Natural Product: NPC128863

Natural Product IDNPC128863
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 5,6-Dihydroxy-2-(4-Hydroxy-3-Methoxyphenyl)-7,8-Dimethoxychromen-4-One
IUPAC Name 5,6-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-7,8-dimethoxychromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL478416
PubChem CID 442662
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 BAIRXMVFPKLWSE-UHFFFAOYSA-N
Standard InCHI InChI=1S/C18H16O8/c1-23-12-6-8(4-5-9(12)19)11-7-10(20)13-14(21)15(22)17(24-2)18(25-3)16(13)26-11/h4-7,19,21-22H,1-3H3
SMILES COc1cc(ccc1O)c1cc(=O)c2c(c(c(c(c2o1)OC)OC)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   360.08 Volume:   343.445
?
Van der Waals volume.
Dense:   1.048 LogP:   2.017
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.123
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.175
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   18.0
TPSA:   118.59
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.608 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.593 Fsp3:   0.167
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:   1
Colloidal aggregators:   0.36 Fluc inhibitor:   0.441
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.829
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.627
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.355 Promiscuous compounds:   0.865

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.192 MDCK Permeability:   -4.804
Pgp-inhibitor:   0.354 Pgp-substrate:   0.139
PAMPA:   0.215
?
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):   0.024
20% Bioavailability (F20%):   0.211 30% Bioavailability (F30%):   0.426
50% Bioavailability (F50%):   0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.008 MRP1:   0.988
Plasma Protein Binding (PPB):   95.932% Volume Distribution (VD):   -0.468
Fu: 4.544%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.98
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.996
BSEP inhibitor:   0.888

ADMET: Metabolism

CYP1A2-inhibitor:   0.332 CYP1A2-substrate:   0.61
CYP2C19-inhibitor:   0.193 CYP2C19-substrate:   0.259
CYP2C9-inhibitor:   0.895 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.977 CYP2D6-substrate:   0.363
CYP3A4-inhibitor:   0.02 CYP3A4-substrate:   0.006
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.917
HLM stability:   0.297
?
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):  8.153 Half-life (T1/2):  1.671

