Natural Product: NPC130833

Natural Product IDNPC130833
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PTNGWSBREHHWFF-ZCFIWIBFSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44577733
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003411] 2-benzopyrans

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 PTNGWSBREHHWFF-ZCFIWIBFSA-N
Standard InCHI InChI=1S/C11H10O4/c1-6-4-8-7(5-12)2-3-9(13)10(8)11(14)15-6/h2-3,5-6,13H,4H2,1H3/t6-/m1/s1
SMILES C[C@@H]1Cc2c(ccc(c2C(=O)O1)O)C=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   206.06 Volume:   203.678
?
Van der Waals volume.
Dense:   1.012 LogP:   1.562
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.678
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.885
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   13.0
TPSA:   63.6
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   1.0 Rings:   2.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.555 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.111 Fsp3:   0.273
MCE-18:   39.429
?
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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.409 Fluc inhibitor:   0.256
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.381
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.277
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.736 Promiscuous compounds:   0.274

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.845 MDCK Permeability:   -4.644
Pgp-inhibitor:   0.808 Pgp-substrate:   0.056
PAMPA:   0.635
?
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):   0.042
20% Bioavailability (F20%):   0.094 30% Bioavailability (F30%):   0.521
50% Bioavailability (F50%):   0.838

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.073 MRP1:   0.463
Plasma Protein Binding (PPB):   93.733% Volume Distribution (VD):   0.133
Fu: 6.64%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.991
OATP1B3 inhibitor:   0.993 BCRP inhibitor:   0.336
BSEP inhibitor:   0.905

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.902
CYP2C19-inhibitor:   0.009 CYP2C19-substrate:   0.421
CYP2C9-inhibitor:   0.01 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.075
CYP3A4-inhibitor:   0.022 CYP3A4-substrate:   0.762
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.983
HLM stability:   0.903
?
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):  4.063 Half-life (T1/2):  1.302

ADMET: Toxicity

hERG Blockers:  0.027 hERG Blockers (10um):  0.333
Human Hepatotoxicity (H-HT):  0.509 Drug-induced Liver Injury (DILI):  0.838
AMES Toxicity:  0.917 Rat Oral Acute Toxicity:  0.69
Maximum Recommended Daily Dose:  0.761 Skin Sensitization:  0.999
Carcinogencity:  0.765 Eye Corrosion:  0.847
Eye Irritation:  0.985 Respiratory Toxicity:  0.795
Drug-induced Neurotoxicity:  0.837 Ototoxicity:  0.137
Hematotoxicity:  0.165 Drug-induced Nephrotoxicity:  0.84
Genotoxicity:  0.968 RPMI-8226 Immunitoxicity:  0.099
A549 Cytotoxicity:  0.342 Hek293 Cytotoxicity:  0.208
BCF:   0.958
?
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:   3.508
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.689
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.131
?
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
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[ 36006216]
NPO27746 Taxus mairei Species Taxaceae Eukaryota stem bark n.a. n.a. PMID[11473432]
NPO25366 Sapium indicum Species Euphorbiaceae Eukaryota Fruits n.a. n.a. PMID[12713411]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[16124776]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota bark n.a. n.a. PMID[17907781]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[18636777]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[18804027]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota bark n.a. n.a. PMID[19646881]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[20233596]
NPO25054 Phaleria macrocarpa Species Thymelaeaceae Eukaryota nut shell n.a. n.a. PMID[23044367]
NPO25252 Nannocystis exedens Species Nannocystaceae Bacteria n.a. n.a. n.a. PMID[24460410]
NPO25311 Guettarda platypoda Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[2553871]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29244495]
NPO284 Albizia procera Species Fabaceae Eukaryota Bark n.a. n.a. PMID[30520635]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[32058711]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36364129]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[8557595]
NPO27746 Taxus mairei Species Taxaceae Eukaryota Roots n.a. n.a. PMID[8991951]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[9644081]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3963 Hortonia floribunda Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3721 Achyranthes obtusifolia Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28460 Achyrocline tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22283 Alhagi maurorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25389 Allium angulosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18706 Anemone thalictroides Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25492 Botryllus leachi Species Styelidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24461 Clusia sandiensis Species Clusiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25441 Desmodium pulchellu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24802 Diploprion bifasciatum Species Serranidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24882 Erythrophleum chlorostachys Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24607 Goniothalamus dolichocarpus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25311 Guettarda platypoda Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24852 Helicia nilagirica Species Proteaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24730 Lactarius deliciosus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25466 Lecanora sulphurella Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24566 Marasmiellus ramealis Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20264 Moonia heterophylla n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO25252 Nannocystis exedens Species Nannocystaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO23994 Ormosia macrophylla Species Limoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14189 Osmundaria spiralis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25054 Phaleria macrocarpa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22618 Psolus eximius Species Psolidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23894 Pulicaria insignis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25366 Sapium indicum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25277 Seiridium cupressi Species Sporocadaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22152 Tecoma undulata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15482 Vanderbylia fraxinea Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27390 Vernonia brevifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4421 Penicillium cyclopium Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3255 Lampranthus sociorum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5981 Achlys triphylla Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3415 Perymenium mendezii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO284 Albizia procera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22283 Alhagi maurorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24852 Helicia nilagirica Species Proteaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28460 Achyrocline tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25389 Allium angulosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4421 Penicillium cyclopium Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25492 Botryllus leachi Species Styelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5981 Achlys triphylla Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18706 Anemone thalictroides Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23894 Pulicaria insignis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14189 Osmundaria spiralis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3963 Hortonia floribunda Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25366 Sapium indicum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO284 Albizia procera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24852 Helicia nilagirica Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25252 Nannocystis exedens Species Nannocystaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24730 Lactarius deliciosus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4952 Pertusaria amara Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25277 Seiridium cupressi Species Sporocadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20264 Moonia heterophylla n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO15482 Vanderbylia fraxinea Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3415 Perymenium mendezii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24566 Marasmiellus ramealis Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7616 Melanargia galathea Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3263 Thea sasanqua n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7464 Uruparia lanosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO22283 Alhagi maurorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23994 Ormosia macrophylla Species Limoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22618 Psolus eximius Species Psolidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24461 Clusia sandiensis Species Clusiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24607 Goniothalamus dolichocarpus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3721 Achyranthes obtusifolia Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24882 Erythrophleum chlorostachys Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27390 Vernonia brevifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24802 Diploprion bifasciatum Species Serranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6844 Bulbophyllum protractum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3255 Lampranthus sociorum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25441 Desmodium pulchellu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2963 Diospyros glaucifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4117 Nauclea rhynchophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15597 Calystegia pubescens Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22152 Tecoma undulata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25466 Lecanora sulphurella Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29287 Alectoria ochroleuca Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25054 Phaleria macrocarpa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25311 Guettarda platypoda Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO855 Elymnias thryallis Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC130833 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC470842
0.725 Intermediate Similarity NPC291454
0.6905 Remote Similarity NPC603067
0.5814 Remote Similarity NPC214702
0.5814 Remote Similarity NPC470831
0.5814 Remote Similarity NPC599777
0.5111 Remote Similarity NPC235115
0.5111 Remote Similarity NPC488349
0.5111 Remote Similarity NPC195964

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC130833 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