Natural Product: NPC113614

Natural Product IDNPC113614
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 DYNISIGUMYFVJW-OCBLOMHFSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 52325853
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

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 DYNISIGUMYFVJW-OCBLOMHFSA-N
Standard InCHI InChI=1S/C20H30O3/c1-12(2)14-10-13-6-7-17-19(3,15(13)11-16(14)21)8-5-9-20(17,4)18(22)23/h6,10,12,15-17,21H,5,7-9,11H2,1-4H3,(H,22,23)/p-1/t15-,16-,17+,19+,20+/m0/s1
SMILES CC(C)C1=CC2=CC[C@@H]3[C@](C)(CCC[C@@]3(C)C(=O)[O-])[C@H]2C[C@@H]1O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   318.22 Volume:   347.268
?
Van der Waals volume.
Dense:   0.916 LogP:   3.584
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.116
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.211
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   17.0
TPSA:   57.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   2.0 Rings:   3.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.803 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.451 Fsp3:   0.75
MCE-18:   56.571
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.644 Fluc inhibitor:   0.016
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.029
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.005
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.489 Promiscuous compounds:   0.081

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.244 MDCK Permeability:   -4.934
Pgp-inhibitor:   0.03 Pgp-substrate:   0.065
PAMPA:   0.948
?
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):   0.002
20% Bioavailability (F20%):   0.108 30% Bioavailability (F30%):   0.039
50% Bioavailability (F50%):   0.508

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.01 MRP1:   0.999
Plasma Protein Binding (PPB):   96.516% Volume Distribution (VD):   -0.297
Fu: 4.114%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.991
OATP1B3 inhibitor:   0.787 BCRP inhibitor:   0.006
BSEP inhibitor:   0.987

ADMET: Metabolism

CYP1A2-inhibitor:   0.013 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.002
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.992 CYP3A4-substrate:   0.958
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.567
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):  3.397 Half-life (T1/2):  1.261

ADMET: Toxicity

hERG Blockers:  0.03 hERG Blockers (10um):  0.069
Human Hepatotoxicity (H-HT):  0.518 Drug-induced Liver Injury (DILI):  0.388
AMES Toxicity:  0.304 Rat Oral Acute Toxicity:  0.524
Maximum Recommended Daily Dose:  0.511 Skin Sensitization:  0.985
Carcinogencity:  0.706 Eye Corrosion:  0.429
Eye Irritation:  0.77 Respiratory Toxicity:  0.88
Drug-induced Neurotoxicity:  0.078 Ototoxicity:  0.5
Hematotoxicity:  0.581 Drug-induced Nephrotoxicity:  0.912
Genotoxicity:  0.596 RPMI-8226 Immunitoxicity:  0.055
A549 Cytotoxicity:  0.134 Hek293 Cytotoxicity:  0.077
BCF:   0.943
?
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:   3.633
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.231
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.529
?
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
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. DOI[10.1023/A:1025674116183]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota seeds Mengha, Yunnan Province, China 1991-Aug PMID[11277741]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota seeds n.a. n.a. PMID[11325233]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota Seeds n.a. n.a. PMID[11430002]
NPO3261 Aplysina archeri Species Aplysinidae Eukaryota n.a. n.a. n.a. PMID[1324982]
NPO6457 Pinus strobus Species Pinaceae Eukaryota n.a. heartwood n.a. PMID[13465274]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[1536925]
NPO14054 Penicillium janczewskii Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[16180822]
NPO422 Euphorbia cornigera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[17512094]
NPO422 Euphorbia cornigera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[19376614]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[2089121]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. seed n.a. PMID[24225786]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[3379416]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[3443857]
NPO2697 Monodora tenuifolia Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[3509958]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[3760882]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[3841557]
NPO11747 Ocimum tenuiflorum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39073007]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[7288443]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[8133299]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. xylem n.a. PMID[8133299]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[8691212]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[9461664]
NPO22470 Corynebacterium glutamicum Species Corynebacteriaceae Bacteria n.a. n.a. n.a. Database[Article]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22470 Corynebacterium glutamicum Species Corynebacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO6457 Pinus strobus Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24089 Alcea rosea Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4274 Alcyonium utinomii Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5584 Aldisa sanguinea Species Dorididae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4564 Anguilla japonica Species Anguillidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3554 Aonidiella aurantii Species Diaspididae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3261 Aplysina archeri Species Aplysinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18993 Araiostegiella perdurans Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5975 Aspergillus carneus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25760 Aspergillus striatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1242 Balanops australiana Species Balanopaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6231 Cortinarius odoratus Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7449 Eleutherobia albiflora Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7007 Eucalyptus jenseni Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO849 Euonymus tingens Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO422 Euphorbia cornigera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15487 Gymnopus confluens Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2250 Hylocomium splendens Species Hylocomiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO295 Kokoona reflexa Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7760 Macrolepiota neomastoidea Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3956 Maesa ramentacea Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1390 Melolontha melolontha Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2408 Millettia laurentii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2697 Monodora tenuifolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2993 Nototodarus sloanii Species Ommastrephidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11747 Ocimum tenuiflorum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14054 Penicillium janczewskii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8058 Pluchea odorata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1489 Pseudoplexaura flagellosa Species Plexauridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7606 Salacia lehmbachii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4949 Salvia yosgadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3743 Sideritis brevibracteata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5261 Sideroxylon cubense Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3408 Viguiera decurrens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17292 Asparagus racemosus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20619 Ougeinia dalbergioides n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO19502 Squamopappus skutchii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4564 Anguilla japonica Species Anguillidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2408 Millettia laurentii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4564 Anguilla japonica Species Anguillidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24089 Alcea rosea Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24089 Alcea rosea Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO422 Euphorbia cornigera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO849 Euonymus tingens Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11747 Ocimum tenuiflorum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2697 Monodora tenuifolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17292 Asparagus racemosus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14054 Penicillium janczewskii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2993 Nototodarus sloanii Species Ommastrephidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6231 Cortinarius odoratus Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3956 Maesa ramentacea Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7606 Salacia lehmbachii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7007 Eucalyptus jenseni Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5261 Sideroxylon cubense Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2250 Hylocomium splendens Species Hylocomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO295 Kokoona reflexa Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3261 Aplysina archeri Species Aplysinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5975 Aspergillus carneus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18993 Araiostegiella perdurans Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2408 Millettia laurentii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15487 Gymnopus confluens Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4949 Salvia yosgadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3743 Sideritis brevibracteata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7449 Eleutherobia albiflora Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8058 Pluchea odorata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1390 Melolontha melolontha Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25760 Aspergillus striatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5584 Aldisa sanguinea Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20619 Ougeinia dalbergioides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1242 Balanops australiana Species Balanopaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24089 Alcea rosea Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3554 Aonidiella aurantii Species Diaspididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4564 Anguilla japonica Species Anguillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7760 Macrolepiota neomastoidea Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19502 Squamopappus skutchii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6457 Pinus strobus Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4274 Alcyonium utinomii Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3408 Viguiera decurrens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1489 Pseudoplexaura flagellosa Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21014 Brucea antidysenterica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22470 Corynebacterium glutamicum Species Corynebacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO21165 Phagnalon atlanticum Species Asteraceae 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 NPC113614 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
0.6604 Remote Similarity NPC309399
0.5172 Remote Similarity NPC279666

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC113614 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