Natural Product: NPC609497

Natural Product IDNPC609497
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 JAOZFCHZESUBKS-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL186433
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 JAOZFCHZESUBKS-UHFFFAOYSA-N
Standard InCHI InChI=1S/C14H10O6/c1-19-14-8(16)5-9-10(12(14)18)11(17)6-3-2-4-7(15)13(6)20-9/h2-5,15-16,18H,1H3
SMILES COc1c(O)cc2oc3c(O)cccc3c(=O)c2c1O

  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
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[15678383]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[16045947]
NPO2737 Calophyllum caledonicum Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. stem n.a. PMID[20188156]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. Malaysian n.a. PMID[7506311]
NPO14730 Bonnetia dinizii Species Bonnetiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO62420 Calophyllum bracteatum Genus Calophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2737 Calophyllum caledonicum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO47332 Tovomita pyrifolium Planch et Triana Genus Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2737 Calophyllum caledonicum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2737 Calophyllum caledonicum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14730 Bonnetia dinizii Species Bonnetiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2804 Calophyllum inophyllum Species Calophyllaceae 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
NPT261 Individual protein Monoamine oxidase A Homo sapiens IC50 = 2700.0 nM PMID[15482934]

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

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 NPC609497 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
0.6604 Remote Similarity NPC29231
0.6538 Remote Similarity NPC603670
0.6538 Remote Similarity NPC611763
0.6346 Remote Similarity NPC209278
0.6346 Remote Similarity NPC206238
0.6346 Remote Similarity NPC39007
0.6275 Remote Similarity NPC251110
0.6275 Remote Similarity NPC272721
0.6226 Remote Similarity NPC11158
0.6111 Remote Similarity NPC246116
0.5882 Remote Similarity NPC59551
0.5849 Remote Similarity NPC603894
0.5769 Remote Similarity NPC607638
0.5714 Remote Similarity NPC610063
0.56 Remote Similarity NPC606736
0.5556 Remote Similarity NPC152951
0.5556 Remote Similarity NPC92564
0.5283 Remote Similarity NPC55557

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC609497 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