Natural Product: NPC9050

Natural Product IDNPC9050
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YILKZADAWNUTTB-QLWRWLBVSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 13491909
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002750] Corynanthean-type alkaloids

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 YILKZADAWNUTTB-QLWRWLBVSA-N
Standard InCHI InChI=1S/C22H26N2O4/c1-4-13-11-24-8-7-21-16-9-14(25)5-6-17(16)23(2)22(21)18(24)10-15(13)20(21,12-28-22)19(26)27-3/h4-6,9,15,18,25H,7-8,10-12H2,1-3H3/b13-4-/t15-,18-,20-,21-,22+/m0/s1
SMILES C/C=C1/CN2CC[C@]34c5cc(ccc5N(C)[C@]54[C@@H]2C[C@@H]1[C@@]3(CO5)C(=O)OC)O

  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
NPO19809 Streptomyces roseoviolaceus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO2065 Eriostemon deserti Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14210 Brugmansia arborea Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6602 Vinca major Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3078 Gentiana pyrenaica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13490 Diospyros tricolor Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12216 Gynura elliptica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13601 Relicina connivens Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25628.1 Abrus pulchellus subsp. cantoniensis Subspecies Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21627 Bambusa chungii Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1409 Drymonia macrophylla Species Gesneriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25599 Gloxinia erinoides Species Gesneriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11862 Ostrinia nubilalis Species Crambidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14590 Ruta oreojasme Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12216 Gynura elliptica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14590 Ruta oreojasme Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14590 Ruta oreojasme Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25628.1 Abrus pulchellus subsp. cantoniensis Subspecies Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14210 Brugmansia arborea Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14590 Ruta oreojasme Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13490 Diospyros tricolor Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21627 Bambusa chungii Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2065 Eriostemon deserti Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1409 Drymonia macrophylla Species Gesneriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25599 Gloxinia erinoides Species Gesneriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6602 Vinca major Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12216 Gynura elliptica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11862 Ostrinia nubilalis Species Crambidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3078 Gentiana pyrenaica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19809 Streptomyces roseoviolaceus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25628.1 Abrus pulchellus subsp. cantoniensis Subspecies Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13601 Relicina connivens Species Parmeliaceae 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
NPT1167 Individual protein Delta opioid receptor Mus musculus IC50 = 19952.62 nM PMID[33326237]
NPT1811 Individual protein Dopamine D5 receptor Homo sapiens Inhibition n.a. n.a. % PMID[33326237]
NPT272 Individual protein Kappa opioid receptor Homo sapiens Inhibition n.a. n.a. % PMID[33326237]
NPT271 Individual protein Delta opioid receptor Homo sapiens Ki = 10400.0 nM PMID[33326237]
NPT272 Individual protein Kappa opioid receptor Homo sapiens Activity = 35.0 % PMID[33326237]
NPT145 Individual protein Mu opioid receptor Homo sapiens Ki = 300.0 nM PMID[33326237]
NPT1168 Individual protein Mu opioid receptor Mus musculus Activity = 62.0 % PMID[33326237]
NPT145 Individual protein Mu opioid receptor Homo sapiens Ki = 316.23 nM PMID[33326237]
NPT1167 Individual protein Delta opioid receptor Mus musculus IC50 = 20300.0 nM PMID[33326237]
NPT295 Individual protein Serotonin transporter Homo sapiens Inhibition < 60.0 % PMID[33326237]
NPT1811 Individual protein Dopamine D5 receptor Homo sapiens Ki > 10000.0 nM PMID[33326237]
NPT271 Individual protein Delta opioid receptor Homo sapiens Ki = 10000.0 nM PMID[33326237]
NPT1167 Individual protein Delta opioid receptor Mus musculus Activity = 50.0 % PMID[33326237]
NPT272 Individual protein Kappa opioid receptor Homo sapiens Ki = 1680.0 nM PMID[33326237]
NPT1168 Individual protein Mu opioid receptor Mus musculus IC50 = 2600.0 nM PMID[33326237]
NPT271 Individual protein Delta opioid receptor Homo sapiens Inhibition n.a. n.a. % PMID[33326237]
NPT145 Individual protein Mu opioid receptor Homo sapiens Inhibition n.a. n.a. % PMID[33326237]
NPT272 Individual protein Kappa opioid receptor Homo sapiens Ki = 1584.89 nM PMID[33326237]
NPT1168 Individual protein Mu opioid receptor Mus musculus IC50 = 2511.89 nM PMID[33326237]
NPT272 Individual protein Kappa opioid receptor Homo sapiens Ki = 1584.89 nM PMID[36827198]
NPT1168 Individual protein Mu opioid receptor Mus musculus EC50 = 2511.89 nM PMID[36827198]
NPT145 Individual protein Mu opioid receptor Homo sapiens Ki = 316.23 nM PMID[36827198]
NPT272 Individual protein Kappa opioid receptor Homo sapiens Ki = 1670.0 nM PMID[36827198]
NPT1168 Individual protein Mu opioid receptor Mus musculus Emax = 62.0 % PMID[36827198]
NPT145 Individual protein Mu opioid receptor Homo sapiens Ki = 300.0 nM PMID[36827198]
NPT1168 Individual protein Mu opioid receptor Mus musculus EC50 = 2600.0 nM PMID[36827198]
NPT987 Individual protein Histamine H3 receptor Homo sapiens Inhibition < 60.0 % PMID[33326237]
NPT3603 Individual protein Kappa opioid receptor Mus musculus IC50 = 73.0 nM PMID[33326237]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT28438 Unchecked Unchecked n.a. Ratio Ki = 5.6 n.a. PMID[36827198]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[33326237]





 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 NPC9050 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
1.0 High Similarity NPC603966
0.7671 Intermediate Similarity NPC604417

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC9050 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