Natural Product: NPC239568

Natural Product IDNPC239568
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 MMPBHSBVPREJQC-GCJOFGIHSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5316301
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins and derivatives
        • [CHEMONTID:0001743] Coumarin 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 MMPBHSBVPREJQC-GCJOFGIHSA-N
Standard InCHI InChI=1S/C15H16O9/c16-5-8-10(19)11(20)12(21)15(22-8)24-14-7(17)3-1-6-2-4-9(18)23-13(6)14/h1-4,8,10-12,15-17,19-21H,5H2/t8-,10-,11+,12-,15+/m1/s1
SMILES c1cc(c(c2c1ccc(=O)o2)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   340.08 Volume:   308.257
?
Van der Waals volume.
Dense:   1.103 LogP:   -1.132
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.104
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.766
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   18.0
TPSA:   149.82
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.429 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.793 Fsp3:   0.4
MCE-18:   66.048
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.755 Fluc inhibitor:   0.111
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.969
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.171
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.332 Promiscuous compounds:   0.302

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.334 MDCK Permeability:   -5.139
Pgp-inhibitor:   0.0 Pgp-substrate:   0.008
PAMPA:   0.988
?
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):   0.013
20% Bioavailability (F20%):   0.404 30% Bioavailability (F30%):   0.898
50% Bioavailability (F50%):   0.72

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.016 MRP1:   0.719
Plasma Protein Binding (PPB):   71.675% Volume Distribution (VD):   -0.349
Fu: 30.287%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.997
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.004

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.014 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.015 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.006
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.056
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.066
HLM stability:   0.407
?
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):  2.92 Half-life (T1/2):  3.141

ADMET: Toxicity

hERG Blockers:  0.018 hERG Blockers (10um):  0.068
Human Hepatotoxicity (H-HT):  0.609 Drug-induced Liver Injury (DILI):  0.861
AMES Toxicity:  0.864 Rat Oral Acute Toxicity:  0.043
Maximum Recommended Daily Dose:  0.047 Skin Sensitization:  0.983
Carcinogencity:  0.338 Eye Corrosion:  0.002
Eye Irritation:  0.63 Respiratory Toxicity:  0.027
Drug-induced Neurotoxicity:  0.014 Ototoxicity:  0.787
Hematotoxicity:  0.299 Drug-induced Nephrotoxicity:  0.475
Genotoxicity:  0.863 RPMI-8226 Immunitoxicity:  0.075
A549 Cytotoxicity:  0.065 Hek293 Cytotoxicity:  0.143
BCF:   0.212
?
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:   2.53
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.958
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.184
?
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
NPO520 Euphorbia lathyris Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[12542364]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. root n.a. PMID[15997133]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. root n.a. PMID[16141313]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. callus n.a. PMID[22368856]
NPO19803 Oxytropis ochrocephala Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22494026]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[23611151]
NPO14508 Aconitum heterophyllum Species Ranunculaceae Eukaryota n.a. root n.a. PMID[24156713]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota roots n.a. n.a. PMID[24931277]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[26562066]
NPO520 Euphorbia lathyris Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[30817151]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[32997496]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[34770847]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. root n.a. Database[Article]
NPO19303 Auricularia auricula-judae Species Auriculariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19479 Trametes feei Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18393 Eugenia sandwicensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19803 Oxytropis ochrocephala Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14508 Aconitum heterophyllum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16416 Serratula strangulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17135 Mikania goyazensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO520 Euphorbia lathyris Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18816 Lindera glauca Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7960 Cicer arietinum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7960 Cicer arietinum Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7960 Cicer arietinum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19303 Auricularia auricula-judae Species Auriculariaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7960 Cicer arietinum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO18816 Lindera glauca Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14508 Aconitum heterophyllum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO520 Euphorbia lathyris Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7960 Cicer arietinum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19303 Auricularia auricula-judae Species Auriculariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7960 Cicer arietinum Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO520 Euphorbia lathyris Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16416 Serratula strangulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7960 Cicer arietinum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14508 Aconitum heterophyllum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18816 Lindera glauca Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18393 Eugenia sandwicensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19303 Auricularia auricula-judae Species Auriculariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7960 Cicer arietinum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO520 Euphorbia lathyris Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO520 Euphorbia lathyris Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10882 Acer caudatifolium Species Aceraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15287 Vernonia megapotamica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17558 Cynoglossum formosanum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7037 Rumohra adiantiformis Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18393 Eugenia sandwicensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO520 Euphorbia lathyris Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17135 Mikania goyazensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19303 Auricularia auricula-judae Species Auriculariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14508 Aconitum heterophyllum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19406 Chrysanthemum leptophyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19479 Trametes feei Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14015 Salacia cordata Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10705 Marshallia graminifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12376 Baccharis macraei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19803 Oxytropis ochrocephala Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7067 Stellera chamaejasme Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18816 Lindera glauca Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16416 Serratula strangulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18247 Globicephala melas Species Delphinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13505 Grateloupia livida Species Halymeniaceae 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 NPC239568 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
0.746 Intermediate Similarity NPC213197
0.6875 Remote Similarity NPC212670
0.6875 Remote Similarity NPC206264
0.6667 Remote Similarity NPC52740
0.6462 Remote Similarity NPC41844
0.625 Remote Similarity NPC103409
0.6061 Remote Similarity NPC96294
0.5714 Remote Similarity NPC92830
0.5714 Remote Similarity NPC94777
0.5616 Remote Similarity NPC474434
0.5541 Remote Similarity NPC73703
0.5479 Remote Similarity NPC611276
0.5467 Remote Similarity NPC471416
0.5333 Remote Similarity NPC85624
0.5294 Remote Similarity NPC604162
0.5185 Remote Similarity NPC215060
0.5128 Remote Similarity NPC282987
0.5128 Remote Similarity NPC8573
0.506 Remote Similarity NPC476352

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC239568 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
0.6875 Remote Similarity NPD1653 Approved

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