Natural Product: NPC256452

Natural Product IDNPC256452
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Piperchabamide A
IUPAC Name 1-(3-phenylpropanoyl)-2,3-dihydropyridin-6-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL270831
PubChem CID 44453778
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000089] Pyridines and derivatives
        • [CHEMONTID:0002224] Hydropyridines

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 GUEXEBNXDLFLBU-UHFFFAOYSA-N
Standard InCHI InChI=1S/C14H15NO2/c16-13-8-4-5-11-15(13)14(17)10-9-12-6-2-1-3-7-12/h1-4,6-8H,5,9-11H2
SMILES O=C(N1CCC=CC1=O)CCc1ccccc1

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO10274 Pothomorphe peltata n.a. n.a. n.a. n.a. Dominican Republic n.a. PMID[11430019]
NPO6544 Carpesium longifolium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[14695795]
NPO3968 Dracontium loretense Species Araceae Eukaryota n.a. n.a. n.a. PMID[19341262]
NPO3968 Dracontium loretense Species Araceae Eukaryota corms Iquitos, Peru 2005-MAY PMID[19341262]
NPO10666 Verbesina virginica Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[19485332]
NPO4251 Photorhabdus luminescens Species Morganellaceae Bacteria n.a. n.a. n.a. PMID[22909174]
NPO12125 Pseudomonas stutzeri Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[23149469]
NPO6648 Piper retrofractum Species Piperaceae Eukaryota Fruits n.a. n.a. PMID[23506561]
NPO6648 Piper retrofractum Species Piperaceae Eukaryota leaves n.a. n.a. PMID[25127165]
NPO4251 Photorhabdus luminescens Species Morganellaceae Bacteria n.a. n.a. n.a. PMID[25988621]
NPO13059 Abies webbiana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8639 Agaricus xanthodermus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10459 Brickellia longifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12488 Bupleurum rigidum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6544 Carpesium longifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11511 Cochlearia officinalis Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9950 Coelogyne nitida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6880 Crocus corsicus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO876 Didymosphaeria enalia Species Didymosphaeriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11137 Dichotomanthes tristaniicarpa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4251 Photorhabdus luminescens Species Morganellaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO10666 Verbesina virginica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27487 Silene banksia Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7158 Schefflera venulosa Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12125 Pseudomonas stutzeri Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO10274 Pothomorphe peltata n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO2840 Podocarpus minor Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6648 Piper retrofractum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3968 Dracontium loretense Species Araceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23642 Penicillium tardum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO230 Palisota barteri Species Commelinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7536 Mycoplasma mycoides Species Mycoplasmataceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO9166 Monascus rubropunctatus Species Fellodistomidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2393 Matsumurella chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO43 Leifsonia aquatica Species Microbacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO964 Homalium laurifolium Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12383 Frullania brasiliensis Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6428 Euphorbia wangii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6544 Carpesium longifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7158 Schefflera venulosa Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7158 Schefflera venulosa Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6544 Carpesium longifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12383 Frullania brasiliensis Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27487 Silene banksia Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6648 Piper retrofractum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6428 Euphorbia wangii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4251 Photorhabdus luminescens Species Morganellaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12383 Frullania brasiliensis Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12125 Pseudomonas stutzeri Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2393 Matsumurella chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6544 Carpesium longifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23642 Penicillium tardum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12488 Bupleurum rigidum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7158 Schefflera venulosa Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO876 Didymosphaeria enalia Species Didymosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9166 Monascus rubropunctatus Species Fellodistomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10274 Pothomorphe peltata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO3968 Dracontium loretense Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10459 Brickellia longifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8639 Agaricus xanthodermus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2840 Podocarpus minor Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO964 Homalium laurifolium Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9950 Coelogyne nitida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO230 Palisota barteri Species Commelinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11511 Cochlearia officinalis Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO43 Leifsonia aquatica Species Microbacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6880 Crocus corsicus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6648 Piper retrofractum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13059 Abies webbiana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10666 Verbesina virginica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27487 Silene banksia Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11137 Dichotomanthes tristaniicarpa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7536 Mycoplasma mycoides Species Mycoplasmataceae Bacteria 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
NPT993 Cell line Hepatocyte Mus musculus Inhibition = 29.0 % PMID[19775895]
NPT993 Cell line Hepatocyte Mus musculus Inhibition = 32.0 % PMID[19775895]
NPT993 Cell line Hepatocyte Mus musculus Inhibition = 70.0 % PMID[19775895]
NPT520 Cell line 3T3-L1 Mus musculus Activity = 10.2 % PMID[18477507]
NPT520 Cell line 3T3-L1 Mus musculus Activity = 8.9 % PMID[18477507]
NPT520 Cell line 3T3-L1 Mus musculus Activity = 14.0 % PMID[18477507]
NPT520 Cell line 3T3-L1 Mus musculus Activity = -5.0 % PMID[18477507]
NPT1460 Cell line L929 Mus musculus Inhibition = 71.0 % PMID[19775895]
NPT1460 Cell line L929 Mus musculus Inhibition = 35.0 % PMID[19775895]
NPT1460 Cell line L929 Mus musculus Inhibition = 23.0 % PMID[19775895]
NPT1460 Cell line L929 Mus musculus Inhibition = 90.0 % PMID[19775895]
NPT1460 Cell line L929 Mus musculus IC50 = 13000.0 nM PMID[19775895]
NPT993 Cell line Hepatocyte Mus musculus IC50 = 14000.0 nM PMID[19775895]
NPT2 Others Unspecified n.a. Inhibition = 3.0 % PMID[19775895]
NPT2 Others Unspecified n.a. Inhibition = 27.0 % PMID[19775895]
NPT2 Others Unspecified n.a. Inhibition = 98.0 % PMID[19775895]
NPT2 Others Unspecified n.a. Inhibition = 100.0 % PMID[19775895]
NPT2 Others Unspecified n.a. IC50 = 20000.0 nM PMID[19775895]

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 NPC256452 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
0.6304 Remote Similarity NPC609996
0.5472 Remote Similarity NPC169742
0.5238 Remote Similarity NPC151405
0.5116 Remote Similarity NPC477703

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC256452 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