Natural Product: NPC227325

Natural Product IDNPC227325
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 5-Hydroxy-2-(4-Hydroxy-3-Methoxyphenyl)-6,7,8-Trimethoxychromen-4-One
IUPAC Name 5-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-6,7,8-trimethoxychromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL74272
PubChem CID 181092
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002593] 8-O-methylated flavonoids

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 UBZBPKARIHPOEC-UHFFFAOYSA-N
Standard InCHI InChI=1S/C19H18O8/c1-23-13-7-9(5-6-10(13)20)12-8-11(21)14-15(22)17(24-2)19(26-4)18(25-3)16(14)27-12/h5-8,20,22H,1-4H3
SMILES COc1cc(ccc1O)c1cc(=O)c2c(o1)c(OC)c(c(c2O)OC)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   374.1 Volume:   360.741
?
Van der Waals volume.
Dense:   1.037 LogP:   2.204
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.32
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.953
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   18.0
TPSA:   107.59
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   2.0 Rings:   3.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.702 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.553 Fsp3:   0.211
MCE-18:   20.0
?
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:   1 PAINS Alert:   0
Colloidal aggregators:   0.158 Fluc inhibitor:   0.391
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.84
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.616
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.326 Promiscuous compounds:   0.644

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.204 MDCK Permeability:   -4.772
Pgp-inhibitor:   0.489 Pgp-substrate:   0.186
PAMPA:   0.068
?
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):   0.005
20% Bioavailability (F20%):   0.139 30% Bioavailability (F30%):   0.148
50% Bioavailability (F50%):   0.966

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.076 MRP1:   0.991
Plasma Protein Binding (PPB):   97.033% Volume Distribution (VD):   -0.448
Fu: 2.556%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.959
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.969
BSEP inhibitor:   0.962

ADMET: Metabolism

CYP1A2-inhibitor:   0.726 CYP1A2-substrate:   0.936
CYP2C19-inhibitor:   0.456 CYP2C19-substrate:   0.642
CYP2C9-inhibitor:   0.654 CYP2C9-substrate:   0.003
CYP2D6-inhibitor:   0.985 CYP2D6-substrate:   0.875
CYP3A4-inhibitor:   0.75 CYP3A4-substrate:   0.062
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.95
HLM stability:   0.584
?
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):  5.399 Half-life (T1/2):  1.517

