Natural Product: NPC541435

Natural Product IDNPC541435
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 5-hydroxy-3-(4-hydroxyphenyl)-7-[(2~{S},3~{R},4~{S},5~{S},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chromen-4-one
IUPAC Name 5-hydroxy-3-(4-hydroxyphenyl)-7-[(2~{S},3~{R},4~{S},5~{S},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic 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 ZCOLJUOHXJRHDI-FZHKGVQDSA-N
Standard InCHI InChI=1S/C21H20O10/c22-7-15-18(26)19(27)20(28)21(31-15)30-11-5-13(24)16-14(6-11)29-8-12(17(16)25)9-1-3-10(23)4-2-9/h1-6,8,15,18-24,26-28H,7H2/t15-,18+,19-,20+,21+/m0/s1
SMILES O=C1C(C2=CC=C(O)C=C2)=COC2=CC(O[C@@H]3O[C@@H](CO)[C@@H](O)[C@H](O)[C@H]3O)=CC(O)=C12

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   432.11 Volume:   404.357
?
Van der Waals volume.
Dense:   1.069 LogP:   0.742
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.3
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.384
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   170.05
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   6.0 Rings:   4.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.331 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.833 Fsp3:   0.286
MCE-18:   84.259
?
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:   0.599 Fluc inhibitor:   0.301
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.931
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.787
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.268 Promiscuous compounds:   0.454

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.438 MDCK Permeability:   -5.097
Pgp-inhibitor:   0.0 Pgp-substrate:   0.514
PAMPA:   1.0
?
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):   0.279
20% Bioavailability (F20%):   0.506 30% Bioavailability (F30%):   0.885
50% Bioavailability (F50%):   0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.238
Plasma Protein Binding (PPB):   84.243% Volume Distribution (VD):   -0.15
Fu: 15.751%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.787
OATP1B3 inhibitor:   0.851 BCRP inhibitor:   0.326
BSEP inhibitor:   0.028

ADMET: Metabolism

CYP1A2-inhibitor:   0.047 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:   0.0 CYP3A4-substrate:   0.767
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.056
HLM stability:   0.0
?
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):  2.995 Half-life (T1/2):  2.901

