Natural Product: NPC608264

Natural Product IDNPC608264
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.
 KIEVPIBIYKKJRJ-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL342343
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 KIEVPIBIYKKJRJ-UHFFFAOYSA-N
Standard InCHI InChI=1S/C16H12O3/c1-18-12-6-4-5-11(9-12)16-10-14(17)13-7-2-3-8-15(13)19-16/h2-10H,1H3
SMILES COc1cccc(-c2cc(=O)c3ccccc3o2)c1

  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
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[21049973]
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19812 Pimelea simplex Species Thymelaeaceae 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
NPT1602 Individual protein Neuraminidase Influenza A virus (A/Puerto Rico/8/1934(H1N1)) IC50 = 10760.0 nM PMID[31744778]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT113 Cell line RAW264.7 Mus musculus Activity = 101.59 % PMID[28408221]
NPT113 Cell line RAW264.7 Mus musculus Inhibition = 15.7 % PMID[28408221]
NPT616 Cell line MDCK Canis lupus familiaris CC50 = 263400.0 nM PMID[31744778]
NPT28438 Unchecked Unchecked n.a. logKi = 0.38 n.a. PMID[18158201]
NPT28438 Unchecked Unchecked n.a. Ratio CC50/EC50 = 20955.0 n.a. PMID[31744778]
NPT742 Organism Influenza A virus Influenza A virus EC50 = 12.57 nM PMID[31744778]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT29 Organism Rattus norvegicus Rattus norvegicus Protection = 48.0 % PMID[8523407]





 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 NPC608264 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
0.78 Intermediate Similarity NPC599976
0.7755 Intermediate Similarity NPC2771
0.7755 Intermediate Similarity NPC483772
0.7647 Intermediate Similarity NPC77955
0.7059 Intermediate Similarity NPC603094
0.6667 Remote Similarity NPC483774
0.6667 Remote Similarity NPC32298
0.6481 Remote Similarity NPC608669
0.6429 Remote Similarity NPC480173
0.6333 Remote Similarity NPC130015
0.6226 Remote Similarity NPC607644
0.6111 Remote Similarity NPC284424
0.6066 Remote Similarity NPC602126
0.5789 Remote Similarity NPC113089
0.5741 Remote Similarity NPC22783
0.5741 Remote Similarity NPC196034
0.5636 Remote Similarity NPC604293
0.5455 Remote Similarity NPC41721
0.5254 Remote Similarity NPC125887
0.5172 Remote Similarity NPC333230
0.5167 Remote Similarity NPC250266
0.5167 Remote Similarity NPC266597
0.5167 Remote Similarity NPC604085
0.5167 Remote Similarity NPC605146
0.5161 Remote Similarity NPC604422
0.5088 Remote Similarity NPC193805

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC608264 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