ADMET: Toxicity

hERG Blockers:  0.084 hERG Blockers (10um):  0.539
Human Hepatotoxicity (H-HT):  0.388 Drug-induced Liver Injury (DILI):  0.668
AMES Toxicity:  0.402 Rat Oral Acute Toxicity:  0.422
Maximum Recommended Daily Dose:  0.49 Skin Sensitization:  0.764
Carcinogencity:  0.706 Eye Corrosion:  0.266
Eye Irritation:  0.946 Respiratory Toxicity:  0.831
Drug-induced Neurotoxicity:  0.228 Ototoxicity:  0.164
Hematotoxicity:  0.3 Drug-induced Nephrotoxicity:  0.172
Genotoxicity:  0.351 RPMI-8226 Immunitoxicity:  0.152
A549 Cytotoxicity:  0.338 Hek293 Cytotoxicity:  0.572
BCF:   1.427
?
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:   3.986
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.544
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.004
?
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
NPO15117 Chromolaena odorata Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)88710-5]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[10096857]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. fruit n.a. PMID[10606547]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Leaves n.a. n.a. PMID[12088434]
NPO25415 Pseudopterogorgia kallos Species Gorgoniidae Eukaryota n.a. n.a. n.a. PMID[15128261]
NPO25294 Merulius incarnatus Species Meruliaceae Eukaryota n.a. n.a. n.a. PMID[16643059]
NPO24744 Chloranthus tianmushanensis Species Chloranthaceae Eukaryota leaves n.a. n.a. PMID[18357995]
NPO24475 Aceriphyllum rossii n.a. n.a. n.a. n.a. n.a. n.a. PMID[19618898]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21707257]
NPO15117 Chromolaena odorata Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23186307]
NPO23805 Arnica nevadensis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23507152]
NPO33595 Stachys glutinosa Species Lamiaceae Eukaryota aerial parts n.a. n.a. PMID[25562563]
NPO22194 Kaempferia pulchra Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[25919052]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29726697]
NPO22194 Kaempferia pulchra Species Zingiberaceae Eukaryota Rhizomes n.a. n.a. PMID[31836445]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[33321838]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[34443694]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[34770961]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[34771092]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[35631245]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36432812]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36840093]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36840093]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36987013]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37020229]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37176852]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37226152]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37751472]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37836118]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37836125]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38257205]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38370080]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38381096]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38695450]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[38786901]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39407547]
NPO24475 Aceriphyllum rossii n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO26042 Agnorhiza bolanderi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7552 Alligator mississippiensis Species Alligatoridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18352 Anaxagorea clavata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25090 Araujia sericifera Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24929 Aria pallescens Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23805 Arnica nevadensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25144 Artemisia monogyna Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24556 Bassia butyracea Species Abylidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20833 Beyeria brevifolia Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25529 Bursaria spinosa Species Pittosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24744 Chloranthus tianmushanensis Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15117 Chromolaena odorata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25471 Chromolaena pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25187 Cladonia evansii Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26128 Clonostachys rosea Species Bionectriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23567 Coccus fagi Species Coccidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25326 Dendrosenecio kilimanjari Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24511 Dipterocarpus alatus Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22736 Drosera peltata Species Droseraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24640 Echinops amplexicaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25234 Epaltes gariepina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24383 Ficus formosana Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24218 Fusarium gibbosum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25671 Gardenia fosbergii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1794 Ilex affinis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25359 Isodon kameba Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22194 Kaempferia pulchra Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25291 Lactarius scrobiculatus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23963 Odixia angusta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23453 Pheidole pallidula Species Formicidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24830 Prosopis glandulosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24068 Prunus laurocerasus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25415 Pseudopterogorgia kallos Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7445 Pteris prolifera Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25390 Pterocarpus grandiflorus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23691 Pyrosoma giganteum Species Pyrosomatidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24675 Quercus aegilops Species Fagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24291 Rhizobium phaseoli Species Rhizobiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6714 Securidaca inappendiculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25045 Senecio squalidus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25258 Seriphidium cinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28665 Sesbania punicea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24987 Simira eliezeriana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20823 Stenostomum lucidum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24599 Streptomyces althioticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO25623 Taxodium mucronatum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25699 Vitex madiensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25294 Merulius incarnatus Species Meruliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8148 Wrightia tomentosa Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6714 Securidaca inappendiculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25258 Seriphidium cinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25623 Taxodium mucronatum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25359 Isodon kameba Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22736 Drosera peltata Species Droseraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25045 Senecio squalidus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15117 Chromolaena odorata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25359 Isodon kameba Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6714 Securidaca inappendiculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25045 Senecio squalidus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25258 Seriphidium cinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22736 Drosera peltata Species Droseraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25623 Taxodium mucronatum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8148 Wrightia tomentosa Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25258 Seriphidium cinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20823 Stenostomum lucidum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24383 Ficus formosana Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23567 Coccus fagi Species Coccidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7552 Alligator mississippiensis Species Alligatoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22194 Kaempferia pulchra Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23691 Pyrosoma giganteum Species Pyrosomatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7445 Pteris prolifera Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24929 Aria pallescens Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23805 Arnica nevadensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22736 Drosera peltata Species Droseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24218 Fusarium gibbosum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24987 Simira eliezeriana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24511 Dipterocarpus alatus Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25529 Bursaria spinosa Species Pittosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6714 Securidaca inappendiculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15117 Chromolaena odorata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25291 Lactarius scrobiculatus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24744 Chloranthus tianmushanensis Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26128 Clonostachys rosea Species Bionectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24068 Prunus laurocerasus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25471 Chromolaena pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1794 Ilex affinis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25258 Seriphidium cinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24599 Streptomyces althioticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24291 Rhizobium phaseoli Species Rhizobiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24475 Aceriphyllum rossii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25415 Pseudopterogorgia kallos Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23453 Pheidole pallidula Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25144 Artemisia monogyna Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24556 Bassia butyracea Species Abylidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25326 Dendrosenecio kilimanjari Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25187 Cladonia evansii Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25234 Epaltes gariepina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18352 Anaxagorea clavata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25671 Gardenia fosbergii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25699 Vitex madiensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26042 Agnorhiza bolanderi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25623 Taxodium mucronatum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25390 Pterocarpus grandiflorus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25090 Araujia sericifera Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24640 Echinops amplexicaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20833 Beyeria brevifolia Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24830 Prosopis glandulosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25359 Isodon kameba Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28665 Sesbania punicea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24675 Quercus aegilops Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23963 Odixia angusta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25045 Senecio squalidus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25294 Merulius incarnatus Species Meruliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13883 Vernonia pooleae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5940 Solanum fraxinifolium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14373 Gutierrezia spathulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10792 Deuterophoma tracheiphila n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO8148 Wrightia tomentosa Species Apocynaceae 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
NPO19472 Thymus vulgaris Other Leaf 0.74 0.74 0.74 mg/100g Database [DUKE]

