Natural Product: NPC130730

Natural Product IDNPC130730
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Picroside Ii
IUPAC Name [(1aS,1bS,2S,5aR,6S,6aS)-1a-(hydroxymethyl)-2-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2,5a,6,6a-tetrahydro-1bH-oxireno[5,6]cyclopenta[1,3-c]pyran-6-yl] 4-hydroxy-3-methoxybenzoate
Synonyms Picroside II
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL510404
PubChem CID 11944602
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000238] Tannins
        • [CHEMONTID:0001710] Hydrolyzable tannins

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 AKNILCMFRRDTEY-NUGKWEEESA-N
Standard InCHI InChI=1S/C23H28O13/c1-31-12-6-9(2-3-11(12)26)20(30)34-18-10-4-5-32-21(14(10)23(8-25)19(18)36-23)35-22-17(29)16(28)15(27)13(7-24)33-22/h2-6,10,13-19,21-22,24-29H,7-8H2,1H3/t10-,13-,14-,15-,16+,17-,18+,19+,21+,22+,23-/m1/s1
SMILES OC[C@H]1O[C@@H](O[C@@H]2OC=C[C@@H]3[C@H]2[C@@]2(CO)O[C@H]2[C@H]3OC(=O)c2ccc(c(c2)OC)O)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   512.15 Volume:   464.672
?
Van der Waals volume.
Dense:   1.102 LogP:   -0.626
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.198
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.615
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   25.0
TPSA:   197.13
?
Topological Polar Surface Area.
 H-Bond Acceptor:   13.0
H-Bond Donor:   6.0 Rings:   5.0
Heavy Atoms:   13.0

MedChem Properties

QED Drug-Likeness Score:   0.173 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.924 Fsp3:   0.609
MCE-18:   115.027
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.562 Fluc inhibitor:   0.11
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.035
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.026
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.215 Promiscuous compounds:   0.315

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.304 MDCK Permeability:   -5.304
Pgp-inhibitor:   0.003 Pgp-substrate:   0.527
PAMPA:   0.952
?
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):   0.267
20% Bioavailability (F20%):   0.371 30% Bioavailability (F30%):   0.941
50% Bioavailability (F50%):   0.971

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.014 MRP1:   0.573
Plasma Protein Binding (PPB):   64.512% Volume Distribution (VD):   -0.501
Fu: 39.389%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.039
BSEP inhibitor:   0.016

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.821
HLM stability:   0.009
?
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):  2.098 Half-life (T1/2):  3.092

