Natural Product: NPC123928

Natural Product IDNPC123928
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XYNUFQXFKOHZQI-IJKLJMITSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 643640
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000324] Fatty acid esters

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 XYNUFQXFKOHZQI-IJKLJMITSA-N
Standard InCHI InChI=1S/C20H28O7/c1-6-9(2)17(22)26-12-8-20(5,25)14-11(21)7-19(4,24)15(14)16-13(12)10(3)18(23)27-16/h6,10-13,16,21,24-25H,7-8H2,1-5H3/b9-6-/t10-,11-,12-,13+,16-,19+,20-/m0/s1
SMILES C/C=C(/C)C(=O)O[C@H]1C[C@@](C)(C2=C([C@@H]3[C@@H]1[C@H](C)C(=O)O3)[C@@](C)(C[C@@H]2O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   380.18 Volume:   379.793
?
Van der Waals volume.
Dense:   1.001 LogP:   0.724
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.198
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.343
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   18.0
TPSA:   113.29
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.372 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.13 Fsp3:   0.7
MCE-18:   63.235
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.443 Fluc inhibitor:   0.002
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.021
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.355 Promiscuous compounds:   0.722

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.201 MDCK Permeability:   -4.888
Pgp-inhibitor:   0.002 Pgp-substrate:   1.0
PAMPA:   0.999
?
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):   0.005
20% Bioavailability (F20%):   0.998 30% Bioavailability (F30%):   0.998
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.005 MRP1:   0.992
Plasma Protein Binding (PPB):   64.289% Volume Distribution (VD):   -0.074
Fu: 35.561%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.997
OATP1B3 inhibitor:   0.73 BCRP inhibitor:   0.007
BSEP inhibitor:   0.86

ADMET: Metabolism

CYP1A2-inhibitor:   0.22 CYP1A2-substrate:   0.005
CYP2C19-inhibitor:   0.005 CYP2C19-substrate:   0.016
CYP2C9-inhibitor:   0.019 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.176
CYP3A4-inhibitor:   0.113 CYP3A4-substrate:   0.987
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.523
HLM stability:   0.644
?
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):  5.942 Half-life (T1/2):  2.494

