Natural Product: NPC285776

Natural Product IDNPC285776
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Veratric Acid
IUPAC Name 3,4-dimethoxybenzoic acid
Synonyms 3,4-Dimethoxy-Benzoic Acid; 3,4-Dimethoxybenzoic Acid
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL118903
PubChem CID 7121
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000176] Benzoic acids and derivatives
          • [CHEMONTID:0002344] Methoxybenzoic acids and derivatives
            • [CHEMONTID:0002346] P-methoxybenzoic acids and derivatives

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 DAUAQNGYDSHRET-UHFFFAOYSA-N
Standard InCHI InChI=1S/C9H10O4/c1-12-7-4-3-6(9(10)11)5-8(7)13-2/h3-5H,1-2H3,(H,10,11)
SMILES COc1cc(ccc1OC)C(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   182.06 Volume:   180.279
?
Van der Waals volume.
Dense:   1.01 LogP:   1.616
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.242
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.268
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   7.0
TPSA:   55.76
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   1.0 Rings:   1.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.767 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.347 Fsp3:   0.222
MCE-18:   7.0
?
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:   0.013 Fluc inhibitor:   0.006
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.02
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.174
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.977 Promiscuous compounds:   0.639

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.938 MDCK Permeability:   -4.767
Pgp-inhibitor:   0.017 Pgp-substrate:   0.205
PAMPA:   0.881
?
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):   0.189
20% Bioavailability (F20%):   0.091 30% Bioavailability (F30%):   0.033
50% Bioavailability (F50%):   0.361

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.009 MRP1:   0.987
Plasma Protein Binding (PPB):   63.408% Volume Distribution (VD):   -0.578
Fu: 29.068%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.851
OATP1B3 inhibitor:   0.98 BCRP inhibitor:   0.06
BSEP inhibitor:   0.274

ADMET: Metabolism

CYP1A2-inhibitor:   0.074 CYP1A2-substrate:   0.02
CYP2C19-inhibitor:   0.243 CYP2C19-substrate:   0.007
CYP2C9-inhibitor:   0.222 CYP2C9-substrate:   0.009
CYP2D6-inhibitor:   0.035 CYP2D6-substrate:   0.004
CYP3A4-inhibitor:   0.241 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.001 CYP2C8-inhibitor:   0.269
HLM stability:   0.032
?
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):  2.082 Half-life (T1/2):  2.556

