Natural Product: NPC186397

Natural Product IDNPC186397
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 1,3,7-Trihydroxy-2-Prenylxanthone
IUPAC Name 1,3,7-trihydroxy-2-(3-methylbut-2-enyl)xanthen-9-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL506229
PubChem CID 5495920
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0002817] Dibenzopyrans
            • [CHEMONTID:0000200] Xanthenes
              • [CHEMONTID:0000204] Xanthones
                • [CHEMONTID:0003517] 2-prenylated xanthones

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 FLWKTILHZPCXDW-UHFFFAOYSA-N
Standard InCHI InChI=1S/C18H16O5/c1-9(2)3-5-11-13(20)8-15-16(17(11)21)18(22)12-7-10(19)4-6-14(12)23-15/h3-4,6-8,19-21H,5H2,1-2H3
SMILES CC(=CCc1c(O)cc2c(c1O)c(=O)c1c(o2)ccc(c1)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   312.1 Volume:   317.074
?
Van der Waals volume.
Dense:   0.984 LogP:   3.184
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.954
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.473
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   18.0
TPSA:   90.9
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.497 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.701 Fsp3:   0.167
MCE-18:   19.0
?
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:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.723 Fluc inhibitor:   0.755
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.979
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.644
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.318 Promiscuous compounds:   0.109

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.106 MDCK Permeability:   -4.776
Pgp-inhibitor:   0.526 Pgp-substrate:   0.089
PAMPA:   0.593
?
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):   0.093
20% Bioavailability (F20%):   0.423 30% Bioavailability (F30%):   0.847
50% Bioavailability (F50%):   0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.017 MRP1:   0.815
Plasma Protein Binding (PPB):   91.613% Volume Distribution (VD):   -0.042
Fu: 9.391%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.915
OATP1B3 inhibitor:   0.939 BCRP inhibitor:   0.868
BSEP inhibitor:   0.951

ADMET: Metabolism

CYP1A2-inhibitor:   0.587 CYP1A2-substrate:   0.998
CYP2C19-inhibitor:   0.75 CYP2C19-substrate:   0.99
CYP2C9-inhibitor:   0.898 CYP2C9-substrate:   0.334
CYP2D6-inhibitor:   0.954 CYP2D6-substrate:   0.798
CYP3A4-inhibitor:   0.039 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.999
?
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):  6.031 Half-life (T1/2):  1.074