ADMET: Toxicity

hERG Blockers:  0.035 hERG Blockers (10um):  0.251
Human Hepatotoxicity (H-HT):  0.606 Drug-induced Liver Injury (DILI):  0.942
AMES Toxicity:  0.799 Rat Oral Acute Toxicity:  0.091
Maximum Recommended Daily Dose:  0.048 Skin Sensitization:  0.935
Carcinogencity:  0.213 Eye Corrosion:  0.0
Eye Irritation:  0.441 Respiratory Toxicity:  0.019
Drug-induced Neurotoxicity:  0.012 Ototoxicity:  0.884
Hematotoxicity:  0.127 Drug-induced Nephrotoxicity:  0.669
Genotoxicity:  0.918 RPMI-8226 Immunitoxicity:  0.075
A549 Cytotoxicity:  0.151 Hek293 Cytotoxicity:  0.236
BCF:   0.438
?
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:   3.046
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.428
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.641
?
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
NPO20835 Medicago truncatula Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/BF00270213]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. Wrocław, Poland 2004–2005 DOI[10.1016/J.FOODCHEM.2006.08.014]
NPO15336 Prunus avium Species Rosaceae Eukaryota Fruit n.a. n.a. DOI[10.1016/j.foodchem.2007.08.004]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO15336 Prunus avium Species Rosaceae Eukaryota n.a. fruit n.a. DOI[10.1016/j.phytochem.2007.01.008]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0021-9258(18)90865-3]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)94679-X]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0168-9452(02)00136-X]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0168-9452(02)00136-X]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf950732o]
NPO19934 Genista ephedroides Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np980112s]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1023/A:1024390522259]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10775096]
NPO6257 Ficus septica Species Moraceae Eukaryota Stems Tainan Hsien, Taiwan, Republic of China 2000-JAN PMID[16038551]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. root n.a. PMID[1622242]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16659156]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16668466]
NPO15336 Prunus avium Species Rosaceae Eukaryota n.a. fruit n.a. PMID[17328933]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO6257 Ficus septica Species Moraceae Eukaryota leaves n.a. n.a. PMID[19938815]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[20963508]
NPO20835 Medicago truncatula Species Fabaceae Eukaryota n.a. root n.a. PMID[21615146]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds Tekirdag, Turkey PMID[24499198]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25053043]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25070365]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25369450]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. PMID[25369450]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[30199256]
NPO58636 Genista tridentata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[37997986]
NPO10942 Retama sphaerocarpa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[38847466]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15336 Prunus avium Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20835 Medicago truncatula Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5203 Ulex minor Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19934 Genista ephedroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2455 Thermopsis mollis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10667 Thermopsis rhombifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6257 Ficus septica Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO55215 Cytisus eriocarpus Genus Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23376 Genista aetnensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29328 Genista tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO47408 Baptisia bracteata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO50272 Baptisia cinerea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO47052 Baptisia lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO53145 Baptisia lecontei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO50310 Baptisia megacarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO48868 Baptisia nuttalliana Genus Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO58636 Genista tridentata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10942 Retama sphaerocarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO53767 Adenocarpus complicatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO64364 Cytisus baeticus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO51977 Genista depressa Genus Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO47416 Lupinus hartwegii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO53943 Thermopsis macrophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO49973 Thermopsis villosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23137 Ulex nanus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Cotyledon n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Hypocotyl n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO24342 Lupinus albus Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO15336 Prunus avium Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15336 Prunus avium Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6257 Ficus septica Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29328 Genista tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23137 Ulex nanus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. Database[MetaboLights]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO15336 Prunus avium Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23137 Ulex nanus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29328 Genista tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6257 Ficus septica Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5203 Ulex minor Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25469 Lupinus luteus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29328 Genista tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2455 Thermopsis mollis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20835 Medicago truncatula Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5203 Ulex minor Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23376 Genista aetnensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10942 Retama sphaerocarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15336 Prunus avium Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6257 Ficus septica Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23137 Ulex nanus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19934 Genista ephedroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10667 Thermopsis rhombifolia Species Fabaceae 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 NPC541435 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 NPC197896
1.0 High Similarity NPC313163
0.8429 Intermediate Similarity NPC348541
0.8312 Intermediate Similarity NPC479405
0.8219 Intermediate Similarity NPC80140
0.8205 Intermediate Similarity NPC479404
0.8194 Intermediate Similarity NPC73511
0.7808 Intermediate Similarity NPC234739
0.76 Intermediate Similarity NPC205076
0.7568 Intermediate Similarity NPC161749
0.7368 Intermediate Similarity NPC100720
0.7297 Intermediate Similarity NPC160515
0.7195 Intermediate Similarity NPC303913
0.7105 Intermediate Similarity NPC105511
0.7105 Intermediate Similarity NPC156457
0.6941 Remote Similarity NPC479403
0.675 Remote Similarity NPC610187
0.6538 Remote Similarity NPC39360
0.6538 Remote Similarity NPC29763
0.6538 Remote Similarity NPC210003
0.65 Remote Similarity NPC138540
0.6471 Remote Similarity NPC303644
0.6456 Remote Similarity NPC297987
0.6456 Remote Similarity NPC258035
0.6456 Remote Similarity NPC323593
0.6456 Remote Similarity NPC203500
0.6429 Remote Similarity NPC487212
0.6386 Remote Similarity NPC48773
0.6329 Remote Similarity NPC211014
0.622 Remote Similarity NPC481043
0.622 Remote Similarity NPC224462
0.6203 Remote Similarity NPC45165
0.619 Remote Similarity NPC479407
0.6071 Remote Similarity NPC307518
0.6071 Remote Similarity NPC116458
0.6071 Remote Similarity NPC479406
0.6071 Remote Similarity NPC246943
0.6053 Remote Similarity NPC191154
0.6024 Remote Similarity NPC307938
0.6 Remote Similarity NPC135345
0.5952 Remote Similarity NPC229729
0.5926 Remote Similarity NPC289667
0.5926 Remote Similarity NPC259070
0.5854 Remote Similarity NPC487213
0.5854 Remote Similarity NPC95090
0.5854 Remote Similarity NPC277205
0.5854 Remote Similarity NPC27408
0.5854 Remote Similarity NPC37919
0.5854 Remote Similarity NPC136042
0.5854 Remote Similarity NPC189142
0.5854 Remote Similarity NPC77660
0.5833 Remote Similarity NPC479402
0.5783 Remote Similarity NPC84362
0.5769 Remote Similarity NPC134819
0.5732 Remote Similarity NPC261866
0.5714 Remote Similarity NPC64425
0.5647 Remote Similarity NPC479401
0.5647 Remote Similarity NPC285197
0.5581 Remote Similarity NPC22832
0.5581 Remote Similarity NPC243930
0.5581 Remote Similarity NPC601144
0.5581 Remote Similarity NPC601607
0.5517 Remote Similarity NPC311830
0.5517 Remote Similarity NPC605784
0.5426 Remote Similarity NPC35119
0.5422 Remote Similarity NPC331652
0.5417 Remote Similarity NPC116632
0.5402 Remote Similarity NPC486578
0.5357 Remote Similarity NPC249281
0.5357 Remote Similarity NPC108831
0.5357 Remote Similarity NPC182634
0.5349 Remote Similarity NPC60966
0.5341 Remote Similarity NPC607707
0.5333 Remote Similarity NPC251417
0.5294 Remote Similarity NPC146792
0.5294 Remote Similarity NPC603782
0.5281 Remote Similarity NPC601586
0.5263 Remote Similarity NPC32641
0.5263 Remote Similarity NPC256188
0.5263 Remote Similarity NPC114192
0.525 Remote Similarity NPC78697
0.5248 Remote Similarity NPC164704
0.5244 Remote Similarity NPC25547
0.5233 Remote Similarity NPC22195
0.5233 Remote Similarity NPC84265
0.5233 Remote Similarity NPC21190
0.5233 Remote Similarity NPC610763
0.5176 Remote Similarity NPC77672
0.5176 Remote Similarity NPC133671
0.5176 Remote Similarity NPC135391
0.5176 Remote Similarity NPC83283
0.5176 Remote Similarity NPC78263
0.5176 Remote Similarity NPC250069
0.5172 Remote Similarity NPC27942
0.5169 Remote Similarity NPC607201
0.5146 Remote Similarity NPC470716
0.5135 Remote Similarity NPC216769
0.5132 Remote Similarity NPC90665
0.5116 Remote Similarity NPC93337
0.5098 Remote Similarity NPC470715
0.5098 Remote Similarity NPC25523
0.5057 Remote Similarity NPC46420
0.5057 Remote Similarity NPC24043
0.5057 Remote Similarity NPC105025

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC541435 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
0.7568 Intermediate Similarity NPD4381 Clinical (unspecified phase)
0.561 Remote Similarity NPD3818 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