Natural Product: NPC65530

Natural Product IDNPC65530
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (2S,3R,4S,5S,6R)-2-[5-[(E)-2-(3,5-Dihydroxyphenyl)Ethenyl]-2-Hydroxyphenoxy]-6-(Hydroxymethyl)Oxane-3,4,5-Triol
IUPAC Name (2S,3R,4S,5S,6R)-2-[5-[(E)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL109802
PubChem CID 11968990
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000253] Stilbenes
        • [CHEMONTID:0000142] Stilbene glycosides

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 UMGCIIXWEFTPOC-CUYWLFDKSA-N
Standard InCHI InChI=1S/C20H22O9/c21-9-16-17(25)18(26)19(27)20(29-16)28-15-7-10(3-4-14(15)24)1-2-11-5-12(22)8-13(23)6-11/h1-8,16-27H,9H2/b2-1+/t16-,17-,18+,19-,20-/m1/s1
SMILES OC[C@H]1O[C@@H](Oc2cc(ccc2O)/C=C/c2cc(O)cc(c2)O)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   406.13 Volume:   389.464
?
Van der Waals volume.
Dense:   1.043 LogP:   1.356
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.621
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.398
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   19.0
TPSA:   160.07
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   7.0 Rings:   3.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.343 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.817 Fsp3:   0.3
MCE-18:   67.692
?
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:   1 PAINS Alert:   0
Colloidal aggregators:   0.62 Fluc inhibitor:   0.945
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.121
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.734
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.498 Promiscuous compounds:   0.356

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.339 MDCK Permeability:   -5.104
Pgp-inhibitor:   0.0 Pgp-substrate:   0.009
PAMPA:   0.949
?
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):   0.02
20% Bioavailability (F20%):   0.86 30% Bioavailability (F30%):   0.988
50% Bioavailability (F50%):   0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.026 MRP1:   0.023
Plasma Protein Binding (PPB):   78.402% Volume Distribution (VD):   -0.153
Fu: 23.212%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.198
BSEP inhibitor:   0.001

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.003 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.096 CYP2D6-substrate:   0.261
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.131
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.211
?
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):  3.169 Half-life (T1/2):  3.31

ADMET: Toxicity

hERG Blockers:  0.043 hERG Blockers (10um):  0.309
Human Hepatotoxicity (H-HT):  0.68 Drug-induced Liver Injury (DILI):  0.308
AMES Toxicity:  0.83 Rat Oral Acute Toxicity:  0.067
Maximum Recommended Daily Dose:  0.221 Skin Sensitization:  0.99
Carcinogencity:  0.08 Eye Corrosion:  0.0
Eye Irritation:  0.855 Respiratory Toxicity:  0.029
Drug-induced Neurotoxicity:  0.014 Ototoxicity:  0.687
Hematotoxicity:  0.033 Drug-induced Nephrotoxicity:  0.523
Genotoxicity:  0.803 RPMI-8226 Immunitoxicity:  0.176
A549 Cytotoxicity:  0.635 Hek293 Cytotoxicity:  0.608
BCF:   0.501
?
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:   2.988
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.642
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.722
?
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
NPO12079 Dysoxylum cumingianum Species Meliaceae Eukaryota n.a. leaf n.a. DOI[10.1021/jo00051a050]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota rhizome n.a. n.a. PMID[10714491]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[11076555]
NPO14520 Bassia muricata Species Chenopodiaceae Eukaryota n.a. aerial part n.a. PMID[11454355]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[11459643]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[1517743]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. root n.a. PMID[16564530]
NPO12477 Dodonaea viscosa Species Sapindaceae Eukaryota n.a. n.a. n.a. PMID[19719093]
NPO12477 Dodonaea viscosa Species Sapindaceae Eukaryota n.a. n.a. n.a. PMID[22512738]
NPO13237 Teucrium yemense Species n.a. n.a. Aerial Parts n.a. n.a. PMID[28581290]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[29359942]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[31944695]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots; Tubers n.a. n.a. PMID[7714535]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[8277318]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12477 Dodonaea viscosa Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14304 Physalis alkekengi Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7819.1 Epichloe festucae var. lolii Varieties Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15297 Aconitum seravschanicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13716 Aconitum tasiromontanum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14217 Adansonia grandidieri Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14412 Aphyllocladus denticulatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2631 Aster sedifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14520 Bassia muricata Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4345 Caulocystis cephalornithos Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16590 Cytophaga hutchinsoni Species Cytophagaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO14104 Dendriopoterium menendezii Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9448 Dictyopteris australis Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12079 Dysoxylum cumingianum Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8386 Enceliopsis argophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11749 Eria mollis Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14014 Eriocheir sinensis Species Varunidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10688 Flacourtia jangomas Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13403 Gadus morhua callarias Species Gadidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO624 Isaria fumosorosea Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22526 Justicia secunda Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3214 Lavandula vera Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9752 Miliusa velutina Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13523 Neobalanocarpus heimii Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11580 Onobrychis arenaria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12252 Psychotria stachyoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO986 Rattus rattus Species Muridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2198 Rivularia firma Species Rivulariaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO1501 Senecio subdentatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13421 Sphaerella laricina n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO13237 Teucrium yemense Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO11861 Rheum sp. Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14014 Eriocheir sinensis Species Varunidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12477 Dodonaea viscosa Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11861 Rheum sp. Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14304 Physalis alkekengi Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11861 Rheum sp. Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12477 Dodonaea viscosa Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14304 Physalis alkekengi Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15297 Aconitum seravschanicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14014 Eriocheir sinensis Species Varunidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12477 Dodonaea viscosa Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14014 Eriocheir sinensis Species Varunidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14304 Physalis alkekengi Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16590 Cytophaga hutchinsoni Species Cytophagaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2631 Aster sedifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12252 Psychotria stachyoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12477 Dodonaea viscosa Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14014 Eriocheir sinensis Species Varunidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO624 Isaria fumosorosea Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14412 Aphyllocladus denticulatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8386 Enceliopsis argophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9448 Dictyopteris australis Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13237 Teucrium yemense Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14520 Bassia muricata Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14304 Physalis alkekengi Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4345 Caulocystis cephalornithos Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2198 Rivularia firma Species Rivulariaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13523 Neobalanocarpus heimii Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11580 Onobrychis arenaria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3214 Lavandula vera Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14217 Adansonia grandidieri Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7819.1 Epichloe festucae var. lolii Varieties Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12079 Dysoxylum cumingianum Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10688 Flacourtia jangomas Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15297 Aconitum seravschanicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13716 Aconitum tasiromontanum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1501 Senecio subdentatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22526 Justicia secunda Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14104 Dendriopoterium menendezii Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13403 Gadus morhua callarias Species Gadidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13421 Sphaerella laricina n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO9752 Miliusa velutina Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11749 Eria mollis Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO986 Rattus rattus Species Muridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28024 Rheum palmatum Species Polygonaceae 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
NPT32 Organism Mus musculus Mus musculus IC50 > 100000.0 nM PMID[10714491]
NPT32 Organism Mus musculus Mus musculus Inhibition = 10.0 % PMID[10714491]