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
NPT1167 Individual protein Delta opioid receptor Mus musculus Ki = 37500.0 nM PMID[25562563]
NPT1168 Individual protein Mu opioid receptor Mus musculus Ki > 50000.0 nM PMID[25562563]
NPT68 Individual protein Aldose reductase Rattus norvegicus IC50 = 45708.82 nM PMID[18585047]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT517 Cell line Panel NCI-60 (60 carcinoma cell lines) Homo sapiens GI50 = 22000.0 nM PMID[9632366]
NPT368 Cell line SN12C Homo sapiens GI50 n.a. 26730.06 nM PubChem BioAssay data set
NPT370 Cell line NCI-H23 Homo sapiens GI50 n.a. 27733.2 nM PubChem BioAssay data set
NPT371 Cell line UO-31 Homo sapiens GI50 n.a. 28840.32 nM PubChem BioAssay data set
NPT369 Cell line ACHN Homo sapiens GI50 n.a. 21428.91 nM PubChem BioAssay data set
NPT116 Cell line HL-60 Homo sapiens GI50 n.a. 31260.79 nM PubChem BioAssay data set
NPT372 Cell line HOP-92 Homo sapiens GI50 n.a. 2333.46 nM PubChem BioAssay data set
NPT374 Cell line SF-539 Homo sapiens GI50 n.a. 11830.42 nM PubChem BioAssay data set
NPT375 Cell line Malme-3M Homo sapiens GI50 n.a. 28707.81 nM PubChem BioAssay data set
NPT373 Cell line SK-MEL-5 Homo sapiens GI50 n.a. 15310.87 nM PubChem BioAssay data set
NPT376 Cell line A498 Homo sapiens GI50 n.a. 2612.16 nM PubChem BioAssay data set
NPT111 Cell line K562 Homo sapiens GI50 n.a. 17782.79 nM PubChem BioAssay data set
NPT377 Cell line OVCAR-3 Homo sapiens GI50 n.a. 32136.61 nM PubChem BioAssay data set
NPT379 Cell line HOP-62 Homo sapiens GI50 n.a. 21577.44 nM PubChem BioAssay data set
NPT112 Cell line MOLT-4 Homo sapiens GI50 n.a. 23067.47 nM PubChem BioAssay data set
NPT380 Cell line U-251 Homo sapiens GI50 n.a. 8974.29 nM PubChem BioAssay data set
NPT382 Cell line OVCAR-5 Homo sapiens GI50 n.a. 100000.0 nM PubChem BioAssay data set
NPT381 Cell line OVCAR-8 Homo sapiens GI50 n.a. 16292.96 nM PubChem BioAssay data set
NPT383 Cell line SNB-19 Homo sapiens GI50 n.a. 33962.53 nM PubChem BioAssay data set
NPT572 Cell line DMS-273 Homo sapiens GI50 n.a. 5081.59 nM PubChem BioAssay data set
NPT385 Cell line SR Homo sapiens GI50 n.a. 23014.42 nM PubChem BioAssay data set
NPT323 Cell line SW-620 Homo sapiens GI50 n.a. 31695.67 nM PubChem BioAssay data set
NPT573 Cell line M19-MEL Homo sapiens GI50 n.a. 22803.42 nM PubChem BioAssay data set
NPT384 Cell line TK-10 Homo sapiens GI50 n.a. 28183.83 nM PubChem BioAssay data set
NPT455 Cell line NCI-H522 Homo sapiens GI50 n.a. 17100.15 nM PubChem BioAssay data set
NPT387 Cell line M14 Homo sapiens GI50 n.a. 23334.58 nM PubChem BioAssay data set
NPT386 Cell line KM12 Homo sapiens GI50 n.a. 29853.83 nM PubChem BioAssay data set