ADMET: Toxicity

hERG Blockers:  0.07 hERG Blockers (10um):  0.516
Human Hepatotoxicity (H-HT):  0.403 Drug-induced Liver Injury (DILI):  0.699
AMES Toxicity:  0.432 Rat Oral Acute Toxicity:  0.406
Maximum Recommended Daily Dose:  0.527 Skin Sensitization:  0.801
Carcinogencity:  0.641 Eye Corrosion:  0.136
Eye Irritation:  0.951 Respiratory Toxicity:  0.806
Drug-induced Neurotoxicity:  0.135 Ototoxicity:  0.182
Hematotoxicity:  0.253 Drug-induced Nephrotoxicity:  0.155
Genotoxicity:  0.54 RPMI-8226 Immunitoxicity:  0.13
A549 Cytotoxicity:  0.402 Hek293 Cytotoxicity:  0.56
BCF:   0.996
?
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:   3.485
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.397
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.881
?
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
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.indcrop.2008.08.002]
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]
NPO11960 Myriastra clavosa Species n.a. n.a. n.a. Philippines n.a. PMID[12193033]
NPO11960 Myriastra clavosa Species n.a. n.a. n.a. n.a. n.a. PMID[12350152]
NPO14579 Mentha spicata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[12776552]
NPO15105 Lyngbya semiplena Species Oscillatoriaceae Bacteria n.a. Papua New Guinea n.a. PMID[14575438]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[16249088]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[17238120]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[18405608]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[18661821]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[20973550]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21417376]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21627108]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21707257]
NPO1762 Citropsis articulata Species Rutaceae Eukaryota Root Bark n.a. n.a. PMID[21985060]
NPO1762 Citropsis articulata Species Rutaceae Eukaryota n.a. root n.a. PMID[21985060]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29726697]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30792999]
NPO5692 Trachyspermum ammi Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[31218527]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[34443694]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[34453492]
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]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[35264638]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[35608311]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[35631245]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36235238]
NPO14579 Mentha spicata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36715796]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36840093]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36840093]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37020229]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37049808]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37175125]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37226152]
NPO5692 Trachyspermum ammi Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37445619]
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]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38474654]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38695450]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38695450]
NPO5692 Trachyspermum ammi Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38714128]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[38786901]
NPO5692 Trachyspermum ammi Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[39064843]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39407547]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39520005]
NPO4995 Thymus serpyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39633960]
NPO4995 Thymus serpyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39683108]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[7700984]
NPO19302 Amathia alternata Species Vesiculariidae Eukaryota n.a. Atlantic n.a. PMID[9249973]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14579 Mentha spicata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26697 Dracocephalum moldavicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4995 Thymus serpyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19302 Amathia alternata Species Vesiculariidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1762 Citropsis articulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12968 Crotalaria spectabilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22538 Dendrobium plicatile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16082 Flindersia bennettiana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14198 Haliclona valliculata Species Chalinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18035 Lagerstroemia flos-reginae Species Lythraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17744 Litsea elliptica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15105 Lyngbya semiplena Species Oscillatoriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO13667 Manoao colensoi Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11960 Myriastra clavosa Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO18669 Myriophyllum verticillatum Species Haloragaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11070 Nervilia purpurea Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10039 Podosphaera fuliginea Species Erysiphaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25840 Sargassum fusiforme Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19237 Sargassum macrocarpum Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13312 Senecio panduriformis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14705 Tanacetopsis mucronata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19079 Vatica pauciflora Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18258 Zanthoxylum rhoifolium Species Rutaceae 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]
NPO14579 Mentha spicata Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO14579 Mentha spicata Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO14579 Mentha spicata Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota Shoot Essent. Oil n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14579 Mentha spicata Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14579 Mentha spicata 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]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
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]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26697 Dracocephalum moldavicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12968 Crotalaria spectabilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5692 Trachyspermum ammi Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4995 Thymus serpyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14579 Mentha spicata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14579 Mentha spicata Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
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]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26697 Dracocephalum moldavicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4995 Thymus serpyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5692 Trachyspermum ammi Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12968 Crotalaria spectabilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14579 Mentha spicata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29401 Bupleurum chinense Species Apiaceae 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]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25840 Sargassum fusiforme Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4995 Thymus serpyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26697 Dracocephalum moldavicum Species Lamiaceae 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]
NPO13857 Mentha canadensis 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]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25840 Sargassum fusiforme Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29169 Origanum vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13667 Manoao colensoi Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25840 Sargassum fusiforme Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19302 Amathia alternata Species Vesiculariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18035 Lagerstroemia flos-reginae Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15105 Lyngbya semiplena Species Oscillatoriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO1762 Citropsis articulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10039 Podosphaera fuliginea Species Erysiphaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14198 Haliclona valliculata Species Chalinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17744 Litsea elliptica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11960 Myriastra clavosa Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14705 Tanacetopsis mucronata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19237 Sargassum macrocarpum Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18258 Zanthoxylum rhoifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18669 Myriophyllum verticillatum Species Haloragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11070 Nervilia purpurea Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12968 Crotalaria spectabilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14579 Mentha spicata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19079 Vatica pauciflora Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22538 Dendrobium plicatile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16082 Flindersia bennettiana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13312 Senecio panduriformis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26697 Dracocephalum moldavicum Species Lamiaceae 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
NPT68 Individual protein Aldose reductase Rattus norvegicus IC50 = 109647.82 nM PMID[18585047]

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 NPC128863 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
0.7736 Intermediate Similarity NPC71334
0.7679 Intermediate Similarity NPC227325
0.6897 Remote Similarity NPC4455
0.6724 Remote Similarity NPC280339
0.6724 Remote Similarity NPC167815
0.65 Remote Similarity NPC47781
0.6441 Remote Similarity NPC83508
0.623 Remote Similarity NPC183950
0.623 Remote Similarity NPC137062
0.6 Remote Similarity NPC312924
0.5902 Remote Similarity NPC20830
0.5833 Remote Similarity NPC231018
0.5806 Remote Similarity NPC115323
0.5738 Remote Similarity NPC201136
0.5714 Remote Similarity NPC19687
0.5714 Remote Similarity NPC606105
0.5574 Remote Similarity NPC198826
0.5556 Remote Similarity NPC18607
0.5556 Remote Similarity NPC196439
0.5556 Remote Similarity NPC2476
0.55 Remote Similarity NPC250822
0.5484 Remote Similarity NPC162313
0.5469 Remote Similarity NPC152166
0.5429 Remote Similarity NPC602497
0.541 Remote Similarity NPC301323
0.5323 Remote Similarity NPC176775
0.5323 Remote Similarity NPC188203
0.5312 Remote Similarity NPC283600
0.5161 Remote Similarity NPC306821
0.5161 Remote Similarity NPC275722
0.5161 Remote Similarity NPC275836
0.5156 Remote Similarity NPC183878
0.5156 Remote Similarity NPC212678
0.5156 Remote Similarity NPC253634
0.5079 Remote Similarity NPC57030
0.5077 Remote Similarity NPC288669
0.5077 Remote Similarity NPC610401
0.5075 Remote Similarity NPC485299
0.5063 Remote Similarity NPC111249

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC128863 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