ADMET: Toxicity

hERG Blockers:  0.04 hERG Blockers (10um):  0.516
Human Hepatotoxicity (H-HT):  0.502 Drug-induced Liver Injury (DILI):  0.629
AMES Toxicity:  0.731 Rat Oral Acute Toxicity:  0.755
Maximum Recommended Daily Dose:  0.686 Skin Sensitization:  0.874
Carcinogencity:  0.693 Eye Corrosion:  0.033
Eye Irritation:  0.981 Respiratory Toxicity:  0.957
Drug-induced Neurotoxicity:  0.079 Ototoxicity:  0.159
Hematotoxicity:  0.089 Drug-induced Nephrotoxicity:  0.155
Genotoxicity:  0.961 RPMI-8226 Immunitoxicity:  0.077
A549 Cytotoxicity:  0.367 Hek293 Cytotoxicity:  0.706
BCF:   1.59
?
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:   4.452
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.549
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.118
?
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
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(74)80113-5]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[10075773]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. whole plant n.a. PMID[10361686]
NPO29752 Cudrania cochinchinensis n.a. n.a. n.a. roots n.a. n.a. PMID[11170668]
NPO29752 Cudrania cochinchinensis n.a. n.a. n.a. roots n.a. n.a. PMID[12932139]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[16724839]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. PMID[16933891]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18464091]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18558747]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19113969]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota stem bark Pangradin village, Jasinga, West Java, Indonesia 2005-AUG PMID[19839614]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[20000780]
NPO15264 Garcinia paucinervis Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[20594858]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[20817450]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. pericarp n.a. PMID[24555285]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota leaves Bobai, Guangxi Province, China 2005-Dec PMID[24679044]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[24717154]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota Barks n.a. n.a. PMID[24754786]
NPO32711 garcinia esculenta Species Clusiaceae Eukaryota twigs n.a. n.a. PMID[24960143]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota fruit hulls Madras, Tamil Nadu, India 1993-MAR PMID[9213587]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18911 Piper umbellatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3707 Chromatium okenii Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO23156 Maclura cochinchinensis Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9741 Actinopyga agassizi Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8560 Aplidium tabascum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8354 Aster bellidiastrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4064 Halimodendron halodendron Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7534 Leptogorgia sarmentosa Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3449 Lonicera hypoleuca Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24931 Myelochroa aurulenta Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10056 Nicotiana sylvestris Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8927 Poria selecta Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25216 Senecio vellereus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27924 Serpocaulon triseriale Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10221 Streptomyces alboniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO12600 Trametes cinnabarina Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9717 Wibelia divaricata Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29752 Cudrania cochinchinensis n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO17885 Eupatorium sachalinense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15264 Garcinia paucinervis Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10228 Ascochyta viciae Species Didymellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6948 Davidsoniella virescens Species Ceratocystidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2812 Lecanora kukunorensis Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1154 Neomeris annulata Species Dasycladaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9298 Piper wightii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15242 Setosphaeria holmii Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26341 Trifolium resupinatum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11057 Artocarpus integra Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19563 Gyrophora hyperborea n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO16291 Leptochloa digitata Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18412 Lobophytum microlobulatum Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1755 Pinus heldreichii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18013 Sceletium subvelutinum n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO7336 Senecio brasiliensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18911 Piper umbellatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29752 Cudrania cochinchinensis n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17885 Eupatorium sachalinense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7336 Senecio brasiliensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11057 Artocarpus integra Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23156 Maclura cochinchinensis Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17885 Eupatorium sachalinense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11057 Artocarpus integra Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7336 Senecio brasiliensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18911 Piper umbellatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8560 Aplidium tabascum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9741 Actinopyga agassizi Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3707 Chromatium okenii Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27924 Serpocaulon triseriale Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16291 Leptochloa digitata Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4064 Halimodendron halodendron Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8354 Aster bellidiastrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12600 Trametes cinnabarina Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3449 Lonicera hypoleuca Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10221 Streptomyces alboniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6775 Cistanche salsa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10056 Nicotiana sylvestris Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7534 Leptogorgia sarmentosa Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24931 Myelochroa aurulenta Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8927 Poria selecta Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23156 Maclura cochinchinensis Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10228 Ascochyta viciae Species Didymellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1154 Neomeris annulata Species Dasycladaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11471 Garcinia oblongifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25216 Senecio vellereus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18911 Piper umbellatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6948 Davidsoniella virescens Species Ceratocystidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9717 Wibelia divaricata Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18412 Lobophytum microlobulatum Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15242 Setosphaeria holmii Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9298 Piper wightii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5276 Zanthoxylum decaryi Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26341 Trifolium resupinatum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2812 Lecanora kukunorensis Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7336 Senecio brasiliensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18013 Sceletium subvelutinum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO1755 Pinus heldreichii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11057 Artocarpus integra Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15264 Garcinia paucinervis Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17885 Eupatorium sachalinense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19563 Gyrophora hyperborea n.a. n.a. n.a. 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
NPT21990 Single protein 7,8-dihydro-8-oxoguanine triphosphatase Homo sapiens IC50 = 1700.0 nM PMID[30771603]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT65 Cell line HepG2 Homo sapiens IC50 > 10000.0 nM PMID[24960143]
NPT83 Cell line MCF7 Homo sapiens IC50 > 10000.0 nM PMID[24960143]
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 > 10000.0 nM PMID[24960143]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 21300.0 nM PMID[24960143]
NPT924 Cell line HSC-2 Homo sapiens CC50 > 640000.0 nM PMID[11170668]
NPT188 Organism Candida parapsilosis Candida parapsilosis MIC > 128.0 ug.mL-1 PMID[12932139]
NPT554 Organism Candida glabrata Candida glabrata MIC > 128.0 ug.mL-1 PMID[12932139]
NPT925 Organism Emericella nidulans Emericella nidulans MIC > 128.0 ug.mL-1 PMID[12932139]
NPT20 Organism Candida albicans Candida albicans MIC > 128.0 ug.mL-1 PMID[12932139]
NPT20 Organism Candida albicans Candida albicans IZ = 9.0 mm PMID[12932139]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans MIC = 128.0 ug.mL-1 PMID[12932139]
NPT187 Organism Issatchenkia orientalis Pichia kudriavzevii MIC > 128.0 ug.mL-1 PMID[12932139]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MIC > 128.0 ug.mL-1 PMID[12932139]
NPT28736 Protein family Alpha-glucosidase Saccharomyces cerevisiae S288c IC50 > 100000.0 nM PMID[30282319]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT610 Others Molecular identity unknown n.a. Survival = 82.87 % PMID[27466696]





 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 NPC186397 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7 Intermediate Similarity NPC37135
0.6508 Remote Similarity NPC266499
0.6129 Remote Similarity NPC142339
0.6032 Remote Similarity NPC100123
0.6 Remote Similarity NPC223988
0.5932 Remote Similarity NPC602367
0.5758 Remote Similarity NPC228785
0.5758 Remote Similarity NPC602307
0.5714 Remote Similarity NPC227337
0.5692 Remote Similarity NPC119224
0.5571 Remote Similarity NPC136674
0.5556 Remote Similarity NPC218313
0.5507 Remote Similarity NPC68093
0.5439 Remote Similarity NPC169479
0.5362 Remote Similarity NPC217677
0.5342 Remote Similarity NPC262286
0.5333 Remote Similarity NPC206238
0.5303 Remote Similarity NPC24821
0.5303 Remote Similarity NPC284220
0.5294 Remote Similarity NPC479167
0.5294 Remote Similarity NPC141549
0.5286 Remote Similarity NPC236132
0.5278 Remote Similarity NPC25152
0.5278 Remote Similarity NPC236796
0.5224 Remote Similarity NPC69769
0.5224 Remote Similarity NPC259166
0.5217 Remote Similarity NPC101957
0.5217 Remote Similarity NPC306488
0.5205 Remote Similarity NPC320359
0.5205 Remote Similarity NPC189473
0.5205 Remote Similarity NPC61010
0.5075 Remote Similarity NPC138243
0.5075 Remote Similarity NPC157784
0.5072 Remote Similarity NPC55018
0.507 Remote Similarity NPC483039

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC186397 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