 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 NPC65530 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
0.7627 Intermediate Similarity NPC59324
0.7581 Intermediate Similarity NPC212770
0.7119 Intermediate Similarity NPC26080
0.7119 Intermediate Similarity NPC165686
0.7097 Intermediate Similarity NPC469661
0.6984 Remote Similarity NPC604095
0.6562 Remote Similarity NPC252169
0.6557 Remote Similarity NPC210015
0.6508 Remote Similarity NPC85799
0.6508 Remote Similarity NPC303422
0.6393 Remote Similarity NPC205054
0.6308 Remote Similarity NPC242028
0.6308 Remote Similarity NPC203230
0.629 Remote Similarity NPC214910
0.6029 Remote Similarity NPC98777
0.6 Remote Similarity NPC218003
0.5821 Remote Similarity NPC294166
0.5821 Remote Similarity NPC115022
0.5818 Remote Similarity NPC10932
0.5781 Remote Similarity NPC481303
0.5735 Remote Similarity NPC8497
0.5652 Remote Similarity NPC260681
0.55 Remote Similarity NPC9248
0.5484 Remote Similarity NPC221090
0.5443 Remote Similarity NPC476869
0.5441 Remote Similarity NPC100389
0.5441 Remote Similarity NPC478871
0.5441 Remote Similarity NPC478870
0.5441 Remote Similarity NPC478872
0.5441 Remote Similarity NPC307110
0.5441 Remote Similarity NPC478873
0.5441 Remote Similarity NPC157554
0.5432 Remote Similarity NPC233467
0.5424 Remote Similarity NPC484157
0.5395 Remote Similarity NPC168358
0.5385 Remote Similarity NPC19470
0.5375 Remote Similarity NPC100936
0.5375 Remote Similarity NPC1253
0.5375 Remote Similarity NPC476868
0.5323 Remote Similarity NPC12308
0.5303 Remote Similarity NPC65942
0.5303 Remote Similarity NPC248307
0.5286 Remote Similarity NPC186418
0.5286 Remote Similarity NPC202700
0.5286 Remote Similarity NPC185778
0.527 Remote Similarity NPC191046
0.5254 Remote Similarity NPC142319
0.5224 Remote Similarity NPC479029
0.5217 Remote Similarity NPC478888
0.519 Remote Similarity NPC199928
0.5181 Remote Similarity NPC157396
0.5176 Remote Similarity NPC59692
0.5156 Remote Similarity NPC166168
0.5152 Remote Similarity NPC479028
0.5152 Remote Similarity NPC479031
0.5139 Remote Similarity NPC475084
0.5135 Remote Similarity NPC186406
0.5135 Remote Similarity NPC88043
0.5082 Remote Similarity NPC192810
0.5077 Remote Similarity NPC40377
0.5072 Remote Similarity NPC473045
0.5067 Remote Similarity NPC88484
0.5063 Remote Similarity NPC469586
0.506 Remote Similarity NPC476865

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC65530 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