Natural Product: NPC274443

Natural Product IDNPC274443
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Lapachol
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL15193
PubChem CID NA
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001534] Quinone and hydroquinone lipids
          • [CHEMONTID:0001547] Vitamin K compounds

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 CIEYTVIYYGTCCI-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H14O3/c1-9(2)7-8-12-13(16)10-5-3-4-6-11(10)14(17)15(12)18/h3-7,18H,8H2,1-2H3
SMILES CC(=CCC1=C(O)C(=O)c2c(C1=O)cccc2)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   242.09 Volume:   258.799
?
Van der Waals volume.
Dense:   0.935 LogP:   3.187
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.828
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.906
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   14.0
TPSA:   54.37
?
Topological Polar Surface Area.
H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   2.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.81 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.518 Fsp3:   0.2
MCE-18:   26.0
?
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:   1 PAINS Alert:   1
Colloidal aggregators:   0.195 Fluc inhibitor:   0.646
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.724
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.243
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.879 Promiscuous compounds:   0.122

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.522 MDCK Permeability:   -4.68
Pgp-inhibitor:   0.967 Pgp-substrate:   0.014
PAMPA:   0.888
?
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):   0.949
20% Bioavailability (F20%):   0.351 30% Bioavailability (F30%):   0.998
50% Bioavailability (F50%):   0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.523
Plasma Protein Binding (PPB):   96.974% Volume Distribution (VD):   -0.106
Fu: 2.815%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.085
BSEP inhibitor:   0.102

ADMET: Metabolism

CYP1A2-inhibitor:   0.256 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.969 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.998
CYP2D6-inhibitor:   0.016 CYP2D6-substrate:   0.122
CYP3A4-inhibitor:   0.356 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   1.0
?
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):  1.793 Half-life (T1/2):  1.303

ADMET: Toxicity

hERG Blockers:  0.043 hERG Blockers (10um):  0.273
Human Hepatotoxicity (H-HT):  0.616 Drug-induced Liver Injury (DILI):  0.633
AMES Toxicity:  0.675 Rat Oral Acute Toxicity:  0.534
Maximum Recommended Daily Dose:  0.19 Skin Sensitization:  0.83
Carcinogencity:  0.639 Eye Corrosion:  0.181
Eye Irritation:  0.972 Respiratory Toxicity:  0.63
Drug-induced Neurotoxicity:  0.408 Ototoxicity:  0.352
Hematotoxicity:  0.566 Drug-induced Nephrotoxicity:  0.496
Genotoxicity:  0.508 RPMI-8226 Immunitoxicity:  0.043
A549 Cytotoxicity:  0.078 Hek293 Cytotoxicity:  0.082
BCF:   1.721
?
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:   4.55
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.012
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.55
?
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
NPO64618 Tabebuia argentea + Aspergillus niger symbiont Species n.a. n.a. n.a. n.a. n.a. DOI[10.3329/bjp.v9i1.15622]
NPO6987 Tolypothrix byssoidea Species Tolypothrichaceae Bacteria n.a. n.a. n.a. PMID[11429991]
NPO3427 Aglaia rubiginosa Species Meliaceae Eukaryota twigs and leaves n.a. n.a. PMID[15043407]
NPO23838 Kitasatospora kifunensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[17191679]
NPO1376 Landsburgia quercifolia Species Sargassaceae Eukaryota n.a. n.a. n.a. PMID[1791483]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. bark n.a. PMID[17950604]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[17950604]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. Brazilian n.a. PMID[19674905]
