Natural Product: NPC19890

Natural Product IDNPC19890
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Hinokinin
IUPAC Name (3R,4R)-3,4-bis(1,3-benzodioxol-5-ylmethyl)oxolan-2-one
Synonyms (-)-Hinokinin; Hinokinin
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL242011
PubChem CID 442879
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0003686] Furanoid lignans
        • [CHEMONTID:0001604] Tetrahydrofuran lignans
          • [CHEMONTID:0003424] 9,9'-epoxylignans
            • [CHEMONTID:0001613] Dibenzylbutyrolactone lignans

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 DDWGQGZPYDSYEL-LSDHHAIUSA-N
Standard InCHI InChI=1S/C20H18O6/c21-20-15(6-13-2-4-17-19(8-13)26-11-24-17)14(9-22-20)5-12-1-3-16-18(7-12)25-10-23-16/h1-4,7-8,14-15H,5-6,9-11H2/t14-,15+/m0/s1
SMILES O=C1OC[C@@H]([C@H]1Cc1ccc2c(c1)OCO2)Cc1ccc2c(c1)OCO2

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   354.11 Volume:   345.98
?
Van der Waals volume.
Dense:   1.023 LogP:   2.505
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.496
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.256
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   26.0
TPSA:   63.22
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   0.0 Rings:   5.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.787 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.24 Fsp3:   0.35
MCE-18:   80.889
?
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:   0.325 Fluc inhibitor:   0.789
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.025
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.104
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.324 Promiscuous compounds:   0.158

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.936 MDCK Permeability:   -4.653
Pgp-inhibitor:   0.829 Pgp-substrate:   0.004
PAMPA:   0.243
?
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):   0.0
20% Bioavailability (F20%):   0.205 30% Bioavailability (F30%):   0.0
50% Bioavailability (F50%):   0.383

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.564 MRP1:   0.552
Plasma Protein Binding (PPB):   97.752% Volume Distribution (VD):   -0.14
Fu: 2.402%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.971
OATP1B3 inhibitor:   0.713 BCRP inhibitor:   0.001
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.534 CYP1A2-substrate:   0.986
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.982
CYP2C9-inhibitor:   0.006 CYP2C9-substrate:   1.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.012
HLM stability:   0.686
?
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):  1.623 Half-life (T1/2):  1.487

