Natural Product: NPC55887

Natural Product IDNPC55887
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YBPSGTZBJNUQAI-HSGHKLBJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10072248
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

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 YBPSGTZBJNUQAI-HSGHKLBJSA-N
Standard InCHI InChI=1S/C24H30O8/c1-8-22(6)10-14(27)18-23(7)11-15(31-12(2)25)19(28)21(4,5)16(23)9-17(32-13(3)26)24(18,30)20(22)29/h8,11,16-18,30H,1,9-10H2,2-7H3/t16-,17+,18+,22-,23-,24-/m0/s1
SMILES C=C[C@@]1(C)CC(=O)[C@@H]2[C@@]3(C)C=C(C(=O)C(C)(C)[C@@H]3C[C@H]([C@]2(C1=O)O)OC(=O)C)OC(=O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   446.19 Volume:   449.857
?
Van der Waals volume.
Dense:   0.992 LogP:   1.41
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.719
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.74
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   22.0
TPSA:   124.04
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   1.0 Rings:   3.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.516 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.104 Fsp3:   0.625
MCE-18:   73.846
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.147 Fluc inhibitor:   0.006
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.005
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.002
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.385 Promiscuous compounds:   0.553

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.291 MDCK Permeability:   -4.889
Pgp-inhibitor:   0.944 Pgp-substrate:   0.015
PAMPA:   0.999
?
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):   0.04
20% Bioavailability (F20%):   0.631 30% Bioavailability (F30%):   0.981
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.876
Plasma Protein Binding (PPB):   83.68% Volume Distribution (VD):   0.073
Fu: 18.185%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.636
BSEP inhibitor:   0.999

ADMET: Metabolism

CYP1A2-inhibitor:   0.027 CYP1A2-substrate:   0.004
CYP2C19-inhibitor:   0.282 CYP2C19-substrate:   0.008
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.017
CYP3A4-inhibitor:   0.259 CYP3A4-substrate:   0.005
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.963
HLM stability:   0.954
?
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):  4.815 Half-life (T1/2):  0.839