NPO10199 Leuconotis griffithii n.a. n.a. n.a. n.a. n.a. n.a. PMID[20153644]
NPO10199 Leuconotis griffithii n.a. n.a. n.a. n.a. n.a. n.a. PMID[23647487]
NPO10199 Leuconotis griffithii n.a. n.a. n.a. n.a. n.a. n.a. PMID[30362746]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[32044231]
NPO19293 Tabebuia cassinoides Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[7153777]
NPO11437 Alluaudia ascendens Species Didiereaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8231 Jaspis digonoxea Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3143 Artemisia carruthii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10199 Leuconotis griffithii n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO6987 Tolypothrix byssoidea Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO3427 Aglaia rubiginosa Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3751 Orthantha lutea n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO228 Physostigma venenosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
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]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO228 Physostigma venenosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8231 Jaspis digonoxea Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO856 Helichrysum mimetes Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3427 Aglaia rubiginosa Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11724 Vernonia venosissima Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10196 Echinocereus blanckii Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3751 Orthantha lutea n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11189 Anabaena sphaerica Species Nostocaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12083 Hydnellum zonatum Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4214 Centaurea collina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23838 Kitasatospora kifunensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10199 Leuconotis griffithii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12727 Rufoplaca arenaria Species Teloschistaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4489 Achillea serbica 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]
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]
NPO449 Trichocentrum cebolletum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3143 Artemisia carruthii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO228 Physostigma venenosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19293 Tabebuia cassinoides Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6710 Sinapis nigra Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5445 Euonymus nanus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11437 Alluaudia ascendens Species Didiereaceae 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
NPT153 Individual protein Androgen Receptor Homo sapiens Potency n.a. 17280.4 nM PubChem BioAssay data set
NPT152 Individual protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 68171.3 nM PubChem BioAssay data set
NPT1566 Individual protein Glyoxalase I Homo sapiens Ki = 37153.52 nM PMID[3290487]
NPT109 Individual protein Cytochrome P450 3A4 Homo sapiens Potency = 25118.9 nM PubChem BioAssay data set
NPT198 Individual protein Vitamin D receptor Homo sapiens Potency n.a. 35481.3 nM PubChem BioAssay data set
NPT198 Individual protein Vitamin D receptor Homo sapiens Potency n.a. 25118.9 nM PubChem BioAssay data set
NPT1627 Individual protein G-protein coupled receptor 35 Homo sapiens EC50 = 2840.0 nM PMID[24900447]
NPT1627 Individual protein G-protein coupled receptor 35 Homo sapiens EC50 = 47900.0 nM PMID[24900447]
