Natural Product: NPC130449

Natural Product IDNPC130449
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Syringaresinol-Beta-D Glucoside
IUPAC Name (2S,3R,4S,5S,6R)-2-[4-[(3S,3aR,6S,6aR)-3-(4-hydroxy-3,5-dimethoxyphenyl)-1,3,3a,4,6,6a-hexahydrofuro[3,4-c]furan-6-yl]-2,6-dimethoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1077080
PubChem CID 443024
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0001511] Lignan glycosides

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 WEKCEGQSIIQPAQ-IRBNZIFYSA-N
Standard InCHI InChI=1S/C28H36O13/c1-34-16-5-12(6-17(35-2)21(16)30)25-14-10-39-26(15(14)11-38-25)13-7-18(36-3)27(19(8-13)37-4)41-28-24(33)23(32)22(31)20(9-29)40-28/h5-8,14-15,20,22-26,28-33H,9-11H2,1-4H3/t14-,15-,20+,22+,23-,24+,25+,26+,28-/m0/s1
SMILES COc1cc(cc(c1O)OC)[C@@H]1[C@H]2CO[C@H](c3cc(c(c(c3)OC)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)OC)[C@H]2CO1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   580.22 Volume:   548.516
?
Van der Waals volume.
Dense:   1.058 LogP:   -0.327
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.189
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.499
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 Rigid Bonds:   27.0
TPSA:   174.99
?
Topological Polar Surface Area.
 H-Bond Acceptor:   13.0
H-Bond Donor:   5.0 Rings:   5.0
Heavy Atoms:   13.0

MedChem Properties

QED Drug-Likeness Score:   0.28 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.615 Fsp3:   0.571
MCE-18:   112.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.553 Fluc inhibitor:   0.024
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.035
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.127
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.097 Promiscuous compounds:   0.126

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.084 MDCK Permeability:   -5.345
Pgp-inhibitor:   0.005 Pgp-substrate:   0.167
PAMPA:   0.045
?
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):   0.079
20% Bioavailability (F20%):   0.023 30% Bioavailability (F30%):   0.242
50% Bioavailability (F50%):   0.96

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.224 MRP1:   0.645
Plasma Protein Binding (PPB):   81.832% Volume Distribution (VD):   -0.315
Fu: 19.288%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.479
BSEP inhibitor:   0.076

ADMET: Metabolism

CYP1A2-inhibitor:   0.082 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.003
CYP3A4-inhibitor:   0.427 CYP3A4-substrate:   0.302
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.497
HLM stability:   0.01
?
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):  3.081 Half-life (T1/2):  4.579