NPT389 Cell line RPMI-8226 Homo sapiens GI50 n.a. 19010.78 nM PubChem BioAssay data set
NPT388 Cell line NCI-H322M Homo sapiens GI50 n.a. 44977.99 nM PubChem BioAssay data set
NPT390 Cell line LOX IMVI Homo sapiens GI50 n.a. 16788.04 nM PubChem BioAssay data set
NPT147 Cell line SK-MEL-2 Homo sapiens GI50 n.a. 17741.89 nM PubChem BioAssay data set
NPT81 Cell line A549 Homo sapiens GI50 n.a. 27289.78 nM PubChem BioAssay data set
NPT575 Cell line KM-20L2 Homo sapiens GI50 n.a. 40179.08 nM PubChem BioAssay data set
NPT391 Cell line HCC 2998 Homo sapiens GI50 n.a. 34593.94 nM PubChem BioAssay data set
NPT148 Cell line HCT-15 Homo sapiens GI50 n.a. 7744.62 nM PubChem BioAssay data set
NPT395 Cell line SF-268 Homo sapiens GI50 n.a. 26485.0 nM PubChem BioAssay data set
NPT393 Cell line HCT-116 Homo sapiens GI50 n.a. 24774.22 nM PubChem BioAssay data set
NPT394 Cell line EKVX Homo sapiens GI50 n.a. 100000.0 nM PubChem BioAssay data set
NPT731 Cell line LXFL 529 Homo sapiens GI50 n.a. 16595.87 nM PubChem BioAssay data set
NPT576 Cell line DMS-114 Homo sapiens GI50 n.a. 23933.16 nM PubChem BioAssay data set
NPT146 Cell line SK-OV-3 Homo sapiens GI50 n.a. 11168.63 nM PubChem BioAssay data set
NPT397 Cell line NCI-H460 Homo sapiens GI50 n.a. 16218.1 nM PubChem BioAssay data set
NPT398 Cell line UACC-62 Homo sapiens GI50 n.a. 14791.08 nM PubChem BioAssay data set
NPT399 Cell line SF-295 Homo sapiens GI50 n.a. 23442.29 nM PubChem BioAssay data set
NPT458 Cell line IGROV-1 Homo sapiens GI50 n.a. 4841.72 nM PubChem BioAssay data set
NPT403 Cell line UACC-257 Homo sapiens GI50 n.a. 20701.41 nM PubChem BioAssay data set
NPT401 Cell line 786-0 Homo sapiens GI50 n.a. 29785.16 nM PubChem BioAssay data set
NPT578 Cell line SNB-78 Homo sapiens GI50 n.a. 27669.42 nM PubChem BioAssay data set
NPT404 Cell line CCRF-CEM Homo sapiens GI50 n.a. 22387.21 nM PubChem BioAssay data set
NPT579 Cell line DLD-1 Homo sapiens GI50 n.a. 23933.16 nM PubChem BioAssay data set
NPT170 Cell line SK-MEL-28 Homo sapiens GI50 n.a. 23496.33 nM PubChem BioAssay data set
NPT406 Cell line RXF 393 Homo sapiens GI50 n.a. 12971.79 nM PubChem BioAssay data set
NPT407 Cell line COLO 205 Homo sapiens GI50 n.a. 10000.0 nM PubChem BioAssay data set
NPT732 Cell line HOP-18 Homo sapiens GI50 n.a. 32433.96 nM PubChem BioAssay data set
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. GI = 64.1 % PMID[23199882]
NPT35 Others n.a. n.a. Activity = 4.53 n.a. PMID[10757712]
NPT35 Others n.a. n.a. Activity = 0.81 n.a. PMID[10757712]
NPT2 Others Unspecified n.a. IC50 = 700.0 nM PMID[22047798]
NPT2 Others Unspecified n.a. IC50 = 10600.0 nM PMID[22047798]
NPT2 Others Unspecified n.a. Ratio IC50 = 6.0 n.a. PMID[22047798]