NPT1627 Individual protein G-protein coupled receptor 35 Homo sapiens IC50 = 4660.0 nM PMID[24900447]
NPT1627 Individual protein G-protein coupled receptor 35 Homo sapiens Efficacy = 328.0 picometer PMID[24900447]
NPT1627 Individual protein G-protein coupled receptor 35 Homo sapiens Ratio = 8.7 n.a. PMID[24900447]
NPT3060 Individual protein Dual specificity phosphatase Cdc25A Homo sapiens IC50 = 33200.0 nM PMID[31563013]
NPT1385 Individual protein Histone-lysine N-methyltransferase SETD7 Homo sapiens Inhibition = 4.0 % PMID[32088124]
NPT1385 Individual protein Histone-lysine N-methyltransferase SETD7 Homo sapiens Inhibition = 3.0 % PMID[32088124]
NPT1705 Individual protein Ribosomal protein S6 kinase alpha 3 Homo sapiens IC50 = 2000.0 nM PMID[36898330]
NPT531 Individual protein Nuclear receptor ROR-gamma Mus musculus Potency = 35481.3 nM PubChem BioAssay data set
NPT55 Individual protein Putative fructose-1,6-bisphosphate aldolase Giardia intestinalis Potency = 1774.1 nM PubChem BioAssay data set
NPT55 Individual protein Putative fructose-1,6-bisphosphate aldolase Giardia intestinalis Potency = 1119.4 nM PubChem BioAssay data set
NPT531 Individual protein Nuclear receptor ROR-gamma Mus musculus Potency = 3162.3 nM PubChem BioAssay data set
NPT72 Individual protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 108.17 % PMID[23571415]
NPT470 Individual protein Rhodesain Trypanosoma brucei rhodesiense IC50 > 100000.0 nM PMID[33992862]
NPT470 Individual protein Rhodesain Trypanosoma brucei rhodesiense Inhibition n.a. n.a. % PMID[33992862]
NPT470 Individual protein Rhodesain Trypanosoma brucei rhodesiense IC50 = 58000.0 nM PMID[33992862]
NPT470 Individual protein Rhodesain Trypanosoma brucei rhodesiense Inhibition = 70.0 % PMID[33992862]
NPT470 Individual protein Rhodesain Trypanosoma brucei rhodesiense Inhibition = 18.0 % PMID[33992862]
NPT48 Individual protein Lysine-specific demethylase 4D-like Homo sapiens Potency = 31622.8 nM PubChem BioAssay data set
NPT48 Individual protein Lysine-specific demethylase 4D-like Homo sapiens Potency = 25118.9 nM PubChem BioAssay data set
NPT94 Individual protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 28183.8 nM PubChem BioAssay data set
NPT444 Individual protein Ubiquitin carboxyl-terminal hydrolase 1 Homo sapiens Potency n.a. 35481.3 nM PubChem BioAssay data set
NPT73 Individual protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 115.5 % PMID[23571415]
NPT911 Individual protein Dual specificity phosphatase Cdc25B Homo sapiens IC50 = 42700.0 nM PMID[31563013]
NPT791 Individual protein Cruzipain Trypanosoma cruzi Inhibition = 35.0 % PMID[33992862]
NPT93 Individual protein Survival motor neuron protein Homo sapiens Potency = 3981.1 nM PubChem BioAssay data set
NPT93 Individual protein Survival motor neuron protein Homo sapiens Potency = 3162.3 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 19952.6 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 28183.8 nM PubChem BioAssay data set
NPT583 Individual protein Inositol monophosphatase 1 Rattus norvegicus Potency = 12589.3 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 17782.8 nM PubChem BioAssay data set
NPT25570 Single protein Dihydroorotate dehydrogenase (quinone), mitochondrial Schistosoma mansoni Activity = 0.0 % PMID[30776695]
NPT25570 Single protein Dihydroorotate dehydrogenase (quinone), mitochondrial Schistosoma mansoni IC50 = 19.0 nM PMID[30776695]
NPT21852 Single protein Dihydroorotate dehydrogenase Homo sapiens IC50 = 100.0 nM PMID[30776695]
NPT21852 Single protein Dihydroorotate dehydrogenase Homo sapiens Inhibition > 40.0 % PMID[37870434]
NPT74 Individual protein Proto-oncogene c-JUN Homo sapiens Potency n.a. 30729.3 nM PubChem BioAssay data set
NPT197 Protein-protein interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 25118.9 nM PubChem BioAssay data set