ADMET: Toxicity

hERG Blockers:  0.027 hERG Blockers (10um):  0.109
Human Hepatotoxicity (H-HT):  0.878 Drug-induced Liver Injury (DILI):  0.986
AMES Toxicity:  0.887 Rat Oral Acute Toxicity:  0.036
Maximum Recommended Daily Dose:  0.07 Skin Sensitization:  0.994
Carcinogencity:  0.326 Eye Corrosion:  0.0
Eye Irritation:  0.031 Respiratory Toxicity:  0.013
Drug-induced Neurotoxicity:  0.047 Ototoxicity:  0.945
Hematotoxicity:  0.605 Drug-induced Nephrotoxicity:  0.845
Genotoxicity:  0.851 RPMI-8226 Immunitoxicity:  0.338
A549 Cytotoxicity:  0.476 Hek293 Cytotoxicity:  0.335
BCF:   0.774
?
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:   3.335
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.987
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.975
?
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
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[11575955]
NPO1287 Coriaria nepalensis Species Coriariaceae Eukaryota n.a. root n.a. PMID[12016873]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. PMID[16268553]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. Fijian red alga n.a. PMID[16724831]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota stems Yunnan Province, China 2004 PMID[17253844]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. PMID[17715978]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[17944538]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota Stems purchased from Kyoungdong Oriental Herbal Market, Seoul, Korea 2006-APR PMID[18052323]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18154272]
NPO16239 Rhodiola rosea Species Crassulaceae Eukaryota roots n.a. n.a. PMID[19729316]
NPO18521 Capparis flavicans Species Capparaceae Eukaryota aerial parts Khon Kaen Province, Thailand 2006-Aug PMID[19943620]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. Fijian red alga n.a. PMID[20141173]
NPO16259 Syringa reticulata Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[21955940]
NPO14559 Acer saccharum Species Sapindaceae Eukaryota n.a. bark n.a. PMID[22032697]
NPO14559 Acer saccharum Species Sapindaceae Eukaryota bark n.a. n.a. PMID[22032697]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota leaves n.a. n.a. PMID[22212722]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[22823026]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota leaves and stems Ha Long, Quang Ninh province, Vietnam 2014-Jul PMID[25769817]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota Stems n.a. n.a. PMID[27310249]
NPO41077 Xanthoceras sorbifolia Bunge Strain Sapindaceae Eukaryota Leaves n.a. n.a. PMID[27623545]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[29792702]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. PMID[30407005]
NPO40254 Opuntia humifusa Species Cactaceae Eukaryota Cladodes n.a. n.a. PMID[32118424]
NPO16693 Byrsonima crassifolia Species Malpighiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16239 Rhodiola rosea Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26304 Hymenocallis littoralis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9588 Atelopus chiriquiensis Species Bufonidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14559 Acer saccharum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16259 Syringa reticulata Species Oleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17757 Plectranthus saccatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11809 Eleutherococcus sessiliflorus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13053 Corydalis conspersa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5016 Glossogyne tenuifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11242 Gynochthodes parvifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15662 Ligustrum ovalifolium Species Oleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5019 Mespilus germanica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1575 Mikania luetzelburgii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO326 Pittosporum brevicalyx Species Pittosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15280 Sideritis grandiflora Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6178 Solanum euacanthum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4581 Ungernia victoris Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9141 Epimedium wushanense Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16210 Androcymbium palaestinum Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18071 Euryops pedunculatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21166 Kalopanax septemlobus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12630 Senecio oxyodontus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15594 Aplidiopsis confluata n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO22493 Xenia crassa Species Xeniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25200 Takifugu niphobles Species Tetraodontidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15954 Pyrenula japonica Species Pyrenulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40254 Opuntia humifusa Species Cactaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16693 Byrsonima crassifolia Species Malpighiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16693 Byrsonima crassifolia Species Malpighiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO5019 Mespilus germanica Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16693 Byrsonima crassifolia Species Malpighiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21166 Kalopanax septemlobus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9141 Epimedium wushanense Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26304 Hymenocallis littoralis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14559 Acer saccharum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5019 Mespilus germanica Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO11809 Eleutherococcus sessiliflorus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14559 Acer saccharum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9141 Epimedium wushanense Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11242 Gynochthodes parvifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15954 Pyrenula japonica Species Pyrenulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21166 Kalopanax septemlobus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26304 Hymenocallis littoralis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16239 Rhodiola rosea Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9141 Epimedium wushanense Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16326 Scopolia parviflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21166 Kalopanax septemlobus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14001 Ceroplastes pseudoceriferus Species Coccidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22493 Xenia crassa Species Xeniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5016 Glossogyne tenuifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13053 Corydalis conspersa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26304 Hymenocallis littoralis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO326 Pittosporum brevicalyx Species Pittosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15740 Garcinia purpurea Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14507.1 Quercus ithaburensis subsp. macrolepis Subspecies Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16049 Cryptocarya pleurosperma Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15662 Ligustrum ovalifolium Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11242 Gynochthodes parvifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16210 Androcymbium palaestinum Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16693 Byrsonima crassifolia Species Malpighiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4581 Ungernia victoris Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15280 Sideritis grandiflora Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5019 Mespilus germanica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9141 Epimedium wushanense Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18071 Euryops pedunculatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1575 Mikania luetzelburgii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9474 Clausena pentaphylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18521 Capparis flavicans Species Capparaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17917 Thamnophis sirtalis Species Colubridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11755 Banisteriopsis caapi Species Malpighiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25200 Takifugu niphobles Species Tetraodontidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21166 Kalopanax septemlobus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6178 Solanum euacanthum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17600 Gnathotrichus sulcatus Species Curculionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15594 Aplidiopsis confluata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO1287 Coriaria nepalensis Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16326 Scopolia parviflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17444 Gleichenia japonica Species Gleicheniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15954 Pyrenula japonica Species Pyrenulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12630 Senecio oxyodontus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16239 Rhodiola rosea Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17757 Plectranthus saccatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11809 Eleutherococcus sessiliflorus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10751 Bothriocline laxa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11280 Aphanoascus terreus Species Onygenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO619 Ankistrodesmus braunii Species Selenastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17141 Lonchocarpus longistylus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14559 Acer saccharum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9588 Atelopus chiriquiensis Species Bufonidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5848 Pimpinella nudicaulis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5594 Notholaena nivea Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16259 Syringa reticulata Species Oleaceae 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
NPT83 Cell line MCF7 Homo sapiens Activity < 0.1 uM PMID[19943620]
NPT396 Cell line T47D Homo sapiens Activity < 0.1 uM PMID[19943620]
NPT396 Cell line T47D Homo sapiens Activity = 19.0 uM PMID[19943620]
NPT396 Cell line T47D Homo sapiens Activity > 100.0 uM PMID[19943620]
NPT393 Cell line HCT-116 Homo sapiens IC50 < 5.0 ug.mL-1 PMID[22032697]
NPT492 Cell line Caco-2 Homo sapiens IC50 < 5.0 ug.mL-1 PMID[22032697]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. EC50 > 100000.0 nM PMID[21955940]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 87.41 % PMID[27623545]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 92.93 % PMID[27623545]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 3080.0 nM PMID[27623545]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 95.44 % PMID[27623545]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 94.43 % PMID[27623545]
NPT1 Others Radical scavenging activity n.a. EC50 > 100000.0 nM PMID[21955940]
NPT2 Others Unspecified n.a. IC50 > 50000.0 nM PMID[25769817]