ADMET: Toxicity

hERG Blockers:  0.017 hERG Blockers (10um):  0.169
Human Hepatotoxicity (H-HT):  0.462 Drug-induced Liver Injury (DILI):  0.765
AMES Toxicity:  0.907 Rat Oral Acute Toxicity:  0.03
Maximum Recommended Daily Dose:  0.014 Skin Sensitization:  0.999
Carcinogencity:  0.226 Eye Corrosion:  0.001
Eye Irritation:  0.346 Respiratory Toxicity:  0.025
Drug-induced Neurotoxicity:  0.025 Ototoxicity:  0.947
Hematotoxicity:  0.388 Drug-induced Nephrotoxicity:  0.564
Genotoxicity:  0.094 RPMI-8226 Immunitoxicity:  0.108
A549 Cytotoxicity:  0.221 Hek293 Cytotoxicity:  0.198
BCF:   0.367
?
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:   3.037
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.647
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.678
?
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
NPO12418 Myroxylon peruiferum Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(79)80020-5]
NPO12418 Myroxylon peruiferum Species Fabaceae Eukaryota n.a. Brazilian n.a. PMID[10328294]
NPO40907 Picrorhiza kurroa Species n.a. n.a. n.a. n.a. n.a. PMID[10395515]
NPO12175 Iostephane heterophylla Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[11473422]
NPO7006 Garcinia subelliptica Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[15568764]
NPO7006 Garcinia subelliptica Species Clusiaceae Eukaryota pericarp n.a. n.a. PMID[16038565]
NPO12653 Diacarnus levii Species Podospongiidae Eukaryota n.a. at a depth of -10 M off the coast of Papua New Guinea 1998-JUN PMID[17253866]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[17944538]
NPO7006 Garcinia subelliptica Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18166016]
NPO23142 Lamium album Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19904996]
NPO7006 Garcinia subelliptica Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[20232858]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[22823026]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota leaves and stems Ha Long, Quang Ninh province, Vietnam 2014-Jul PMID[25769817]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota stem bark Medicinal Plant Garden, College of Pharmacy, Ewha Womans University 2013-DEC PMID[28787158]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[29792702]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. PMID[30892891]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[9599262]
NPO7006 Garcinia subelliptica Species Clusiaceae Eukaryota n.a. xylem n.a. Database[Article]
NPO12175 Iostephane heterophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1790 Plectranthus comosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7006 Garcinia subelliptica Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5311 Isertia haenkeana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12653 Diacarnus levii Species Podospongiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11674 Viburnum lantanoides Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7648 Geigeria plumosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5908 Dianella tasmanica Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7323 Lindera pipericarpa Species Tineidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2289 Vicia hirsuta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40907 Picrorhiza kurroa Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO12418 Myroxylon peruiferum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12526 Veronica turrilliana Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12762 Elattostachys apetala Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23142 Lamium album Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3432 Tovomita brasiliensis Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2289 Vicia hirsuta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3671 Rhodiola coccinea Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7006 Garcinia subelliptica Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3671 Rhodiola coccinea Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2289 Vicia hirsuta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12418 Myroxylon peruiferum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9550 Eritrichium incanum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5311 Isertia haenkeana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12047 Solanum unguiculatum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10092 Hesperocyparis bakeri Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4923 Ononis hircina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11255 Veronica thomsonii Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3093 Phyllanthus tenellus Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2289 Vicia hirsuta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11491 Vellozia declinans Species Velloziaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10102 Pithecellobium albicans Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14818 Neofusicoccum mangiferae Species Botryosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14462 Jasonia tuberosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7648 Geigeria plumosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12653 Diacarnus levii Species Podospongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5908 Dianella tasmanica Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9561 Preussia australis Species Sporormiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13096 Lecidea kochiana Species Lecideaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10553 Heterophyllaea pustulata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9908 Adenium somalense Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9254 Scutellaria racemosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO396 Ventilago goughii Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12175 Iostephane heterophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1790 Plectranthus comosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13466 Atroxima afzeliana Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26737 Solanum mauritianum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7006 Garcinia subelliptica Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3432 Tovomita brasiliensis Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3671 Rhodiola coccinea Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12762 Elattostachys apetala Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1314 Goodenia strophiolata Species Goodeniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5173 Antidesma pentandrum Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1455 Aspergillus caelatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11397 Cladophora rupestris Species Cladophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12526 Veronica turrilliana Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7323 Lindera pipericarpa Species Tineidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11674 Viburnum lantanoides Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2576 Eusideroxylon zwageri Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14776 Petrosia weinbergi Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23142 Lamium album 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

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1135 Cell line Hepatocyte Rattus norvegicus Activity = 103.0 % PMID[6677713]
NPT1135 Cell line Hepatocyte Rattus norvegicus Activity = 101.0 % PMID[6677713]
NPT1135 Cell line Hepatocyte Rattus norvegicus Activity = 78.0 % PMID[6677713]
NPT1135 Cell line Hepatocyte Rattus norvegicus Activity = 27.0 IU/L PMID[6677713]
NPT1135 Cell line Hepatocyte Rattus norvegicus Activity = 28.0 IU/L PMID[6677713]
NPT1135 Cell line Hepatocyte Rattus norvegicus Activity = 40.0 IU/L PMID[6677713]
NPT191 Organism Hepatitis C virus Hepatitis C virus Inhibition = 31.6 % PMID[19904996]
NPT191 Organism Hepatitis C virus Hepatitis C virus Inhibition = 59.4 % PMID[19904996]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Activity = 46.0 % PMID[10395515]





 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 NPC130730 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
0.8442 Intermediate Similarity NPC301910
0.8052 Intermediate Similarity NPC206815
0.8 Intermediate Similarity NPC194705
0.7895 Intermediate Similarity NPC138993
0.75 Intermediate Similarity NPC229548
0.7439 Intermediate Similarity NPC474234
0.6977 Remote Similarity NPC89693
0.6395 Remote Similarity NPC18789
0.6395 Remote Similarity NPC46644
0.6216 Remote Similarity NPC107594
0.619 Remote Similarity NPC475824
0.5747 Remote Similarity NPC229354
0.5698 Remote Similarity NPC473149
0.5376 Remote Similarity NPC476011
0.5319 Remote Similarity NPC282551
0.5275 Remote Similarity NPC486494

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC130730 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
0.5192 Remote Similarity NPD7685 Pre-registration

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