Natural Product: NPC609084

Natural Product IDNPC609084
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XXSOVMSTJJYBOO-QWHCGFSZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL190851
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002719] Lupin alkaloids
        • [CHEMONTID:0002722] Cytisine and derivatives

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 XXSOVMSTJJYBOO-QWHCGFSZSA-N
Standard InCHI InChI=1S/C15H20N2O2/c1-11(18)5-6-16-8-12-7-13(10-16)14-3-2-4-15(19)17(14)9-12/h2-4,12-13H,5-10H2,1H3/t12-,13+/m0/s1
SMILES CC(=O)CCN1C[C@@H]2C[C@H](C1)c1cccc(=O)n1C2

  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
NPO1347 Maackia amurensis Species Fabaceae Eukaryota n.a. stem n.a. PMID[19252325]
NPO1347 Maackia amurensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24252334]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1347 Maackia amurensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO56123 Echinosophora koreensis Nakai Genus Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO58431 Maackia hupehensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1347 Maackia amurensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1347 Maackia amurensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16775 Thermopsis lanceolata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1347 Maackia amurensis Species Fabaceae 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
NPT414 Individual protein Neuronal acetylcholine receptor protein alpha-7 subunit Rattus norvegicus Ki = 1240.0 nM PMID[19548687]
NPT414 Individual protein Neuronal acetylcholine receptor protein alpha-7 subunit Rattus norvegicus Rmax > 100.0 % PMID[16033252]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT29138 Protein complex Neuronal acetylcholine receptor; alpha3/beta4 Homo sapiens Rmax = 11.0 % PMID[16033252]
NPT28922 Protein complex Neuronal acetylcholine receptor; alpha4/beta2 Rattus norvegicus Ki = 8.7 nM PMID[19548687]
NPT28922 Protein complex Neuronal acetylcholine receptor; alpha4/beta2 Rattus norvegicus Ki = 3.2 nM PMID[19548687]
NPT29611 Protein complex Neuronal acetylcholine receptor; alpha4/beta2 Homo sapiens Rmax = 3.0 % PMID[16033252]

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 NPC609084 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
0.8 Intermediate Similarity NPC604550
0.6909 Remote Similarity NPC214125
0.6909 Remote Similarity NPC320667
0.5152 Remote Similarity NPC78058
0.5152 Remote Similarity NPC135639

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC609084 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