NPT197 Protein-protein interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 19952.6 nM PubChem BioAssay data set
NPT539 Individual protein Cellular tumor antigen p53 Homo sapiens Potency = 2511.9 nM PubChem BioAssay data set
NPT49 Individual protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 4466.8 nM PubChem BioAssay data set
NPT52 Individual protein Pyruvate kinase isozymes M1/M2 Homo sapiens IC50 = 1400.0 nM PMID[34355179]
NPT52 Individual protein Pyruvate kinase isozymes M1/M2 Homo sapiens deltaG = 9.34 kcal/mol PMID[34355179]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT91 Cell line KB Homo sapiens ED50 = 4.4 ug ml-1 PMID[7153777]
NPT116 Cell line HL-60 Homo sapiens IC50 = 3180.0 nM PMID[17249647]
NPT80 Cell line Raji Homo sapiens Activity = 50.0 % PMID[19674905]
NPT80 Cell line Raji Homo sapiens Activity = 60.0 % PMID[19674905]
NPT80 Cell line Raji Homo sapiens Activity > 80.0 % PMID[17950604]
NPT168 Cell line P388 Mus musculus IC50 = 0.2 ug.mL-1 PMID[1791483]
NPT90 Cell line DU-145 Homo sapiens IC50 = 64.59 nM PMID[18829316]
NPT90 Cell line DU-145 Homo sapiens Inhibition = 78.12 % PMID[18829316]
NPT941 Cell line HaCaT Homo sapiens IC50 > 10000.0 nM PMID[10479319]
NPT306 Cell line PC-3 Homo sapiens EC50 = 1970.0 nM PMID[19674905]
NPT81 Cell line A549 Homo sapiens EC50 = 4780.0 nM PMID[19674905]
NPT83 Cell line MCF7 Homo sapiens EC50 = 10150.0 nM PMID[19674905]
NPT179 Cell line A2780 Homo sapiens GI50 = 1900.0 nM PMID[20304655]
NPT1723 Cell line HBL-100 Homo sapiens GI50 = 7800.0 nM PMID[22560628]
NPT165 Cell line HeLa Homo sapiens GI50 = 2300.0 nM PMID[22560628]
NPT1577 Cell line SW1573 Homo sapiens GI50 = 34000.0 nM PMID[22560628]
NPT396 Cell line T47D Homo sapiens GI50 = 76000.0 nM PMID[20304655]
NPT1183 Cell line WiDr Homo sapiens GI50 = 36000.0 nM PMID[22560628]
NPT927 Cell line PBMC Homo sapiens IC50 = 2100.0 nM PMID[20378360]
NPT927 Cell line PBMC Homo sapiens IC50 > 103190.0 nM PMID[21820768]
NPT368 Cell line SN12C Homo sapiens GI50 n.a. 31332.86 nM PubChem BioAssay data set
NPT367 Cell line MDA-N Homo sapiens GI50 n.a. 17378.01 nM PubChem BioAssay data set
NPT370 Cell line NCI-H23 Homo sapiens GI50 n.a. 23442.29 nM PubChem BioAssay data set
NPT369 Cell line ACHN Homo sapiens GI50 n.a. 34914.03 nM PubChem BioAssay data set
NPT371 Cell line UO-31 Homo sapiens GI50 n.a. 48865.24 nM PubChem BioAssay data set
NPT372 Cell line HOP-92 Homo sapiens GI50 n.a. 79615.94 nM PubChem BioAssay data set
NPT116 Cell line HL-60 Homo sapiens GI50 n.a. 6501.3 nM PubChem BioAssay data set
NPT374 Cell line SF-539 Homo sapiens GI50 n.a. 7852.36 nM PubChem BioAssay data set
NPT90 Cell line DU-145 Homo sapiens GI50 n.a. 36897.76 nM PubChem BioAssay data set
NPT373 Cell line SK-MEL-5 Homo sapiens GI50 n.a. 11694.99 nM PubChem BioAssay data set
NPT375 Cell line Malme-3M Homo sapiens GI50 n.a. 35075.19 nM PubChem BioAssay data set
NPT111 Cell line K562 Homo sapiens GI50 n.a. 6622.17 nM PubChem BioAssay data set
NPT376 Cell line A498 Homo sapiens GI50 n.a. 60394.86 nM PubChem BioAssay data set
NPT377 Cell line OVCAR-3 Homo sapiens GI50 n.a. 24266.1 nM PubChem BioAssay data set
NPT112 Cell line MOLT-4 Homo sapiens GI50 n.a. 5807.64 nM PubChem BioAssay data set
NPT379 Cell line HOP-62 Homo sapiens GI50 n.a. 34833.73 nM PubChem BioAssay data set
NPT378 Cell line NCI/ADR-RES Homo sapiens GI50 n.a. 32284.94 nM PubChem BioAssay data set
NPT380 Cell line U-251 Homo sapiens GI50 n.a. 10864.26 nM PubChem BioAssay data set
NPT382 Cell line OVCAR-5 Homo sapiens GI50 n.a. 100000.0 nM PubChem BioAssay data set
NPT381 Cell line OVCAR-8 Homo sapiens GI50 n.a. 26730.06 nM PubChem BioAssay data set
NPT572 Cell line DMS-273 Homo sapiens GI50 n.a. 9141.13 nM PubChem BioAssay data set
NPT82 Cell line MDA-MB-231 Homo sapiens GI50 n.a. 8531.0 nM PubChem BioAssay data set
