Natural Product: NPC238861

Natural Product IDNPC238861
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 1,6,6-Trimethyl-2,7,8,9-Tetrahydro-1H-Naphtho[1,2-G][1]Benzofuran-10,11-Dione
IUPAC Name 1,6,6-trimethyl-2,7,8,9-tetrahydro-1H-naphtho[1,2-g][1]benzofuran-10,11-dione
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1518673
PubChem CID 496348
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 GVKKJJOMQCNPGB-UHFFFAOYSA-N
Standard InCHI InChI=1S/C19H20O3/c1-10-9-22-18-12-6-7-13-11(5-4-8-19(13,2)3)15(12)17(21)16(20)14(10)18/h6-7,10H,4-5,8-9H2,1-3H3
SMILES CC1COC2=C1C(=O)C(=O)c1c3CCCC(C)(C)c3ccc21

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   296.14 Volume:   313.506
?
Van der Waals volume.
Dense:   0.945 LogP:   3.161
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.092
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.915
?
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:   0.689 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.563 Fsp3:   0.474
MCE-18:   82.286
?
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:   0.208 Fluc inhibitor:   0.509
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.575
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.617
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.37 Promiscuous compounds:   0.047

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.595 MDCK Permeability:   -4.743
Pgp-inhibitor:   1.0 Pgp-substrate:   0.0
PAMPA:   0.051
?
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):   0.979
20% Bioavailability (F20%):   0.032 30% Bioavailability (F30%):   0.86
50% Bioavailability (F50%):   0.603

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.304
Plasma Protein Binding (PPB):   99.066% Volume Distribution (VD):   0.626
Fu: 0.774%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.989
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.001
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.931 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.934 CYP2C19-substrate:   0.999
CYP2C9-inhibitor:   0.032 CYP2C9-substrate:   0.998
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.979
CYP3A4-inhibitor:   0.476 CYP3A4-substrate:   0.972
CYP2B6-substrate:   0.004 CYP2C8-inhibitor:   1.0
HLM stability:   0.983
?
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):  5.067 Half-life (T1/2):  0.558

ADMET: Toxicity

hERG Blockers:  0.058 hERG Blockers (10um):  0.418
Human Hepatotoxicity (H-HT):  0.865 Drug-induced Liver Injury (DILI):  0.896
AMES Toxicity:  0.889 Rat Oral Acute Toxicity:  0.576
Maximum Recommended Daily Dose:  0.846 Skin Sensitization:  0.992
Carcinogencity:  0.968 Eye Corrosion:  0.003
Eye Irritation:  0.682 Respiratory Toxicity:  0.497
Drug-induced Neurotoxicity:  0.754 Ototoxicity:  0.616
Hematotoxicity:  0.918 Drug-induced Nephrotoxicity:  0.963
Genotoxicity:  0.975 RPMI-8226 Immunitoxicity:  0.202
A549 Cytotoxicity:  0.195 Hek293 Cytotoxicity:  0.761
BCF:   2.104
?
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:   5.307
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.898
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.614
?
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]
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]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[22264035]
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]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36982252]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36987013]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37836125]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38611827]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39147955]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota roots n.a. n.a. PMID[9834151]
NPO11138 Veronicastrum sibiricum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16750 Salvia castanea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18449 Salvia yunnanensis 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]
NPO25813 Salvia przewalskii Species Lamiaceae 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]
NPO27947 Salvia flava Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14213 Salvia bulleyana 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]
NPO25813 Salvia przewalskii 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]
NPO5743 Salvia miltiorrhiza 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]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14822 Salvia sclarea 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]
NPO14979 Salvia trijuga 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]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11138 Veronicastrum sibiricum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2385 Salvia bowleyana 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]
NPO19925 Salvia sinica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza 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]
NPO25813.1 Salvia przewalskii var. mandarinorum Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16750 Salvia castanea 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]
NPO18449 Salvia yunnanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11138 Veronicastrum sibiricum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11138 Veronicastrum sibiricum Species Plantaginaceae 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]
NPO30139 Salvia przewalskll Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5743 Salvia miltiorrhiza Species Lamiaceae 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]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11138 Veronicastrum sibiricum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16750 Salvia castanea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5743 Salvia miltiorrhiza 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]
NPO18449 Salvia yunnanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

