Natural Product: NPC295295

Natural Product IDNPC295295
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Orcinol
IUPAC Name 5-methylbenzene-1,3-diol
Synonyms 5-Methyl Resorcinol; 5-Methylresorcinol; Orcinol; Oricinol
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL110059
PubChem CID 10436
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000134] Phenols
        • [CHEMONTID:0001286] Benzenediols
          • [CHEMONTID:0000137] Resorcinols

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 OIPPWFOQEKKFEE-UHFFFAOYSA-N
Standard InCHI InChI=1S/C7H8O2/c1-5-2-6(8)4-7(9)3-5/h2-4,8-9H,1H3
SMILES Cc1cc(O)cc(c1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   124.05 Volume:   130.743
?
Van der Waals volume.
Dense:   0.949 LogP:   1.283
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.452
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.196
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   6.0
TPSA:   40.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   1.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.549 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.078 Fsp3:   0.143
MCE-18:   6.0
?
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:   Rejected
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.084 Fluc inhibitor:   0.003
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.999 Promiscuous compounds:   0.568

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.938 MDCK Permeability:   -4.741
Pgp-inhibitor:   0.008 Pgp-substrate:   0.068
PAMPA:   0.309
?
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):   0.002
20% Bioavailability (F20%):   0.148 30% Bioavailability (F30%):   0.24
50% Bioavailability (F50%):   0.851

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.471 MRP1:   0.699
Plasma Protein Binding (PPB):   46.481% Volume Distribution (VD):   0.032
Fu: 42.883%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.958
OATP1B3 inhibitor:   0.987 BCRP inhibitor:   0.261
BSEP inhibitor:   0.023

ADMET: Metabolism

CYP1A2-inhibitor:   0.912 CYP1A2-substrate:   0.948
CYP2C19-inhibitor:   0.026 CYP2C19-substrate:   0.841
CYP2C9-inhibitor:   0.587 CYP2C9-substrate:   0.905
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.789
CYP3A4-inhibitor:   0.016 CYP3A4-substrate:   0.66
CYP2B6-substrate:   0.001 CYP2C8-inhibitor:   1.0
HLM stability:   0.99
?
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):  10.833 Half-life (T1/2):  1.405

ADMET: Toxicity

hERG Blockers:  0.171 hERG Blockers (10um):  0.692
Human Hepatotoxicity (H-HT):  0.448 Drug-induced Liver Injury (DILI):  0.173
AMES Toxicity:  0.437 Rat Oral Acute Toxicity:  0.466
Maximum Recommended Daily Dose:  0.556 Skin Sensitization:  0.929
Carcinogencity:  0.757 Eye Corrosion:  0.993
Eye Irritation:  0.999 Respiratory Toxicity:  0.631
Drug-induced Neurotoxicity:  0.351 Ototoxicity:  0.216
Hematotoxicity:  0.133 Drug-induced Nephrotoxicity:  0.048
Genotoxicity:  0.884 RPMI-8226 Immunitoxicity:  0.024
A549 Cytotoxicity:  0.237 Hek293 Cytotoxicity:  0.457
BCF:   0.857
?
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:   2.669
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.71
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.153
?
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
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. whole plant n.a. DOI[10.1007/BF02329610]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.lwt.2014.11.023]
NPO996 Acacia confusa Species Fabaceae Eukaryota leaves n.a. n.a. PMID[10843598]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. PMID[15270561]
NPO32513 Penicillium citrinum Under-species n.a. n.a. n.a. n.a. n.a. PMID[18281952]
NPO31451 Aspergillus sydowii Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[18505285]
NPO996 Acacia confusa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[20047272]
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. PMID[20524638]
NPO31451 Aspergillus sydowii Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21718031]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. root n.a. PMID[22233034]
NPO31451 Aspergillus sydowii Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23647825]
NPO31451 Aspergillus sydowii Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24057165]
NPO33336 Penicillium sp. HN29-3B1 Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[26230970]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Leaves n.a. n.a. PMID[27140807]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota leaves n.a. n.a. PMID[33127538]
NPO4633 Calypogeia integristipula Species Calypogeiaceae Eukaryota n.a. n.a. n.a. PMID[37959695]
NPO53835 Cnicus benedictus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37997548]
NPO3729 Cetraria islandica Species Parmeliaceae Eukaryota n.a. n.a. n.a. PMID[7561895]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota fresh sarcotestas Kwanak Campus of Seoul National University, Seoul, Korea 1996-Sep PMID[9677265]
NPO18110 Lilium maximowiczii Species Liliaceae Eukaryota diseased bulbs n.a. n.a. PMID[9677274]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota leaves St. Louis 1996-SEP PMID[9834151]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. PMID[9834158]
NPO25424 Putterlickia verrucosa Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO32513 Penicillium citrinum Under-species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO13107 Rumex patientia Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4633 Calypogeia integristipula Species Calypogeiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3729 Cetraria islandica Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2777 Cirsium brevistylum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5786 Desmodium oxyphyllum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6513 Vernonia condensata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO33336 Penicillium sp. HN29-3B1 Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18110 Lilium maximowiczii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO53835 Cnicus benedictus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4725 Isodon lihsienensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18807 Coffea pseudozanguebariae Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1919 Erica arborea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6118 Erica umbellata Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21293 Parmelia tinctorum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO996 Acacia confusa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31451 Aspergillus sydowii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2851 Acanthella acuta Species Axinellidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5664 Davallia mariesii Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Wood n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8365 Gymnadenia albida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13107 Rumex patientia Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2602 Usnea longissima Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6118 Erica umbellata Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21293 Parmelia tinctorum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1919 Erica arborea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5664 Davallia mariesii Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8365 Gymnadenia albida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13107 Rumex patientia Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5664 Davallia mariesii Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2602 Usnea longissima Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1919 Erica arborea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6118 Erica umbellata Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2131 Dactylorhiza viridis Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4725 Isodon lihsienensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21293 Parmelia tinctorum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25424 Putterlickia verrucosa Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13107 Rumex patientia Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21293 Parmelia tinctorum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1919 Erica arborea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8365 Gymnadenia albida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6118 Erica umbellata Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6513 Vernonia condensata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2131 Dactylorhiza viridis Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20304 Astragalus pectinatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18110 Lilium maximowiczii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3729 Cetraria islandica Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO996 Acacia confusa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4725 Isodon lihsienensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO66 Siphula decumbens Species Icmadophilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2851 Acanthella acuta Species Axinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4633 Calypogeia integristipula Species Calypogeiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1919 Erica arborea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27 Gentiana dahurica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2777 Cirsium brevistylum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5786 Desmodium oxyphyllum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25424 Putterlickia verrucosa Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6619 Phoebe clemensii Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17423 Solanum coccineum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5664 Davallia mariesii Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19943 Fleischmannia hymenophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18807 Coffea pseudozanguebariae Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13015 Pilosella officinarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20689 Roystonea regia Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21293 Parmelia tinctorum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2258 Johnius belangerii Species Sciaenidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13107 Rumex patientia Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2602 Usnea longissima Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8365 Gymnadenia albida Species Orchidaceae 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
NPO53835 Cnicus benedictus Hydro-methanolic extract Roots 0.10±0.01 n.a. n.a. % PMID[37997548]
NPO53835 Cnicus benedictus Hydro-methanolic extract Roots 0.42±0.05 n.a. n.a. % PMID[37997548]
NPO53835 Cnicus benedictus Hydro-methanolic extract Roots 0.04±0.01 n.a. n.a. % PMID[37997548]
NPO53835 Cnicus benedictus Hydro-methanolic extract Roots 0.04±0.02 n.a. n.a. % PMID[37997548]

