Natural Product: NPC259732

Natural Product IDNPC259732
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XQINTCORIZHGFD-AWEZNQCLSA-O
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 161487
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0000381] Aporphines

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 XQINTCORIZHGFD-AWEZNQCLSA-O
Standard InCHI InChI=1S/C21H25NO4/c1-22(2)9-8-13-11-16(25-4)21(26-5)19-17(13)14(22)10-12-6-7-15(24-3)20(23)18(12)19/h6-7,11,14H,8-10H2,1-5H3/p+1/t14-/m0/s1
SMILES C[N+]1(C)CCc2cc(c(c3-c4c(ccc(c4O)OC)C[C@H]1c23)OC)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   356.19 Volume:   369.203
?
Van der Waals volume.
Dense:   0.965 LogP:   1.31
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.586
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.805
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   20.0
TPSA:   47.92
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   1.0 Rings:   4.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.857 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.47 Fsp3:   0.429
MCE-18:   81.667
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.88 Fluc inhibitor:   0.004
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.442
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.06
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.025 Promiscuous compounds:   0.319

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.527 MDCK Permeability:   -4.976
Pgp-inhibitor:   0.003 Pgp-substrate:   1.0
PAMPA:   0.435
?
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):   0.991
20% Bioavailability (F20%):   1.0 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.79
Plasma Protein Binding (PPB):   46.308% Volume Distribution (VD):   -0.319
Fu: 55.128%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.468
OATP1B3 inhibitor:   0.141 BCRP inhibitor:   0.207
BSEP inhibitor:   0.008

ADMET: Metabolism

CYP1A2-inhibitor:   0.999 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.956 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.011 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.002
CYP3A4-inhibitor:   0.235 CYP3A4-substrate:   0.555
CYP2B6-substrate:   0.622 CYP2C8-inhibitor:   0.0
HLM stability:   0.226
?
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):  6.681 Half-life (T1/2):  2.157