ADMET: Toxicity

hERG Blockers:  0.236 hERG Blockers (10um):  0.57
Human Hepatotoxicity (H-HT):  0.96 Drug-induced Liver Injury (DILI):  0.992
AMES Toxicity:  0.878 Rat Oral Acute Toxicity:  0.335
Maximum Recommended Daily Dose:  0.658 Skin Sensitization:  0.797
Carcinogencity:  0.921 Eye Corrosion:  0.002
Eye Irritation:  0.882 Respiratory Toxicity:  0.225
Drug-induced Neurotoxicity:  0.853 Ototoxicity:  0.609
Hematotoxicity:  0.732 Drug-induced Nephrotoxicity:  0.915
Genotoxicity:  0.997 RPMI-8226 Immunitoxicity:  0.223
A549 Cytotoxicity:  0.31 Hek293 Cytotoxicity:  0.586
BCF:   1.691
?
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:   4.246
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.985
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.354
?
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
NPO17839 Machaerium mucronulatum Species Dolichopodidae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)94598-9]
NPO25454 Plumbago europaea Species Plumbaginaceae Eukaryota n.a. root n.a. DOI[10.2225/vol5-issue3-fulltext-4]
NPO21302 Cladosporium herbarum Species Cladosporiaceae Eukaryota n.a. n.a. n.a. PMID[11325242]
NPO7174 Callyspongia truncata Species Callyspongiidae Eukaryota n.a. n.a. n.a. PMID[12088440]
NPO7174 Callyspongia truncata Species Callyspongiidae Eukaryota n.a. n.a. n.a. PMID[12713420]
NPO7090 Ammi majus Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15009205]
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[15679319]
NPO21302 Cladosporium herbarum Species Cladosporiaceae Eukaryota n.a. n.a. n.a. PMID[16038560]
NPO33321 aristolochia constricta Species Aristolochiaceae Eukaryota n.a. n.a. n.a. PMID[18570470]
NPO1338 Arcangelisia gusanlung Species Menispermaceae Eukaryota n.a. stem n.a. PMID[21500777]
NPO9604 Amycolatopsis lurida Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. PMID[25323720]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota rhizomes Liaoning province, China 2011-SEP PMID[25927664]
NPO16966 Leptospermum scoparium Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[26731565]
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[31096694]
NPO18983 Cleidion brevipetiolatum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[31419126]
NPO16966 Leptospermum scoparium Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[32078653]
NPO40168 Hypoestes aristata Species Acanthaceae Eukaryota n.a. n.a. n.a. PMID[32786879]
NPO17802 Simmondsia chinensis Species Simmondsiaceae Eukaryota n.a. n.a. n.a. PMID[35889256]
NPO18707 Allium ursinum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[37241721]
NPO25454 Plumbago europaea Species Plumbaginaceae Eukaryota n.a. n.a. n.a. PMID[37800169]
NPO16966 Leptospermum scoparium Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38370080]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[38790803]
NPO18707 Allium ursinum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[39684509]
NPO33321 aristolochia constricta Species Aristolochiaceae Eukaryota n.a. n.a. n.a. PMID[9392875]
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO28392 Macrosiphum liriodendri Species Aphididae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7090 Ammi majus Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28510 Aspergillus pseudodeflectus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28218 Asplenium adiantum-nigrum Species Aspleniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28036 Distemonanthus benthamianus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12801 Aglaia meridionalis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18707 Allium ursinum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9604 Amycolatopsis lurida Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO18061 Anacystis cyanea n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO1338 Arcangelisia gusanlung Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17718 Artemisia schmidtiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16293 Babylonia japonica Species Buccinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19189 Brickellia pendula Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7174 Callyspongia truncata Species Callyspongiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18377 Chaetomium retardatum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17275 Chamaemelum scariosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19127 Citrus tankan Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3050 Cladonia pseudodidyma Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21302 Cladosporium herbarum Species Cladosporiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18983 Cleidion brevipetiolatum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21938 Coleus carnosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18847 Copaifera paupera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9535 Cortinarius basirubescens Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18792 Crotalaria lechnaultii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16829 Dunaliella acidophila Species Dunaliellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15358 Entandrophragma cylindricum Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12072 Escallonia philippiana Species Escalloniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17596 Ficus maxima Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18242 Gleichenia glauca Species Gleicheniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18520 Helipterum strictum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3746 Hesperocyparis nevadensis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13594 Hippocratea indica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18306 Juniperus thurifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11677 Lactobacillus acidophilus Species Lactobacillaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO11603 Lathyrus macrorrhizus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13963 Laurencia elata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19057 Lentinellus omphalodes Species Auriscalpiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16966 Leptospermum scoparium Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17839 Machaerium mucronulatum Species Dolichopodidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17831 Millettia racemosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18575 Ochtodes crockeri Species Rhizophyllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5764 Ophioglossum vulgatum Species Ophioglossaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12282 Parmelia conspersa Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25454 Plumbago europaea Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7807 Polyporus sulphureus Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18173 Pyrocystis lunula Species Pyrocystaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17190 Senecio erraticus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17802 Simmondsia chinensis Species Simmondsiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10712 Tabebuia rosea Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17068 Talaromyces wortmanni Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15608 Tanacetum santolina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17709 Timonius kaniensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. Database[FooDB]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19127 Citrus tankan Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16293 Babylonia japonica Species Buccinidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7090 Ammi majus Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25454 Plumbago europaea Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18306 Juniperus thurifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28036 Distemonanthus benthamianus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13963 Laurencia elata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5764 Ophioglossum vulgatum Species Ophioglossaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15358 Entandrophragma cylindricum Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19127 Citrus