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



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

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
NPT149 Individual protein Endoplasmic reticulum-associated amyloid beta-peptide-binding protein Homo sapiens Potency = 25118.9 nM PubChem BioAssay data set
NPT1226 Individual protein Caspase-7 Homo sapiens Potency = 25118.9 nM PubChem BioAssay data set
NPT151 Individual protein 15-hydroxyprostaglandin dehydrogenase [NAD+] Homo sapiens Potency = 19952.6 nM PubChem BioAssay data set
NPT151 Individual protein 15-hydroxyprostaglandin dehydrogenase [NAD+] Homo sapiens Potency = 28183.8 nM PubChem BioAssay data set
NPT109 Individual protein Cytochrome P450 3A4 Homo sapiens Potency = 15848.9 nM PubChem BioAssay data set
NPT1139 Individual protein Arachidonate 15-lipoxygenase, type II Homo sapiens Potency n.a. 25118.9 nM PubChem BioAssay data set
NPT198 Individual protein Vitamin D receptor Homo sapiens Potency n.a. 7079.5 nM PubChem BioAssay data set
NPT199 Individual protein DNA polymerase kappa Homo sapiens Potency n.a. 28183.8 nM PubChem BioAssay data set
NPT199 Individual protein DNA polymerase kappa Homo sapiens Potency n.a. 19952.6 nM PubChem BioAssay data set
NPT198 Individual protein Vitamin D receptor Homo sapiens Potency n.a. 19952.6 nM PubChem BioAssay data set
NPT198 Individual protein Vitamin D receptor Homo sapiens Potency n.a. 15848.9 nM PubChem BioAssay data set
NPT198 Individual protein Vitamin D receptor Homo sapiens Potency n.a. 14125.4 nM PubChem BioAssay data set
NPT50 Individual protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency = 17782.8 nM PubChem BioAssay data set
NPT50 Individual protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency = 14125.4 nM PubChem BioAssay data set
NPT55 Individual protein Putative fructose-1,6-bisphosphate aldolase Giardia intestinalis Potency = 9976.3 nM PubChem BioAssay data set
NPT55 Individual protein Putative fructose-1,6-bisphosphate aldolase Giardia intestinalis Potency = 1581.1 nM PubChem BioAssay data set
NPT58 Individual protein Bloom syndrome protein Homo sapiens Potency = 39810.7 nM PubChem BioAssay data set
NPT48 Individual protein Lysine-specific demethylase 4D-like Homo sapiens Potency = 35481.3 nM PubChem BioAssay data set
NPT791 Individual protein Cruzipain Trypanosoma cruzi Potency = 39810.7 nM PubChem BioAssay data set
NPT94 Individual protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 22387.2 nM PubChem BioAssay data set
NPT94 Individual protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 10000.0 nM PubChem BioAssay data set
NPT444 Individual protein Ubiquitin carboxyl-terminal hydrolase 1 Homo sapiens Potency n.a. 79432.8 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 3981.1 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 12589.3 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 3548.1 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 7943.3 nM PubChem BioAssay data set
NPT197 Protein-protein interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 35481.3 nM PubChem BioAssay data set
NPT47 Individual protein ATP-dependent DNA helicase Q1 Homo sapiens Potency = 12589.3 nM PubChem BioAssay data set
NPT53 Individual protein 4'-phosphopantetheinyl transferase ffp Bacillus subtilis Potency = 19952.6 nM PubChem BioAssay data set
NPT442 Individual protein Ferritin light chain Equus caballus Potency = 35481.3 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
NPT197 Protein-protein interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 17782.8 nM PubChem BioAssay data set
NPT47 Individual protein ATP-dependent DNA helicase Q1 Homo sapiens Potency = 100000.0 nM PubChem BioAssay data set
NPT443 Individual protein Histone acetyltransferase GCN5 Homo sapiens Potency n.a. 28183.8 nM PubChem BioAssay data set
NPT5 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens Potency n.a. 7079.5 nM PubChem BioAssay data set
NPT49 Individual protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 39810.7 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT2 Others Unspecified n.a. Potency = 28183.8 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 NPC238861 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 NPC77000
0.7586 Intermediate Similarity NPC602717
0.6897 Remote Similarity NPC51079
0.6452 Remote Similarity NPC310662
0.625 Remote Similarity NPC212207
0.5333 Remote Similarity NPC239185

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC238861 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
1.0 High Similarity NPD3412 Clinical (unspecified phase)
0.5333 Remote Similarity NPD3495 Discontinued

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