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 NPC227325 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
0.7778 Intermediate Similarity NPC231018
0.7679 Intermediate Similarity NPC128863
0.7636 Intermediate Similarity NPC201136
0.7407 Intermediate Similarity NPC250822
0.7368 Intermediate Similarity NPC4455
0.7368 Intermediate Similarity NPC196439
0.7368 Intermediate Similarity NPC2476
0.7241 Intermediate Similarity NPC19687
0.7193 Intermediate Similarity NPC280339
0.7193 Intermediate Similarity NPC167815
0.7143 Intermediate Similarity NPC176775
0.6949 Remote Similarity NPC47781
0.6897 Remote Similarity NPC183878
0.661 Remote Similarity NPC83508
0.6393 Remote Similarity NPC183950
0.6333 Remote Similarity NPC608498
0.623 Remote Similarity NPC92659
0.6129 Remote Similarity NPC137062
0.5902 Remote Similarity NPC312924
0.5873 Remote Similarity NPC606105
0.5833 Remote Similarity NPC71334
0.5806 Remote Similarity NPC20830
0.5738 Remote Similarity NPC105242
0.5714 Remote Similarity NPC115323
0.5645 Remote Similarity NPC22472
0.5574 Remote Similarity NPC275836
0.5571 Remote Similarity NPC602497
0.5469 Remote Similarity NPC189179
0.5469 Remote Similarity NPC235215
0.5469 Remote Similarity NPC474520
0.5469 Remote Similarity NPC4481
0.541 Remote Similarity NPC226973
0.541 Remote Similarity NPC607196
0.5385 Remote Similarity NPC261004
0.5385 Remote Similarity NPC152166
0.5323 Remote Similarity NPC301323
0.5323 Remote Similarity NPC138360
0.5323 Remote Similarity NPC292107
0.5312 Remote Similarity NPC183597
0.5312 Remote Similarity NPC146165
0.5303 Remote Similarity NPC227192
0.5238 Remote Similarity NPC120163
0.5238 Remote Similarity NPC188203
0.5238 Remote Similarity NPC143828
0.5238 Remote Similarity NPC276409
0.5238 Remote Similarity NPC608038
0.5231 Remote Similarity NPC224137
0.5231 Remote Similarity NPC288669
0.5231 Remote Similarity NPC7846
0.519 Remote Similarity NPC602805
0.5161 Remote Similarity NPC75279
0.5161 Remote Similarity NPC602963
0.5156 Remote Similarity NPC163780
0.5156 Remote Similarity NPC50715
0.5156 Remote Similarity NPC25270
0.5079 Remote Similarity NPC274327
0.5079 Remote Similarity NPC241498
0.5079 Remote Similarity NPC284552
0.5079 Remote Similarity NPC306821
0.5077 Remote Similarity NPC69394
0.5077 Remote Similarity NPC253634

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC227325 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