Natural Product: NPC38041

Natural Product IDNPC38041
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (-)-Pinoresinol 4-O-Beta-D-Glucopyranoside
IUPAC Name (2S,3R,4S,5S,6R)-2-[4-[(3R,3aS,6R,6aS)-3-(4-hydroxy-3-methoxyphenyl)-1,3,3a,4,6,6a-hexahydrofuro[3,4-c]furan-6-yl]-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL573336
PubChem CID 11168362
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 QLJNETOQFQXTLI-JKUDBEEXSA-N
Standard InCHI InChI=1S/C26H32O11/c1-32-18-7-12(3-5-16(18)28)24-14-10-35-25(15(14)11-34-24)13-4-6-17(19(8-13)33-2)36-26-23(31)22(30)21(29)20(9-27)37-26/h3-8,14-15,20-31H,9-11H2,1-2H3/t14-,15-,20-,21-,22+,23-,24+,25+,26-/m1/s1
SMILES OC[C@H]1O[C@@H](Oc2ccc(cc2OC)[C@@H]2OC[C@@H]3[C@H]2CO[C@H]3c2ccc(c(c2)OC)O)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   520.19 Volume:   496.344
?
Van der Waals volume.
Dense:   1.048 LogP:   -0.263
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.347
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.214
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   27.0
TPSA:   156.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   11.0
H-Bond Donor:   5.0 Rings:   5.0
Heavy Atoms:   11.0

MedChem Properties

QED Drug-Likeness Score:   0.349 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.464 Fsp3:   0.538
MCE-18:   106.5
?
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:   0.546 Fluc inhibitor:   0.354
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.13
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.102
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.118 Promiscuous compounds:   0.203

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.093 MDCK Permeability:   -5.242
Pgp-inhibitor:   0.001 Pgp-substrate:   0.336
PAMPA:   0.14
?
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):   0.035
20% Bioavailability (F20%):   0.058 30% Bioavailability (F30%):   0.929
50% Bioavailability (F50%):   0.921

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.033 MRP1:   0.353
Plasma Protein Binding (PPB):   70.42% Volume Distribution (VD):   -0.305
Fu: 29.656%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.207
BSEP inhibitor:   0.002

ADMET: Metabolism

CYP1A2-inhibitor:   0.83 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.994 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.585 CYP3A4-substrate:   0.255
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.106
HLM stability:   0.004
?
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):  3.247 Half-life (T1/2):  4.396