NPT383 Cell line SNB-19 Homo sapiens GI50 n.a. 16368.17 nM PubChem BioAssay data set
NPT384 Cell line TK-10 Homo sapiens GI50 n.a. 37757.22 nM PubChem BioAssay data set
NPT385 Cell line SR Homo sapiens GI50 n.a. 20606.3 nM PubChem BioAssay data set
NPT573 Cell line M19-MEL Homo sapiens GI50 n.a. 20796.97 nM PubChem BioAssay data set
NPT323 Cell line SW-620 Homo sapiens GI50 n.a. 34593.94 nM PubChem BioAssay data set
NPT386 Cell line KM12 Homo sapiens GI50 n.a. 9246.98 nM PubChem BioAssay data set
NPT455 Cell line NCI-H522 Homo sapiens GI50 n.a. 19724.23 nM PubChem BioAssay data set
NPT574 Cell line XF498 Homo sapiens GI50 n.a. 42364.3 nM PubChem BioAssay data set
NPT387 Cell line M14 Homo sapiens GI50 n.a. 45814.19 nM PubChem BioAssay data set
NPT388 Cell line NCI-H322M Homo sapiens GI50 n.a. 30408.85 nM PubChem BioAssay data set
NPT389 Cell line RPMI-8226 Homo sapiens GI50 n.a. 25763.21 nM PubChem BioAssay data set
NPT456 Cell line OVCAR-4 Homo sapiens GI50 n.a. 33651.16 nM PubChem BioAssay data set
NPT390 Cell line LOX IMVI Homo sapiens GI50 n.a. 8298.51 nM PubChem BioAssay data set
NPT457 Cell line BT-549 Homo sapiens GI50 n.a. 51760.68 nM PubChem BioAssay data set
NPT147 Cell line SK-MEL-2 Homo sapiens GI50 n.a. 35481.34 nM PubChem BioAssay data set
NPT575 Cell line KM-20L2 Homo sapiens GI50 n.a. 48865.24 nM PubChem BioAssay data set
NPT81 Cell line A549 Homo sapiens GI50 n.a. 17258.38 nM PubChem BioAssay data set
NPT392 Cell line SNB-75 Homo sapiens GI50 n.a. 57147.86 nM PubChem BioAssay data set
NPT391 Cell line HCC 2998 Homo sapiens GI50 n.a. 86297.85 nM PubChem BioAssay data set
NPT148 Cell line HCT-15 Homo sapiens GI50 n.a. 3681.29 nM PubChem BioAssay data set
NPT393 Cell line HCT-116 Homo sapiens GI50 n.a. 5023.43 nM PubChem BioAssay data set
NPT395 Cell line SF-268 Homo sapiens GI50 n.a. 11857.69 nM PubChem BioAssay data set
NPT83 Cell line MCF7 Homo sapiens GI50 n.a. 24378.11 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. 2924.15 nM PubChem BioAssay data set
NPT731 Cell line LXFL 529 Homo sapiens GI50 n.a. 16180.8 nM PubChem BioAssay data set
NPT576 Cell line DMS-114 Homo sapiens GI50 n.a. 60255.96 nM PubChem BioAssay data set
NPT146 Cell line SK-OV-3 Homo sapiens GI50 n.a. 47752.93 nM PubChem BioAssay data set
NPT396 Cell line T47D Homo sapiens GI50 n.a. 61376.2 nM PubChem BioAssay data set
NPT397 Cell line NCI-H460 Homo sapiens GI50 n.a. 5000.35 nM PubChem BioAssay data set
NPT398 Cell line UACC-62 Homo sapiens GI50 n.a. 13396.77 nM PubChem BioAssay data set
NPT308 Cell line CAKI-1 Homo sapiens GI50 n.a. 54954.09 nM PubChem BioAssay data set
NPT400 Cell line MDA-MB-435 Homo sapiens GI50 n.a. 18535.32 nM PubChem BioAssay data set
NPT399 Cell line SF-295 Homo sapiens GI50 n.a. 22646.44 nM PubChem BioAssay data set
NPT458 Cell line IGROV-1 Homo sapiens GI50 n.a. 46131.76 nM PubChem BioAssay data set
NPT402 Cell line Hs-578T Homo sapiens GI50 n.a. 34833.73 nM PubChem BioAssay data set
NPT577 Cell line RXF 631 Homo sapiens GI50 n.a. 22181.96 nM PubChem BioAssay data set
NPT578 Cell line SNB-78 Homo sapiens GI50 n.a. 100000.0 nM PubChem BioAssay data set
NPT403 Cell line UACC-257 Homo sapiens GI50 n.a. 28641.78 nM PubChem BioAssay data set
NPT401 Cell line 786-0 Homo sapiens GI50 n.a. 21627.19 nM PubChem BioAssay data set
NPT579 Cell line DLD-1 Homo sapiens GI50 n.a. 25468.3 nM PubChem BioAssay data set
NPT404 Cell line CCRF-CEM Homo sapiens GI50 n.a. 18365.38 nM PubChem BioAssay data set
NPT405 Cell line NCI-H226 Homo sapiens GI50 n.a. 53826.98 nM PubChem BioAssay data set
NPT139 Cell line HT-29 Homo sapiens GI50 n.a. 22284.35 nM PubChem BioAssay data set
NPT170 Cell line SK-MEL-28 Homo sapiens GI50 n.a. 22961.49 nM PubChem BioAssay data set
NPT406 Cell line RXF 393 Homo sapiens GI50 n.a. 40738.03 nM PubChem BioAssay data set