ADMET: Toxicity

hERG Blockers:  0.053 hERG Blockers (10um):  0.12
Human Hepatotoxicity (H-HT):  0.502 Drug-induced Liver Injury (DILI):  0.636
AMES Toxicity:  0.392 Rat Oral Acute Toxicity:  0.287
Maximum Recommended Daily Dose:  0.103 Skin Sensitization:  0.409
Carcinogencity:  0.5 Eye Corrosion:  0.874
Eye Irritation:  0.993 Respiratory Toxicity:  0.667
Drug-induced Neurotoxicity:  0.467 Ototoxicity:  0.355
Hematotoxicity:  0.471 Drug-induced Nephrotoxicity:  0.492
Genotoxicity:  0.096 RPMI-8226 Immunitoxicity:  0.028
A549 Cytotoxicity:  0.018 Hek293 Cytotoxicity:  0.031
BCF:   0.329
?
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:   2.561
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.555
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.11
?
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
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)94679-X]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(99)00119-3]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[11575955]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. leaf n.a. PMID[11816040]
NPO24588 Phellinus igniarius Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. PMID[15165144]
NPO19805 Forsythia viridissima Species Oleaceae Eukaryota n.a. flower n.a. PMID[15481244]
NPO24588 Phellinus igniarius Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. PMID[15844878]
NPO24588 Phellinus igniarius Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. PMID[16209522]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[16309325]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. root n.a. PMID[16564530]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. Seoul, Korea 2000-Jun PMID[16643034]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. PMID[17125224]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[17156960]
NPO9294 Eupatorium rufescens Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[17252501]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota stems Yunnan Province, China 2004 PMID[17253844]
NPO24588 Phellinus igniarius Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. PMID[17279797]
NPO21404 Anagallis monelli Species Primulaceae Eukaryota n.a. aerial part n.a. PMID[17329877]
NPO7712 Nylandtia spinosa Species Polygalaceae Eukaryota Roots n.a. n.a. PMID[17927264]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[17950604]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. bark n.a. PMID[17950604]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota Stems purchased from Kyoungdong Oriental Herbal Market, Seoul, Korea 2006-APR PMID[18052323]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[18505286]
NPO2188 Dendrobium candidum Species Orchidaceae Eukaryota n.a. stem n.a. PMID[19182417]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[19650637]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. Brazilian n.a. PMID[19674905]
NPO24588 Phellinus igniarius Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. PMID[20583752]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[23265871]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[23305920]
NPO23332 Dendrobium fimbriatum Species Orchidaceae Eukaryota stems n.a. n.a. PMID[25316316]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[26422318]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota Stems n.a. n.a. PMID[27310249]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota Fruits n.a. n.a. PMID[28218000]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[29359942]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[30199256]
NPO19805 Forsythia viridissima Species Oleaceae Eukaryota Roots n.a. n.a. PMID[30676026]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. Barks Iksan, Chunbuk, Korea n.a. PMID[3127544]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[31291099]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[31944695]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[32044231]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[32141747]
NPO19632 Terminalia ivorensis Species Combretaceae Eukaryota n.a. n.a. n.a. PMID[36964494]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[37049761]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots; Tubers n.a. n.a. PMID[7714535]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2188 Dendrobium candidum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12945 Agelas schmidti Species Agelasidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24588 Phellinus igniarius Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9394 Herba artemisiae scopariae n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11889 Dendrobium chrysanthum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7712 Nylandtia spinosa Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO12883 Papaver albiflorum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23807 Trollius macropetalus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19805 Forsythia viridissima Species Oleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11805 Decaryia madagascariensis n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO10731 Delphinium trifoliolatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3751 Orthantha lutea n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO491 Jeotgalibacillus marinus Species Planococcaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO21404 Anagallis monelli Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23332 Dendrobium fimbriatum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23807 Trollius macropetalus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20900 Dendrobium chrysotoxum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24588 Phellinus igniarius Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19805 Forsythia viridissima Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11889 Dendrobium chrysanthum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9394 Herba artemisiae scopariae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO11230 Herba glechomae longitubae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24588 Phellinus igniarius Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20900 Dendrobium chrysotoxum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10731 Delphinium trifoliolatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19805 Forsythia viridissima Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23807 Trollius macropetalus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24588 Phellinus igniarius Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9518 Gardenia jasminoides Species Rubiaceae 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]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23807 Trollius macropetalus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19805 Forsythia viridissima Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11889 Dendrobium chrysanthum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23332 Dendrobium fimbriatum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2188 Dendrobium candidum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20900 Dendrobium chrysotoxum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24588 Phellinus igniarius Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12083 Hydnellum zonatum Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO487 Tabebuia avellanedae Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21404 Anagallis monelli Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11410 Corydalis speciosa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3751 Orthantha lutea n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20329 Gymnacranthera paniculata Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7700 Lomatium columbianum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27877 Eliokarmos thyrsoides Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12945 Agelas schmidti Species Agelasidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15524 Protea rubropilosa Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23807 Trollius macropetalus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20900 Dendrobium chrysotoxum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9294 Eupatorium rufescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19632 Terminalia ivorensis Species Combretaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12883 Papaver albiflorum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1487 Datura cornigera Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2188 Dendrobium candidum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23332 Dendrobium fimbriatum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11805 Decaryia madagascariensis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7712 Nylandtia spinosa Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11889 Dendrobium chrysanthum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29528 Anaxyrus fowleri Species Bufonidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10731 Delphinium trifoliolatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4068 Croton dichogamus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO491 Jeotgalibacillus marinus Species Planococcaceae Bacteria 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
NPO19632 Terminalia ivorensis Ethyl acetate extract n.a. 99.6±24.9 n.a. n.a. ng/mg PMID[36964494]
NPO19632 Terminalia ivorensis Chloroform extract n.a. 30±7.5 n.a. n.a. ng/mg PMID[36964494]