ADMET: Toxicity

hERG Blockers:  0.024 hERG Blockers (10um):  0.1
Human Hepatotoxicity (H-HT):  0.867 Drug-induced Liver Injury (DILI):  0.98
AMES Toxicity:  0.963 Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.025 Skin Sensitization:  0.998
Carcinogencity:  0.283 Eye Corrosion:  0.0
Eye Irritation:  0.313 Respiratory Toxicity:  0.016
Drug-induced Neurotoxicity:  0.022 Ototoxicity:  0.902
Hematotoxicity:  0.373 Drug-induced Nephrotoxicity:  0.827
Genotoxicity:  0.854 RPMI-8226 Immunitoxicity:  0.18
A549 Cytotoxicity:  0.437 Hek293 Cytotoxicity:  0.285
BCF:   0.687
?
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:   3.245
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.826
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.903
?
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
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1002/ejlt.201100207]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1007/s11746-010-1670-2]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.foodcont.2016.09.002]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.jfca.2010.08.006]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2010.06.003]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2010.12.007]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2016.02.010]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2018.06.017]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.12691/jfnr-2-5-9]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.5219/332]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[10336650]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[15217296]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[15679315]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[16252923]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[16499319]
NPO13478 Scorzonera pseudodivaricata Species Asteraceae Eukaryota n.a. Mongolian n.a. PMID[17542634]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[17624889]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. sand-covered bottom at -10 to -15 m at Hurghada, on the Egyptian Red Sea coast 2003-JUN PMID[18298079]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18611049]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18768384]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[18942825]
NPO12339 Daphne feddei Species Thymelaeaceae Eukaryota stem bark Kunming, Yunnan Province, China n.a. PMID[18986199]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[19476340]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[19628108]
NPO4001 Berberis koreana Species Berberidaceae Eukaryota n.a. n.a. n.a. PMID[19813743]
NPO12855 Alkanna cappadocica Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[20405844]
NPO4001 Berberis koreana Species Berberidaceae Eukaryota trunk Jeju island, Korea 2005-Dec PMID[21420296]
NPO4001 Berberis koreana Species Berberidaceae Eukaryota n.a. n.a. n.a. PMID[21420296]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[21912858]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[22111577]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. flower n.a. PMID[22166201]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[22538527]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[23790907]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[24811150]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[24948953]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[25564559]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[28274428]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[29154541]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[30236698]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[30384263]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds Guangzhou, China PMID[30563201]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[30583361]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[30599958]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[31159190]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[31861466]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36613240]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[37631012]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[38354824]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[39199155]
NPO12855 Alkanna cappadocica Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13030 Artemisia dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1834 Atalantia racemosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21830 Buddleja cordata Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12196 Buphane fischeri n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO5930 Crambe tatarica Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12700 Diospyros eriantha Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9313 Fritillaria ningguoensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO252 Hoffmannia strigillosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24390.1 Juniperus rigida var. conferta Varieties Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11848 Lemaireocereus griseus Species Cactaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2398 Millettia erythrocalyx Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9934 Mycobacterium leprae Species Mycobacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13671 Ononis vaginalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14578 Prorocentrum micans Species Prorocentraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8928 Pteris semipinnata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13585 Rapanea lancifolia Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13478 Scorzonera pseudodivaricata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10783 Syncarpia hillii Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6360 Xenoacremonium recifei Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23754 Solanum aculeatissimum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12339 Daphne feddei Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21329 Ilyonectria destructans Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10211 Pajanelia multijuga n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2398 Millettia erythrocalyx Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2398 Millettia erythrocalyx Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23754 Solanum aculeatissimum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9313 Fritillaria ningguoensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24390.1 Juniperus rigida var. conferta Varieties Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1834 Atalantia racemosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9313 Fritillaria ningguoensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8928 Pteris semipinnata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9934 Mycobacterium leprae Species Mycobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO21329 Ilyonectria destructans Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10783 Syncarpia hillii Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13585 Rapanea lancifolia Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13030 Artemisia dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21830 Buddleja cordata Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12855 Alkanna cappadocica Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12700 Diospyros eriantha Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6360 Xenoacremonium recifei Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11848 Lemaireocereus griseus Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24390.1 Juniperus rigida var. conferta Varieties Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9313 Fritillaria ningguoensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23754 Solanum aculeatissimum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13478 Scorzonera pseudodivaricata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO252 Hoffmannia strigillosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14578 Prorocentrum micans Species Prorocentraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10211 Pajanelia multijuga n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO5930 Crambe tatarica Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12196 Buphane fischeri n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO1834 Atalantia racemosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2398 Millettia erythrocalyx Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12339 Daphne feddei Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13671 Ononis vaginalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4001 Berberis koreana Species Berberidaceae 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
NPT113 Cell line RAW264.7 Mus musculus IC50 > 300000.0 nM PMID[18986199]
NPT34 Cell line BV-2 Mus musculus IC50 = 144330.0 nM PMID[21420296]
NPT81 Cell line A549 Homo sapiens IC50 > 30000.0 nM PMID[21420296]
NPT147 Cell line SK-MEL-2 Homo sapiens IC50 > 30000.0 nM PMID[21420296]
NPT574 Cell line XF498 Homo sapiens IC50 = 25370.0 nM PMID[21420296]
NPT146 Cell line SK-OV-3 Homo sapiens IC50 > 30000.0 nM PMID[21420296]
NPT848 Cell line N9 Homo sapiens IC50 > 100000.0 nM PMID[28073678]
NPT4727 Cell line C3H 10T1/2 Mus musculus FC = 1.3 n.a. PMID[34407463]