tankan Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7090 Ammi majus Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25454 Plumbago europaea Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28036 Distemonanthus benthamianus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17831 Millettia racemosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18306 Juniperus thurifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13963 Laurencia elata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16293 Babylonia japonica Species Buccinidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19127 Citrus tankan Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28036 Distemonanthus benthamianus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7090 Ammi majus Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11169 Piper cubeba Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11677 Lactobacillus acidophilus Species Lactobacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17839 Machaerium mucronulatum Species Dolichopodidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18173 Pyrocystis lunula Species Pyrocystaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3050 Cladonia pseudodidyma Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9535 Cortinarius basirubescens Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21302 Cladosporium herbarum Species Cladosporiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7807 Polyporus sulphureus Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17709 Timonius kaniensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17802 Simmondsia chinensis Species Simmondsiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3746 Hesperocyparis nevadensis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18847 Copaifera paupera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19127 Citrus tankan Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13594 Hippocratea indica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5764 Ophioglossum vulgatum Species Ophioglossaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7090 Ammi majus Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21938 Coleus carnosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17718 Artemisia schmidtiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18575 Ochtodes crockeri Species Rhizophyllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1338 Arcangelisia gusanlung Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18983 Cleidion brevipetiolatum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18306 Juniperus thurifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17385 Magnolia acuminata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13963 Laurencia elata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16966 Leptospermum scoparium Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16653 Matteuccia struthiopteris Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12282 Parmelia conspersa Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18707 Allium ursinum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12072 Escallonia philippiana Species Escalloniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17068 Talaromyces wortmanni Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11603 Lathyrus macrorrhizus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10712 Tabebuia rosea Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15358 Entandrophragma cylindricum Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16293 Babylonia japonica Species Buccinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19189 Brickellia pendula Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17831 Millettia racemosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25454 Plumbago europaea Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28218 Asplenium adiantum-nigrum Species Aspleniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15608 Tanacetum santolina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18520 Helipterum strictum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17275 Chamaemelum scariosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7174 Callyspongia truncata Species Callyspongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18061 Anacystis cyanea n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO9604 Amycolatopsis lurida Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17190 Senecio erraticus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18242 Gleichenia glauca Species Gleicheniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17596 Ficus maxima Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18377 Chaetomium retardatum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16829 Dunaliella acidophila Species Dunaliellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19057 Lentinellus omphalodes Species Auriscalpiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12801 Aglaia meridionalis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18792 Crotalaria lechnaultii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28392 Macrosiphum liriodendri Species Aphididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28510 Aspergillus pseudodeflectus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28036 Distemonanthus benthamianus Species Fabaceae 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
NPT109 Individual protein Cytochrome P450 3A4 Homo sapiens IC50 = 8000.0 nM PMID[15679319]
NPT110 Individual protein Cytochrome P450 2D6 Homo sapiens IC50 = 26500.0 nM PMID[15679319]
NPT109 Individual protein Cytochrome P450 3A4 Homo sapiens Ki = 373.0 nM PMID[16248836]
NPT109 Individual protein Cytochrome P450 3A4 Homo sapiens Kinact = 0.315 min-1 PMID[16248836]
NPT1517 Individual protein Glycine transporter 1 Homo sapiens IC50 > 500000.0 nM PMID[24112084]
NPT1518 Individual protein Excitatory amino acid transporter 3 Homo sapiens IC50 > 500000.0 nM PMID[24112084]
NPT1519 Individual protein Excitatory amino acid transporter 2 Homo sapiens IC50 > 100000.0 nM PMID[24112084]
NPT1520 Individual protein Excitatory amino acid transporter 1 Homo sapiens IC50 > 500000.0 nM PMID[24112084]
NPT295 Individual protein Serotonin transporter Homo sapiens IC50 = 175000.0 nM PMID[24112084]
NPT228 Individual protein Norepinephrine transporter Homo sapiens IC50 = 8760.0 nM PMID[24112084]
NPT246 Individual protein Dopamine transporter Homo sapiens IC50 = 8350.0 nM PMID[24112084]
NPT810 Individual protein GABA transporter 3 Homo sapiens IC50 > 500000.0 nM PMID[24112084]
NPT808 Individual protein GABA transporter 1 Homo sapiens IC50 = 20600.0 nM PMID[24112084]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1229 Cell line Huh-7 Homo sapiens FC = 2.0 n.a. PMID[26774581]
NPT461 Cell line PANC-1 Homo sapiens PC50 = 64.1 uM PMID[28947153]
NPT783 Cell line MIA PaCa-2 Homo sapiens PC50 = 21.3 uM PMID[28947153]
NPT2309 Cell line CAPAN-1 Homo sapiens PC50 = 50.1 uM PMID[28947153]
NPT2107 Cell line PSN1 Homo sapiens PC50 = 60.1 uM PMID[28947153]
NPT189 Cell line Vero Chlorocebus aethiops CC50 > 750000.0 nM PMID[17663539]
NPT548 Tissue Ileum Cavia porcellus Inhibition = 69.8 % PMID[18570470]
NPT548 Tissue Ileum Cavia porcellus Inhibition = 27.3 % PMID[18570470]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 0.6 ug.mL-1 PMID[19128011]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Inhibition = 24.7 % PMID[19128011]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 10400.0 nM PMID[26774581]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 31300.0 nM PMID[26774581]
NPT1515 Organism SARS coronavirus SARS coronavirus EC50 > 10000.0 nM PMID[17663539]
NPT1515 Organism SARS coronavirus SARS coronavirus Inhibition < 25.0 % PMID[17663539]
NPT1515 Organism SARS coronavirus SARS coronavirus Inhibition = 25.0 % PMID[17663539]
NPT1515 Organism SARS coronavirus SARS coronavirus Inhibition = 50.0 % PMID[17663539]
NPT2 Others Unspecified n.a. IC50 > 100000.0 nM PMID[17663539]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 43.2 % PMID[25297647]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 50.4 % PMID[25297647]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 54.7 % PMID[25297647]