NPT407 Cell line COLO 205 Homo sapiens GI50 n.a. 52360.04 nM PubChem BioAssay data set
NPT732 Cell line HOP-18 Homo sapiens GI50 n.a. 15240.53 nM PubChem BioAssay data set
NPT114 Cell line LoVo Homo sapiens IC50 = 9000.0 nM PMID[24374273]
NPT306 Cell line PC-3 Homo sapiens IC50 = 4000.0 nM PMID[24374273]
NPT170 Cell line SK-MEL-28 Homo sapiens IC50 = 8000.0 nM PMID[24374273]
NPT81 Cell line A549 Homo sapiens IC50 = 8000.0 nM PMID[24374273]
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 > 10000.0 nM PMID[30003778]
NPT111 Cell line K562 Homo sapiens IC50 > 10000.0 nM PMID[30003778]
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 > 30000.0 nM PMID[32044231]
NPT83 Cell line MCF7 Homo sapiens IC50 > 30000.0 nM PMID[32044231]
NPT81 Cell line A549 Homo sapiens IC50 > 30000.0 nM PMID[32044231]
NPT65 Cell line HepG2 Homo sapiens CC50 > 4130700.0 nM PMID[29324340]
NPT171 Cell line MRC5 Homo sapiens CC50 >= 285000.0 nM PMID[33333397]
NPT81 Cell line A549 Homo sapiens CC50 >= 285000.0 nM PMID[33333397]
NPT857 Cell line LLC-PK1 Sus scrofa CC50 >= 285000.0 nM PMID[33333397]
NPT65 Cell line HepG2 Homo sapiens CC50 >= 285000.0 nM PMID[33333397]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 123500.0 nM PMID[29324340]
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM DOI[10.6019/CHEMBL4651402]
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM DOI[10.6019/CHEMBL4651402]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 80400.0 nM PMID[38421618]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 80000.0 nM PMID[33333397]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi IC50 = 31300.0 nM PMID[18029184]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Activity = 51.8 % PMID[18029184]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Activity = 82.0 % PMID[18029184]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Activity = 41.7 % PMID[18029184]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi IC50 = 410800.0 nM PMID[23279867]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 206600.0 nM PMID[21820768]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 413200.0 nM PMID[21820768]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MBC = 645.66 uM DOI[10.1007/s00044-011-9788-9]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 161400.0 nM DOI[10.1007/s00044-011-9788-9]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 24100.0 nM PMID[23353747]
NPT634 Organism Leishmania amazonensis Leishmania amazonensis IC50 = 63280.0 nM PMID[23535320]
NPT634 Organism Leishmania amazonensis Leishmania amazonensis IC50 = 102050.0 nM PMID[23535320]
NPT1021 Organism Leishmania infantum Leishmania infantum IC50 = 99880.0 nM PMID[23535320]
NPT1021 Organism Leishmania infantum Leishmania infantum IC50 = 34720.0 nM PMID[23535320]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 11000.0 nM PMID[24374273]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 8000.0 nM PMID[24374273]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 12560.0 nM PMID[27667553]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 20360.0 nM PMID[27667553]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 20230.0 nM PMID[27667553]
NPT474 Organism Plasmodium berghei Plasmodium berghei Inhibition = 0.0 % PMID[14980653]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Inhibition = 65.2 % PMID[17950604]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Inhibition = 8.9 % PMID[17950604]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Inhibition = 32.8 % PMID[17950604]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Inhibition = 86.6 % PMID[17950604]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 IC50 = 311400.0 nM PMID[17950604]
NPT176 Organism Artemia salina Artemia salina Activity = 5.0 ppm PMID[20304655]