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 NPC38041 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 NPC22150
0.8636 High Similarity NPC286235
0.8548 High Similarity NPC276753
0.8548 High Similarity NPC205796
0.8507 High Similarity NPC279298
0.8413 Intermediate Similarity NPC246947
0.8358 Intermediate Similarity NPC51328
0.8358 Intermediate Similarity NPC55158
0.8333 Intermediate Similarity NPC478055
0.75 Intermediate Similarity NPC112861
0.7465 Intermediate Similarity NPC18979
0.7368 Intermediate Similarity NPC185307
0.7368 Intermediate Similarity NPC470950
0.7 Intermediate Similarity NPC216129
0.7 Intermediate Similarity NPC130449
0.7 Intermediate Similarity NPC248132
0.6914 Remote Similarity NPC11411
0.6835 Remote Similarity NPC129417
0.6835 Remote Similarity NPC470235
0.6716 Remote Similarity NPC95392
0.6716 Remote Similarity NPC84013
0.6716 Remote Similarity NPC55715
0.6716 Remote Similarity NPC35877
0.6667 Remote Similarity NPC27843
0.6667 Remote Similarity NPC7171
0.6625 Remote Similarity NPC283995
0.6463 Remote Similarity NPC486097
0.6456 Remote Similarity NPC186316
0.6447 Remote Similarity NPC471063
0.6296 Remote Similarity NPC46092
0.625 Remote Similarity NPC486098
0.625 Remote Similarity NPC39657
0.6216 Remote Similarity NPC486102
0.617 Remote Similarity NPC475224
0.6092 Remote Similarity NPC149873
0.6 Remote Similarity NPC469586
0.6 Remote Similarity NPC486104
0.5974 Remote Similarity NPC114119
0.5974 Remote Similarity NPC471415
0.5942 Remote Similarity NPC88640
0.5942 Remote Similarity NPC101153
0.5942 Remote Similarity NPC193666
0.5942 Remote Similarity NPC123526
0.5942 Remote Similarity NPC608725
0.5904 Remote Similarity NPC163635
0.589 Remote Similarity NPC486107
0.5854 Remote Similarity NPC299706
0.5854 Remote Similarity NPC115466
0.5854 Remote Similarity NPC61604
0.5823 Remote Similarity NPC486106
0.5806 Remote Similarity NPC115207
0.5806 Remote Similarity NPC158079
0.5806 Remote Similarity NPC228346
0.5806 Remote Similarity NPC40432
0.5806 Remote Similarity NPC161557
0.5714 Remote Similarity NPC486099
0.5658 Remote Similarity NPC470097
0.5647 Remote Similarity NPC486549
0.5647 Remote Similarity NPC486548
0.5625 Remote Similarity NPC84181
0.5588 Remote Similarity NPC166040
0.5581 Remote Similarity NPC486546
0.5556 Remote Similarity NPC7191
0.5556 Remote Similarity NPC486100
0.5556 Remote Similarity NPC486101
0.5556 Remote Similarity NPC486105
0.5479 Remote Similarity NPC302378
0.5476 Remote Similarity NPC486545
0.5467 Remote Similarity NPC604095
0.5455 Remote Similarity NPC126409
0.5455 Remote Similarity NPC99572
0.5432 Remote Similarity NPC486109
0.5432 Remote Similarity NPC486108
0.5417 Remote Similarity NPC248355
0.5352 Remote Similarity NPC472024
0.5352 Remote Similarity NPC270849
0.5352 Remote Similarity NPC205054
0.5342 Remote Similarity NPC55040
0.5309 Remote Similarity NPC324492
0.5309 Remote Similarity NPC317053
0.5301 Remote Similarity NPC605526
0.5294 Remote Similarity NPC245615
0.5278 Remote Similarity NPC26653
0.5278 Remote Similarity NPC80600
0.5263 Remote Similarity NPC470098
0.5263 Remote Similarity NPC473266
0.5238 Remote Similarity NPC44452
0.5238 Remote Similarity NPC236934
0.5233 Remote Similarity NPC486103
0.5217 Remote Similarity NPC221090
0.5217 Remote Similarity NPC478955
0.5217 Remote Similarity NPC478700
0.5181 Remote Similarity NPC472711
0.5132 Remote Similarity NPC278961
0.5132 Remote Similarity NPC113680
0.5128 Remote Similarity NPC212770
0.5122 Remote Similarity NPC483499
0.5068 Remote Similarity NPC210015
0.5065 Remote Similarity NPC37468
0.5065 Remote Similarity NPC265154
0.5062 Remote Similarity NPC158635
0.5062 Remote Similarity NPC191046
0.5062 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 NPC38041 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