ADMET: Toxicity

hERG Blockers:  0.235 hERG Blockers (10um):  0.427
Human Hepatotoxicity (H-HT):  0.24 Drug-induced Liver Injury (DILI):  0.009
AMES Toxicity:  0.117 Rat Oral Acute Toxicity:  0.807
Maximum Recommended Daily Dose:  0.987 Skin Sensitization:  0.316
Carcinogencity:  0.669 Eye Corrosion:  0.008
Eye Irritation:  0.852 Respiratory Toxicity:  0.997
Drug-induced Neurotoxicity:  0.837 Ototoxicity:  0.153
Hematotoxicity:  0.07 Drug-induced Nephrotoxicity:  0.265
Genotoxicity:  0.511 RPMI-8226 Immunitoxicity:  0.129
A549 Cytotoxicity:  0.011 Hek293 Cytotoxicity:  0.266
BCF:   2.049
?
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:   4.491
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.239
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.389
?
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
NPO1315 Sinomenium acutum Species Menispermaceae Eukaryota n.a. n.a. n.a. DOI[10.3987/COM-96-7609.]
NPO15018.1 Dioscorea collettii var. hypoglauca Varieties Dioscoreaceae Eukaryota n.a. n.a. n.a. PMID[10075765]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota rhizomes n.a. n.a. PMID[11000020]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. n.a. n.a. PMID[11473438]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. leaf n.a. PMID[15388977]
NPO1315 Sinomenium acutum Species Menispermaceae Eukaryota n.a. n.a. n.a. PMID[16038566]
NPO1315 Sinomenium acutum Species Menispermaceae Eukaryota n.a. stem n.a. PMID[16964757]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. stem n.a. PMID[17202689]
NPO10008 Tinospora capillipes Species Menispermaceae Eukaryota n.a. root n.a. PMID[17340259]
NPO1315 Sinomenium acutum Species Menispermaceae Eukaryota n.a. n.a. n.a. PMID[18081254]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. root n.a. PMID[20030508]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. pericarp n.a. PMID[20628994]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota n.a. rhizome n.a. PMID[21401114]
NPO28410 Nandina domestica Species Berberidaceae Eukaryota n.a. n.a. n.a. PMID[22029392]
NPO1315 Sinomenium acutum Species Menispermaceae Eukaryota n.a. rhizome n.a. PMID[23059629]
NPO28410 Nandina domestica Species Berberidaceae Eukaryota n.a. fruit n.a. PMID[24897106]
NPO25734 Tinospora sagittata Species Menispermaceae Eukaryota n.a. n.a. n.a. PMID[28836430]
NPO14045 Corydalis decumbens Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[31599578]
NPO17129 Melodinus hemsleyanus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[32683864]
NPO17656 Drimys brasiliensis Species Winteraceae Eukaryota n.a. n.a. n.a. PMID[33232149]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. PMID[3728032]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. rhizome n.a. PMID[8281582]
NPO11385 Chondria atropurpurea Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[9868166]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22622 Coptis deltoidea Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1315 Sinomenium acutum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22242 Phellodendron chinense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26538 Phellodendron chinese Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15018.1 Dioscorea collettii var. hypoglauca Varieties Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19855 Oxalis acetosella Species Oxalidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28410 Nandina domestica Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10008 Tinospora capillipes Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11385 Chondria atropurpurea Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17129 Melodinus hemsleyanus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25921 Papaver nudicaule Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14045 Corydalis decumbens Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27900 Mizuhopecten yessoensis Species Pectinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5649 Coptis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29008 Coptis teeta Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota Tubers n.a. Database[FooDB]
NPO14045 Corydalis decumbens Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28410 Nandina domestica Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5649 Coptis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22622 Coptis deltoidea Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10008 Tinospora capillipes Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25921 Papaver nudicaule Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1315 Sinomenium acutum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22242 Phellodendron chinense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6595 Dicranostigma franchetianum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19463 Crotalaria nana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19855 Oxalis acetosella Species Oxalidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14045 Corydalis decumbens Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1315 Sinomenium acutum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22242 Phellodendron chinense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22622 Coptis deltoidea Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10008 Tinospora capillipes Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15018.1 Dioscorea collettii var. hypoglauca Varieties Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19855 Oxalis acetosella Species Oxalidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5649 Coptis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28410 Nandina domestica Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25734 Tinospora sagittata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5493 Rhizoma menispermi n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO25921 Papaver nudicaule Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6595 Dicranostigma franchetianum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19463 Crotalaria nana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17129 Melodinus hemsleyanus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22242 Phellodendron chinense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5649 Coptis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1315 Sinomenium acutum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25921 Papaver nudicaule Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14045 Corydalis decumbens Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28410 Nandina domestica Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22242 Phellodendron chinense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5649 Coptis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10008 Tinospora capillipes Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29008 Coptis teeta Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22622 Coptis deltoidea Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14045 Corydalis decumbens Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1315 Sinomenium acutum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25734 Tinospora sagittata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26538 Phellodendron chinese Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22622 Coptis deltoidea Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12773 Stephania tetrandra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22242 Phellodendron chinense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15018.1 Dioscorea collettii var. hypoglauca Varieties Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13757 Coptis japonica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1315 Sinomenium acutum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19463 Crotalaria nana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25921 Papaver nudicaule Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19855 Oxalis acetosella Species Oxalidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17656 Drimys brasiliensis Species Winteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10008 Tinospora capillipes Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5649 Coptis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28410 Nandina domestica Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27900 Mizuhopecten yessoensis Species Pectinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29008 Coptis teeta Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26653 Amomum giganteum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14045 Corydalis decumbens Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25734 Tinospora sagittata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11385 Chondria atropurpurea Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17129 Melodinus hemsleyanus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26265 Rumex alpinus Species Polygonaceae 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 NPC259732 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 NPC306555
0.8246 Intermediate Similarity NPC81218
0.7818 Intermediate Similarity NPC12053
0.7818 Intermediate Similarity NPC490754
0.6667 Remote Similarity NPC479650
0.6667 Remote Similarity NPC479649
0.6452 Remote Similarity NPC602351
0.5873 Remote Similarity NPC1229
0.5873 Remote Similarity NPC96603
0.5068 Remote Similarity NPC324144

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC259732 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