histone demethylase 1 Homo sapiens IC50 = 15850.0 nM PMID[35101649]
NPT21762 Single protein Lysine-specific histone demethylase 1 Homo sapiens IC50 = 15850.0 nM PMID[33581557]
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 IC50 = 590.0 nM PMID[35620927]
NPT66 Individual protein Acetylcholinesterase Electrophorus electricus Inhibition = 3.53 % PMID[23062825]
NPT197 Protein-protein interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 17782.8 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT196 Cell line AGS Homo sapiens IC50 > 50000.0 nM PMID[17583950]
NPT196 Cell line AGS Homo sapiens IC50 = 47700.0 nM PMID[17583950]
NPT65 Cell line HepG2 Homo sapiens EC50 = 2500.0 nM PMID[20455578]
NPT65 Cell line HepG2 Homo sapiens EC50 = 4700.0 nM PMID[20455578]
NPT65 Cell line HepG2 Homo sapiens FC = 2.0 n.a. PMID[20455578]
NPT4611 Cell line PLC-PRF-5 Homo sapiens FC = 2.5 n.a. PMID[20455578]
NPT933 Cell line U373 MG Homo sapiens FC = 9.9 n.a. PMID[23286284]
NPT83 Cell line MCF7 Homo sapiens IC50 = 3730.0 nM PMID[29313684]
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 = 8990.0 nM PMID[29313684]
NPT461 Cell line PANC-1 Homo sapiens IC50 = 2910.0 nM PMID[29313684]
NPT65 Cell line HepG2 Homo sapiens IC50 relative = 1800.0 nM ECBD screening data for assay EOS300108
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 6.24 % DOI[10.6019/CHEMBL4495565]
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 EC50 = 8150.0 nM PMID[35620927]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 50000.0 nM PMID[17583950]
NPT20904 Cell line Hep 3B2 Homo sapiens IC50 = 3200.0 nM PMID[17583950]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. EC50 = 5500.0 nM PMID[20455578]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. EC50 > 10000.0 nM PMID[20455578]
NPT21802 Protein family Hypoxia inducible factors; HIF-1-alpha, HIF-2-alpha Homo sapiens IC50 = 2050.0 nM PMID[17583950]
NPT21802 Protein family Hypoxia inducible factors; HIF-1-alpha, HIF-2-alpha Homo sapiens IC50 = 2290.0 nM PMID[17583950]
NPT21772 Protein complex GroEL/GroES Escherichia coli Inhibition = 103.0 % PMID[30852084]
NPT21772 Protein complex GroEL/GroES Escherichia coli Inhibition = 84.0 % PMID[30852084]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa Survival = 90.0 % PMID[33479641]





 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 NPC988 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
1.0 High Similarity NPC289432
0.7091 Intermediate Similarity NPC144547
0.6066 Remote Similarity NPC309056

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC988 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