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
NPT2230 Individual protein Thiopurine S-methyltransferase Homo sapiens IC50 = 100000.0 nM PMID[3950915]
NPT233 Individual protein Carbonic anhydrase II Homo sapiens Ki = 6180.0 nM PMID[21282059]
NPT154 Individual protein Mothers against decapentaplegic homolog 3 Homo sapiens Potency n.a. 35481.3 nM PubChem BioAssay data set
NPT1062 Individual protein Carbonic anhydrase IV Homo sapiens Ki = 6480.0 nM PMID[22687439]
NPT1063 Individual protein Carbonic anhydrase VI Homo sapiens Ki = 24420.0 nM PMID[22687439]
NPT955 Individual protein Carbonic anhydrase VII Homo sapiens Ki = 7150.0 nM PMID[22668600]
NPT72 Individual protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 106.94 % PMID[23571415]
NPT73 Individual protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 111.28 % PMID[23571415]
NPT948 Individual protein Carbonic anhydrase IX Homo sapiens Ki = 8250.0 nM PMID[21282059]
NPT949 Individual protein Carbonic anhydrase XII Homo sapiens Ki = 6700.0 nM PMID[21282059]
NPT947 Individual protein Carbonic anhydrase I Homo sapiens Ki = 6830.0 nM PMID[21282059]
NPT954 Individual protein Carbonic anhydrase XIV Homo sapiens Ki = 740.0 nM PMID[22668600]
NPT43 Individual protein Tyrosinase Agaricus bisporus Inhibition = -3.2 % PMID[24268551]
NPT43 Individual protein Tyrosinase Agaricus bisporus IC50 > 100000.0 nM PMID[24268551]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT65 Cell line HepG2 Homo sapiens Potency n.a. 35481.3 nM PubChem BioAssay data set
NPT21 Organism Aspergillus niger Aspergillus niger MIC = 14.0 ug.mL-1 PMID[18597896]
NPT21 Organism Aspergillus niger Aspergillus niger -logMIC = 1.11 n.a. PMID[18597896]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 9.0 ug.mL-1 PMID[18597896]
NPT79 Organism Bacillus subtilis Bacillus subtilis -logMIC = 1.31 n.a. PMID[18597896]
NPT20 Organism Candida albicans Candida albicans MIC = 11.0 ug.mL-1 PMID[18597896]
NPT20 Organism Candida albicans Candida albicans -logMIC = 1.22 n.a. PMID[18597896]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 0.02 equiv PMID[24268551]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 18.0 ug.mL-1 PMID[18597896]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus -logMIC = 1.01 n.a. PMID[18597896]
NPT19 Organism Escherichia coli Escherichia coli MIC = 16.0 ug.mL-1 PMID[18597896]
NPT19 Organism Escherichia coli Escherichia coli -logMIC = 1.06 n.a. PMID[18597896]
NPT21912 Organism Hylobius abietis Hylobius abietis AFI = 7.0 % PMID[17927202]
NPT2 Others Unspecified n.a. Potency n.a. 398.1 nM PubChem BioAssay data set

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT22576 Organism Heterodera zeae Heterodera zeae mortality = 90.0 % PMID[21780738]
NPT22576 Organism Heterodera zeae Heterodera zeae mortality = 60.0 % PMID[21780738]
NPT22576 Organism Heterodera zeae Heterodera zeae mortality = 100.0 % PMID[21780738]
NPT22576 Organism Heterodera zeae Heterodera zeae mortality = 50.0 % PMID[21780738]
NPT22576 Organism Heterodera zeae Heterodera zeae mortality = 80.0 % PMID[21780738]
NPT22576 Organism Heterodera zeae Heterodera zeae mortality = 20.0 % PMID[21780738]
NPT22576 Organism Heterodera zeae Heterodera zeae mortality = 40.0 % PMID[21780738]
NPT22576 Organism Heterodera zeae Heterodera zeae mortality = 10.0 % PMID[21780738]
NPT22576 Organism Heterodera zeae Heterodera zeae mortality = 30.0 % PMID[21780738]





 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
- Mus musculus LD50 = 2.357398791 mg/kg TOXRIC

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 NPC285776 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
0.8065 Intermediate Similarity NPC607154
0.7097 Intermediate Similarity NPC283823
0.6667 Remote Similarity NPC45404
0.6333 Remote Similarity NPC155098
0.6333 Remote Similarity NPC61779
0.6061 Remote Similarity NPC240664
0.5312 Remote Similarity NPC145134
0.5312 Remote Similarity NPC603104
0.5161 Remote Similarity NPC184658
0.5135 Remote Similarity NPC111888
0.5135 Remote Similarity NPC125417

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC285776 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