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 NPC130449 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 NPC216129
1.0 High Similarity NPC248132
0.8772 High Similarity NPC95392
0.8772 High Similarity NPC84013
0.8772 High Similarity NPC55715
0.8772 High Similarity NPC35877
0.8438 Intermediate Similarity NPC51328
0.8438 Intermediate Similarity NPC55158
0.8154 Intermediate Similarity NPC286235
0.7429 Intermediate Similarity NPC605526
0.7164 Intermediate Similarity NPC486104
0.7164 Intermediate Similarity NPC486102
0.7 Intermediate Similarity NPC38041
0.7 Intermediate Similarity NPC22150
0.6923 Remote Similarity NPC276753
0.6923 Remote Similarity NPC205796
0.6818 Remote Similarity NPC246947
0.6761 Remote Similarity NPC279298
0.6575 Remote Similarity NPC486100
0.6575 Remote Similarity NPC486101
0.6567 Remote Similarity NPC486107
0.6494 Remote Similarity NPC486099
0.6234 Remote Similarity NPC39657
0.6216 Remote Similarity NPC486109
0.6216 Remote Similarity NPC486108
0.6207 Remote Similarity NPC165155
0.6207 Remote Similarity NPC24490
0.6133 Remote Similarity NPC486105
0.6111 Remote Similarity NPC606627
0.6026 Remote Similarity NPC486098
0.6 Remote Similarity NPC486106
0.5875 Remote Similarity NPC478055
0.5854 Remote Similarity NPC486097
0.5806 Remote Similarity NPC299144
0.5775 Remote Similarity NPC118385
0.5645 Remote Similarity NPC152722
0.5625 Remote Similarity NPC185071
0.5625 Remote Similarity NPC69513
0.5614 Remote Similarity NPC141765
0.5614 Remote Similarity NPC34103
0.5606 Remote Similarity NPC49074
0.5556 Remote Similarity NPC486103
0.5541 Remote Similarity NPC328567
0.5541 Remote Similarity NPC470826
0.5538 Remote Similarity NPC48863
0.5538 Remote Similarity NPC251981
0.5538 Remote Similarity NPC13745
0.5522 Remote Similarity NPC162093
0.5484 Remote Similarity NPC192810
0.5455 Remote Similarity NPC215833
0.5395 Remote Similarity NPC320671
0.5393 Remote Similarity NPC59516
0.5323 Remote Similarity NPC217854
0.5301 Remote Similarity NPC185307
0.5301 Remote Similarity NPC470950
0.527 Remote Similarity NPC475084
0.5256 Remote Similarity NPC18979
0.5244 Remote Similarity NPC186316
0.5238 Remote Similarity NPC112861
0.5217 Remote Similarity NPC210478
0.5211 Remote Similarity NPC232673
0.5205 Remote Similarity NPC470098
0.5205 Remote Similarity NPC473266
0.52 Remote Similarity NPC470097
0.519 Remote Similarity NPC471063
0.5156 Remote Similarity NPC126409
0.5156 Remote Similarity NPC99572
0.5139 Remote Similarity NPC470236
0.5128 Remote Similarity NPC114119
0.5128 Remote Similarity NPC471415
0.5067 Remote Similarity NPC475096
0.5065 Remote Similarity NPC472713

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC130449 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