ADMET: Toxicity

hERG Blockers:  0.005 hERG Blockers (10um):  0.043
Human Hepatotoxicity (H-HT):  0.552 Drug-induced Liver Injury (DILI):  0.649
AMES Toxicity:  0.596 Rat Oral Acute Toxicity:  0.544
Maximum Recommended Daily Dose:  0.621 Skin Sensitization:  0.963
Carcinogencity:  0.86 Eye Corrosion:  0.104
Eye Irritation:  0.849 Respiratory Toxicity:  0.625
Drug-induced Neurotoxicity:  0.151 Ototoxicity:  0.268
Hematotoxicity:  0.669 Drug-induced Nephrotoxicity:  0.774
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.111
A549 Cytotoxicity:  0.056 Hek293 Cytotoxicity:  0.215
BCF:   0.482
?
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:   3.213
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.913
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.322
?
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
NPO22900 Orthosiphon stamineus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[11374950]
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]
NPO22900 Orthosiphon stamineus Species Lamiaceae Eukaryota n.a. Indonesia n.a. PMID[12467611]
NPO22900 Orthosiphon stamineus Species Lamiaceae Eukaryota aerial parts Bangdung, Indonesia 2000-Aug PMID[12608860]
NPO22900 Orthosiphon stamineus Species Lamiaceae Eukaryota n.a. Taiwan n.a. PMID[15104497]
NPO21944 Laurencia mariannensis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[18076141]
NPO5877 Morus yunnanensis Species Moraceae Eukaryota n.a. n.a. n.a. PMID[22165973]
NPO19152 Empetrum nigrum Species Ericaceae Eukaryota n.a. n.a. n.a. PMID[26473275]
NPO23000 Zephyranthes carinata Species Amaryllidaceae Eukaryota Whole Plants n.a. n.a. PMID[28898076]
NPO3549 Euonymus maackii Species Celastraceae Eukaryota Seeds n.a. n.a. PMID[31713425]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[32933154]
NPO23226 Satureja montana Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[33081385]
NPO23183 Pinus halepensis Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[34847783]
NPO23226 Satureja montana Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36671383]
NPO23226 Satureja montana Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36840093]
NPO23183 Pinus halepensis Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[38202742]
NPO23226 Satureja montana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14529 Asterias rubens Species Asteriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23183 Pinus halepensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22911 Enterococcus faecalis Species Enterococcaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO22900 Orthosiphon stamineus 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]
NPO22773 Teucrium alyssifolium Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22071 Gentiana olivieri Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23141 Angelica ursina Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22395 Ardisia macrocarpa Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22462 Chlorophytum malayense Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22015 Clausena indica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19152 Empetrum nigrum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20100 Ephedra lomatolepis Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22197 Eriogaster lanestris Species Lasiocampidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3549 Euonymus maackii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22518 Gnetum cleistostachyum Species Gnetaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21140 Igernella notabilis Species Dictyodendrillidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23101 Ircinia aruensis Species Irciniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19929 Jateorhiza palmata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21944 Laurencia mariannensis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21545 Maytenus guianensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23062 Melibe leonina Species Dendronotidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5877 Morus yunnanensis Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7320 Nicotiana gossei Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20726 Ophioplocus japonicus Species Ophiolepididae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21745 Phleum africanum Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20964 Picradeniopsis oppositifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22717 Pinus thunbergii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16275 Pterocaulon rugosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10353 Rauvolfia tetraphylla Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21680 Saussurea triangulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22952 Senecio grandiflorus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21881 Stephania succifera Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14664 Stevia salicifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21384 Tetraria capillaris Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22137 Vernonia serratuloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23000 Zephyranthes carinata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23226 Satureja montana Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO19152 Empetrum nigrum Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22900 Orthosiphon stamineus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19929 Jateorhiza palmata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23141 Angelica ursina Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19152 Empetrum nigrum Species Ericaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO19152 Empetrum nigrum Species Ericaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO23226 Satureja montana Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO19929 Jateorhiza palmata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22900 Orthosiphon stamineus 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]
NPO22462 Chlorophytum malayense Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23141 Angelica ursina Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22071 Gentiana olivieri Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3549 Euonymus maackii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21881 Stephania succifera Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22900 Orthosiphon stamineus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19929 Jateorhiza palmata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21545 Maytenus guianensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19152 Empetrum nigrum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20726 Ophioplocus japonicus Species Ophiolepididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21384 Tetraria capillaris Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22462 Chlorophytum malayense Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21881 Stephania succifera Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22900 Orthosiphon stamineus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21140 Igernella notabilis Species Dictyodendrillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23226 Satureja montana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21680 Saussurea triangulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22518 Gnetum cleistostachyum Species Gnetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22952 Senecio grandiflorus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22717 Pinus thunbergii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23000 Zephyranthes carinata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5877 Morus yunnanensis Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16275 Pterocaulon rugosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23141 Angelica ursina Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23101 Ircinia aruensis Species Irciniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14664 Stevia salicifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20100 Ephedra lomatolepis Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22773 Teucrium alyssifolium Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20964 Picradeniopsis oppositifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21944 Laurencia mariannensis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7320 Nicotiana gossei Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21745 Phleum africanum Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19929 Jateorhiza palmata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22197 Eriogaster lanestris Species Lasiocampidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23183 Pinus halepensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22911 Enterococcus faecalis Species Enterococcaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10353 Rauvolfia tetraphylla Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22137 Vernonia serratuloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22015 Clausena indica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22395 Ardisia macrocarpa Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3549 Euonymus maackii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14529 Asterias rubens Species Asteriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22071 Gentiana olivieri Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23062 Melibe leonina Species Dendronotidae 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

In vitro activity

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

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 NPC55887 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
0.7 Intermediate Similarity NPC198539
0.5833 Remote Similarity NPC306799
0.5692 Remote Similarity NPC90769
0.5132 Remote Similarity NPC101043

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC55887 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