NPT1365 Organism Trichoplusia ni Trichoplusia ni FDI = 9.1 % DOI[10.1016/j.cropro.2011.09.009]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 78.12 ug.mL-1 DOI[10.1007/s00044-011-9788-9]
NPT19 Organism Escherichia coli Escherichia coli MIC > 78.12 ug.mL-1 DOI[10.1007/s00044-011-9788-9]
NPT2 Others Unspecified n.a. Potency n.a. 4870.3 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 38335.6 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 217.5 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 48702.7 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 1090.3 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 1526.2 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 96294.6 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 24188.1 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 54150.4 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 30451 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 771.9 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 171.2 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 1540.1 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 48261.6 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 1938.9 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 24409.2 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 54.6 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 60757.8 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 76489.5 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 13602 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 3447.9 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Activity = 8.9 % PMID[19674905]
NPT2 Others Unspecified n.a. Activity = 32.8 % PMID[19674905]
NPT2 Others Unspecified n.a. Activity = 65.2 % PMID[19674905]
NPT2 Others Unspecified n.a. Activity = 86.6 % PMID[19674905]
NPT2 Others Unspecified n.a. IC50 = 311400.0 nM PMID[19674905]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC = 206600.0 nM PMID[21820768]
NPT314 Organism Bacillus cereus Bacillus cereus MIC > 78.12 ug.mL-1 DOI[10.1007/s00044-011-9788-9]
NPT2 Others Unspecified n.a. Ratio CC50/IC50 = 0.94 n.a. PMID[23535320]
NPT2 Others Unspecified n.a. Ratio CC50/IC50 = 0.58 n.a. PMID[23535320]
NPT2 Others Unspecified n.a. Ratio CC50/IC50 = 0.59 n.a. PMID[23535320]
NPT2 Others Unspecified n.a. Ratio CC50/IC50 = 1.71 n.a. PMID[23535320]
NPT2 Others Unspecified n.a. Potency n.a. 3548.1 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 25118.9 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 5011.9 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 35481.3 nM PubChem BioAssay data set
NPT21772 Protein complex GroEL/GroES Escherichia coli Inhibition = 62.0 % PMID[30852084]
NPT21772 Protein complex GroEL/GroES Escherichia coli Inhibition = 89.0 % PMID[30852084]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Lysis = 65.0 % DOI[10.1016/S0960-894X(97)00354-5]
NPT1365 Organism Trichoplusia ni Trichoplusia ni mortality = 10.0 % DOI[10.1016/j.cropro.2011.09.009]





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference
Rattus norvegicus Plasma Drug metabolism = 0.6 ug ml-1 PMID[22796040]
Rattus norvegicus Plasma Drug metabolism = 1.4 ug ml-1 PMID[22796040]
Rattus norvegicus Plasma Drug metabolism = 6.0 ug ml-1 PMID[22796040]
Rattus norvegicus Plasma Drug metabolism = 0.7 ug ml-1 PMID[22796040]





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference
- Mus musculus LD50 = 487.0 mg/kg ToxVal

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 NPC274443 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
0.6818 Remote Similarity NPC231774
0.6667 Remote Similarity NPC244427
0.6216 Remote Similarity NPC222390
0.5789 Remote Similarity NPC600797
0.5556 Remote Similarity NPC603835
0.5116 Remote Similarity NPC157778

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC274443 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