Natural Product: NPC608938

Natural Product IDNPC608938
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XSIFPSYPOVKYCO-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1868953
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 XSIFPSYPOVKYCO-UHFFFAOYSA-N
Standard InCHI InChI=1S/C11H14O2/c1-2-3-9-13-11(12)10-7-5-4-6-8-10/h4-8H,2-3,9H2,1H3
SMILES CCCCOC(=O)c1ccccc1

  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
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota Bark n.a. n.a. PMID[33151073]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[34684884]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[36364159]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[36401242]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO59131 Streptomyces sp. strain GWS-BW-H5 Genus Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota n.a. n.a. Database[FooDB]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3689 Cinnamomum verum Species Lauraceae 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
NPO3689 Cinnamomum verum Oil Leaves 0.05 n.a. n.a. % PMID[36364159]
NPO3689 Cinnamomum verum Oil Leaves 0.06 n.a. n.a. % PMID[36364159]
NPO3689 Cinnamomum verum Oil Leaves 0.04 n.a. n.a. % PMID[36364159]
NPO3689 Cinnamomum verum Oil Leaves 0.02 n.a. n.a. % PMID[36364159]

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
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens Potency n.a. 50118.7 nM PubChem BioAssay data set
NPT46 Individual protein Thyroid hormone receptor beta-1 Homo sapiens Potency n.a. 5011.9 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT521 Cell line RBL-2H3 Rattus norvegicus Inhibition n.a. n.a. % PMID[27324979]

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 = 735.0 mg/kg ToxVal
- Mus musculus LD50 = 3450.0 mg/kg ToxVal
- Oryctolagus cuniculus LD50 = 4000.0 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 NPC608938 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
0.8387 Intermediate Similarity NPC78701
0.7931 Intermediate Similarity NPC92754
0.7419 Intermediate Similarity NPC146351
0.7097 Intermediate Similarity NPC10251
0.6897 Remote Similarity NPC249912
0.6571 Remote Similarity NPC35448
0.6286 Remote Similarity NPC93084
0.6286 Remote Similarity NPC251854
0.6286 Remote Similarity NPC601045
0.625 Remote Similarity NPC225060
0.6176 Remote Similarity NPC604461
0.575 Remote Similarity NPC604244
0.5676 Remote Similarity NPC156124
0.5641 Remote Similarity NPC607895
0.5588 Remote Similarity NPC486840
0.5429 Remote Similarity NPC469574
0.5385 Remote Similarity NPC603245
0.5333 Remote Similarity NPC130398
0.5278 Remote Similarity NPC42211
0.5238 Remote Similarity NPC196246
0.5135 Remote Similarity NPC94298
0.5128 Remote Similarity NPC270699
0.5116 Remote Similarity NPC260818

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC608938 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
0.7097 Intermediate Similarity NPD2182 Pre-clinical
0.6571 Remote Similarity NPD553 Phase 4

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