ADMET: Toxicity

hERG Blockers:  0.013 hERG Blockers (10um):  0.063
Human Hepatotoxicity (H-HT):  0.727 Drug-induced Liver Injury (DILI):  0.274
AMES Toxicity:  0.701 Rat Oral Acute Toxicity:  0.511
Maximum Recommended Daily Dose:  0.616 Skin Sensitization:  0.999
Carcinogencity:  0.733 Eye Corrosion:  0.059
Eye Irritation:  0.533 Respiratory Toxicity:  0.386
Drug-induced Neurotoxicity:  0.337 Ototoxicity:  0.412
Hematotoxicity:  0.362 Drug-induced Nephrotoxicity:  0.954
Genotoxicity:  0.78 RPMI-8226 Immunitoxicity:  0.186
A549 Cytotoxicity:  0.901 Hek293 Cytotoxicity:  0.263
BCF:   0.424
?
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:   3.077
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.638
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.859
?
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
NPO17790 Trigonostemon reidioides Species Euphorbiaceae Eukaryota roots Rat Buri Province, Thailand 1988-DEC PMID[14987064]
NPO17790 Trigonostemon reidioides Species Euphorbiaceae Eukaryota n.a. root n.a. PMID[16204992]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[16309325]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. Seoul, Korea 2000-Jun PMID[16643034]
NPO8524 Pithecellobium clypearia Species Fabaceae Eukaryota n.a. leaf n.a. PMID[16724853]
NPO8524 Pithecellobium clypearia Species Fabaceae Eukaryota leaves n.a. n.a. PMID[16724853]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[18505286]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[19650637]
NPO16660 Phomopsis archeri Species Valsaceae Eukaryota n.a. mycelium n.a. PMID[21341709]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[23305920]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[25590529]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[32141747]
NPO13180 Jasminum officinale Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[39524716]
NPO2733 Sarcomelicope argyrophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5634 Wallago attu Species Siluridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11020 Streptomyces purpeofuscus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO11831 Achillea collina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18962 Actinobacillus pleuropneumoniae Species Pasteurellaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO13422 Amoora yunnanensis n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO9428 Annona rensoniana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17945 Arachniodes dimorphophylla Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10436 Aristolochia maxima Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17100 Artemisia vachanica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13856 Bergenia purpurascens Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11559 Betula mandshurica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17355 Bischofia trifoliata Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17706 Caragana tibetica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14408 Chrysolina fastuosa Species Chrysomelidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17327 Cotoneaster orbicularis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16374 Crataegus sinaica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18709 Discaria crenata Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11420 Dolichospermum affine Species Aphanizomenonaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO17870 Euphorbia ferganensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16510 Ganoderma australe Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13180 Jasminum officinale Species Oleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21802 Julocroton camporum n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO17175 Lasiocephalus ovatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15667 Ligularia platyglossa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17739 Macrotyloma axillare Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16620 Malus asiatica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12559 Mikania obtusata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11925 Mola mola Species Molidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17244 Montrouziera sphaeroidea Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9523 Nephroma antarcticum Species Nephromataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18027 Oreosolen wattii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12733 Pentapora fascialis Species Bitectiporidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1148 Phalium undulatum Species Cassidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16660 Phomopsis archeri Species Valsaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14698 Phyllospongia madagascarensis Species Thorectidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17637 Pimpinella saxifraga Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8524 Pithecellobium clypearia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15079 Polygala myrtifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16253 Rapanea myricoides Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15814 Rhodiola krylovii Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2733 Sarcomelicope argyrophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2589 Solanum bahamense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26487 Tinospora smilacina Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17029 Tridacna gigas Species Tridacnidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17790 Trigonostemon reidioides Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22469 Tropaeolum speciosum Species Tropaeolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15964 Tropiometra afra Species Tropiometridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6939 Vatica diospyroides Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17706 Caragana tibetica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10436 Aristolochia maxima Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13180 Jasminum officinale Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16620 Malus asiatica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13856 Bergenia purpurascens Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17637 Pimpinella saxifraga Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17244 Montrouziera sphaeroidea Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13856 Bergenia purpurascens Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17706 Caragana tibetica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17637 Pimpinella saxifraga Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13180 Jasminum officinale Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17790 Trigonostemon reidioides Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10436 Aristolochia maxima Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13180 Jasminum officinale Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11925 Mola mola Species Molidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22469 Tropaeolum speciosum Species Tropaeolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8524 Pithecellobium clypearia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16374 Crataegus sinaica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11559 Betula mandshurica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2589 Solanum bahamense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15667 Ligularia platyglossa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2733 Sarcomelicope argyrophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16510 Ganoderma australe Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11420 Dolichospermum affine Species Aphanizomenonaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17327 Cotoneaster orbicularis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12733 Pentapora fascialis Species Bitectiporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18027 Oreosolen wattii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17706 Caragana tibetica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16253 Rapanea myricoides Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15079 Polygala myrtifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9523 Nephroma antarcticum Species Nephromataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15814 Rhodiola krylovii Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16620 Malus asiatica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15964 Tropiometra afra Species Tropiometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16660 Phomopsis archeri Species Valsaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17739 Macrotyloma axillare Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10436 Aristolochia maxima Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18709 Discaria crenata Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13856 Bergenia purpurascens Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13422 Amoora yunnanensis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO13180 Jasminum officinale Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21802 Julocroton camporum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO17029 Tridacna gigas Species Tridacnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1148 Phalium undulatum Species Cassidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17244 Montrouziera sphaeroidea Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17790 Trigonostemon reidioides Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6939 Vatica diospyroides Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11020 Streptomyces purpeofuscus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17355 Bischofia trifoliata Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5634 Wallago attu Species Siluridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14408 Chrysolina fastuosa Species Chrysomelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11831 Achillea collina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17175 Lasiocephalus ovatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12559 Mikania obtusata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18962 Actinobacillus pleuropneumoniae Species Pasteurellaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17945 Arachniodes dimorphophylla Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17100 Artemisia vachanica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14698 Phyllospongia madagascarensis Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26487 Tinospora smilacina Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9428 Annona rensoniana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17870 Euphorbia ferganensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17637 Pimpinella saxifraga Species Apiaceae 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 NPC123928 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
0.5246 Remote Similarity NPC488066
0.5246 Remote Similarity NPC488065

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC123928 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