 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 NPC19890 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 NPC110958
0.9111 High Similarity NPC205915
0.8723 High Similarity NPC176586
0.8723 High Similarity NPC210354
0.8542 High Similarity NPC191158
0.8542 High Similarity NPC177644
0.7885 Intermediate Similarity NPC145569
0.7727 Intermediate Similarity NPC476748
0.7593 Intermediate Similarity NPC282291
0.7593 Intermediate Similarity NPC166137
0.7556 Intermediate Similarity NPC223807
0.7292 Intermediate Similarity NPC92693
0.7143 Intermediate Similarity NPC40237
0.6939 Remote Similarity NPC211386
0.6889 Remote Similarity NPC600801
0.68 Remote Similarity NPC143895
0.6667 Remote Similarity NPC3982
0.6383 Remote Similarity NPC72796
0.6271 Remote Similarity NPC216223
0.625 Remote Similarity NPC293757
0.625 Remote Similarity NPC668
0.6207 Remote Similarity NPC56184
0.6154 Remote Similarity NPC158737
0.6078 Remote Similarity NPC192255
0.6078 Remote Similarity NPC474288
0.6071 Remote Similarity NPC5310
0.6071 Remote Similarity NPC300776
0.6071 Remote Similarity NPC176814
0.6071 Remote Similarity NPC4982
0.6071 Remote Similarity NPC606629
0.5962 Remote Similarity NPC171550
0.5962 Remote Similarity NPC134764
0.5778 Remote Similarity NPC80241
0.5778 Remote Similarity NPC301641
0.5778 Remote Similarity NPC485483
0.5738 Remote Similarity NPC174512
0.5686 Remote Similarity NPC11453
0.5667 Remote Similarity NPC487679
0.5667 Remote Similarity NPC487678
0.5614 Remote Similarity NPC230968
0.5614 Remote Similarity NPC102260
0.5556 Remote Similarity NPC68779
0.5556 Remote Similarity NPC108598
0.5517 Remote Similarity NPC218092
0.5517 Remote Similarity NPC106920
0.5517 Remote Similarity NPC15811
0.5517 Remote Similarity NPC246474
0.5517 Remote Similarity NPC162851
0.5439 Remote Similarity NPC18576
0.5417 Remote Similarity NPC40352
0.5417 Remote Similarity NPC213711
0.5345 Remote Similarity NPC47181
0.5345 Remote Similarity NPC185908
0.5345 Remote Similarity NPC482891
0.5312 Remote Similarity NPC478705
0.5306 Remote Similarity NPC344161
0.5231 Remote Similarity NPC478703
0.5231 Remote Similarity NPC478704
0.5172 Remote Similarity NPC273657
0.5161 Remote Similarity NPC482889
0.5075 Remote Similarity NPC158635
0.5075 Remote Similarity NPC229882

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC19890 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