Natural Product: NPC608162

Natural Product IDNPC608162
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 LSTDYDRCKUBPDI-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL137354
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 LSTDYDRCKUBPDI-UHFFFAOYSA-N
Standard InCHI InChI=1S/C18H36O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-20-18(2)19/h3-17H2,1-2H3
SMILES CCCCCCCCCCCCCCCCOC(C)=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
NPO47617 Echinops polyceras Genus Asteraceae Eukaryota n.a. n.a. n.a. PMID[37241978]
NPO21084 Nymphaea caerulea Species Nymphaeaceae Eukaryota n.a. n.a. n.a. PMID[37894493]
NPO21084 Nymphaea caerulea Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO45204 Flavobacterium aRK10267 Genus Flavobacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO21084 Nymphaea caerulea Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21084 Nymphaea caerulea Species Nymphaeaceae 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
NPO21084 Nymphaea caerulea n.a. n.a. 0.87 n.a. n.a. % PMID[37894493]
NPO21084 Nymphaea caerulea n.a. n.a. 0.94 n.a. n.a. % PMID[37894493]
NPO21084 Nymphaea caerulea n.a. n.a. 1.27 n.a. n.a. % PMID[37894493]
NPO21084 Nymphaea caerulea n.a. n.a. 0.83 n.a. n.a. % PMID[37894493]
NPO21084 Nymphaea caerulea n.a. n.a. 1.39 n.a. n.a. % PMID[37894493]
NPO21084 Nymphaea caerulea n.a. n.a. 1.03 n.a. n.a. % PMID[37894493]
NPO47617 Echinops polyceras Hydro distillation Inflorescences 0.24 n.a. n.a. % PMID[37241978]
NPO47617 Echinops polyceras Hydro distillation Inflorescences 0.57 n.a. n.a. % PMID[37241978]
NPO47617 Echinops polyceras Hydro distillation Inflorescences 0.18 n.a. n.a. % PMID[37241978]

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
NPT232 Individual protein Cannabinoid CB1 receptor Homo sapiens Inhibition = 10.0 % PMID[14521402]
NPT1260 Individual protein Anandamide amidohydrolase Rattus norvegicus Inhibition < 0.0 % PMID[14521402]
NPT1287 Individual protein Cannabinoid CB2 receptor Homo sapiens Inhibition = 9.0 % PMID[14521402]
NPT4445 Individual protein N-acylsphingosine-amidohydrolase Homo sapiens Inhibition = 68.0 % PMID[14521402]

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
- Rattus norvegicus LD50 > 5000.0 mg/kg ToxVal
- Oryctolagus cuniculus LD50 > 5000.0 mg/kg ToxVal

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 NPC608162 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 NPC86545
1.0 High Similarity NPC286498
1.0 High Similarity NPC223374
1.0 High Similarity NPC196442
1.0 High Similarity NPC301398
1.0 High Similarity NPC609004
0.95 High Similarity NPC40965
0.8095 Intermediate Similarity NPC248233
0.72 Intermediate Similarity NPC80641
0.7143 Intermediate Similarity NPC3693
0.7143 Intermediate Similarity NPC476549
0.7083 Intermediate Similarity NPC322892
0.6923 Remote Similarity NPC149299
0.6923 Remote Similarity NPC223675
0.6923 Remote Similarity NPC68577
0.68 Remote Similarity NPC154396
0.68 Remote Similarity NPC155872
0.6538 Remote Similarity NPC80396
0.6429 Remote Similarity NPC207815
0.6296 Remote Similarity NPC14608
0.6 Remote Similarity NPC147054
0.5926 Remote Similarity NPC154642
0.5926 Remote Similarity NPC603612
0.5769 Remote Similarity NPC223249
0.5769 Remote Similarity NPC12904
0.56 Remote Similarity NPC159398
0.5556 Remote Similarity NPC286695
0.5417 Remote Similarity NPC140229
0.5217 Remote Similarity NPC99700
0.52 Remote Similarity NPC166804
0.5185 Remote Similarity NPC476550

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC608162 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
0.5455 Remote Similarity NPD631 Phase 4
0.5294 Remote Similarity NPD630 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