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
NPT657 Individual protein 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-1 Bos taurus IC50 > 250.0 ug.mL-1 PMID[9677265]
NPT741 Individual protein Tyrosinase Homo sapiens Activity = 31.0 % PMID[23352755]
NPT741 Individual protein Tyrosinase Homo sapiens Activity = 28.0 % PMID[23352755]
NPT741 Individual protein Tyrosinase Homo sapiens Activity = 46.0 % PMID[23352755]
NPT741 Individual protein Tyrosinase Homo sapiens Activity = 63.0 % PMID[23352755]
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens IC50 > 100000.0 nM PMID[26230970]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT79 Organism Bacillus subtilis Bacillus subtilis IC50 = 16800000.0 nM PMID[6802973]
NPT79 Organism Bacillus subtilis Bacillus subtilis Log 1/I50 = 1.77 1/M PMID[6802973]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis EC50 = 4030.0 nM PMID[17035037]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus EC50 = 4030.0 nM PMID[17035037]
NPT965 Organism Amaranthus hypochondriacus Amaranthus hypochondriacus IC50 = 1000000.0 nM PMID[11076561]
NPT117 Organism Echinochloa crus-galli Echinochloa crus-galli IC50 = 1100000.0 nM PMID[11076561]
NPT965 Organism Amaranthus hypochondriacus Amaranthus hypochondriacus IC50 = 1700000.0 nM PMID[11076561]
NPT117 Organism Echinochloa crus-galli Echinochloa crus-galli IC50 > 8100000.0 nM PMID[11076561]
NPT1 Others Radical scavenging activity n.a. IC50 = 800.0 nM PMID[18281952]
NPT5063 Organism Bipolaris leersiae Bipolaris leersiae Inhibition = 30.0 % PMID[9677274]
NPT5063 Organism Bipolaris leersiae Bipolaris leersiae Inhibition = 80.0 % PMID[9677274]

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
- Rattus norvegicus LD50 = 844.0 mg/kg ToxVal
- Mus musculus LD50 = 2.486453219 mg/kg TOXRIC
- Mus musculus LD50 = 772.0 mg/kg ToxVal
- Oryctolagus cuniculus LD50 = 2400.0 mg/kg ToxVal
- Cavia porcellus LD50 = 1687.0 mg/kg ToxVal

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 NPC295295 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
0.6 Remote Similarity NPC150837
0.5714 Remote Similarity NPC606581
0.5217 Remote Similarity NPC602068

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC295295 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