Natural Product: NPC607196

Natural Product IDNPC607196
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.
 IODGQWWTJYDCLN-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL487196
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002592] 7-O-methylated flavonoids

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 IODGQWWTJYDCLN-UHFFFAOYSA-N
Standard InCHI InChI=1S/C17H14O7/c1-22-16-13(20)12-10(19)7-11(8-3-5-9(18)6-4-8)24-15(12)14(21)17(16)23-2/h3-7,18,20-21H,1-2H3
SMILES COc1c(OC)c(O)c2c(=O)cc(-c3ccc(O)cc3)oc2c1O

  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
NPO25377 Ocimum gratissimum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29192771]
NPO25377 Ocimum gratissimum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37939623]
NPO25377 Ocimum gratissimum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38641286]
NPO25377 Ocimum gratissimum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[6114991]
NPO24693 Prunus cerasus Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[9917288]
NPO59796 Ocimum tenuiflorum L. Genus Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO42914 Ocimum selloi Benth. Genus Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO51842 Ocimum americanum cv.Sacred Genus Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO48476 Nepeta spp. Genus Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23427 Becium grandiflorum n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO61257 Agastache barberi Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25377 Ocimum gratissimum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24693 Prunus cerasus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24693 Prunus cerasus Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO24693 Prunus cerasus Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO24693 Prunus cerasus Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO24693 Prunus cerasus Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO24693 Prunus cerasus Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO25377 Ocimum gratissimum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24693 Prunus cerasus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23427 Becium grandiflorum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25377 Ocimum gratissimum Species Lamiaceae 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
NPT29665 Single protein Quinone reductase 1 Homo sapiens CD > 20.0 ug ml-1 PMID[16038568]

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 NPC607196 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
0.7692 Intermediate Similarity NPC280339
0.717 Intermediate Similarity NPC163780
0.6981 Remote Similarity NPC231018
0.6981 Remote Similarity NPC120163
0.6481 Remote Similarity NPC71334
0.6481 Remote Similarity NPC241498
0.6481 Remote Similarity NPC275836
0.6182 Remote Similarity NPC301323
0.6071 Remote Similarity NPC198826
0.6071 Remote Similarity NPC234133
0.5965 Remote Similarity NPC159275
0.5965 Remote Similarity NPC78913
0.5962 Remote Similarity NPC216318
0.5893 Remote Similarity NPC187498
0.5789 Remote Similarity NPC250266
0.5789 Remote Similarity NPC604462
0.5741 Remote Similarity NPC296197
0.5714 Remote Similarity NPC226973
0.569 Remote Similarity NPC201136
0.569 Remote Similarity NPC25270
0.5667 Remote Similarity NPC610914
0.5614 Remote Similarity NPC239128
0.5614 Remote Similarity NPC47815
0.5517 Remote Similarity NPC176775
0.5517 Remote Similarity NPC145379
0.5517 Remote Similarity NPC101830
0.541 Remote Similarity NPC227325
0.541 Remote Similarity NPC47781
0.5352 Remote Similarity NPC93337
0.5278 Remote Similarity NPC105025
0.5273 Remote Similarity NPC50898
0.5254 Remote Similarity NPC100887
0.5254 Remote Similarity NPC105242
0.5179 Remote Similarity NPC45873
0.5179 Remote Similarity NPC130230
0.5179 Remote Similarity NPC222713
0.5172 Remote Similarity NPC293183
0.5172 Remote Similarity NPC250822
0.5172 Remote Similarity NPC75279
0.5172 Remote Similarity NPC602963
0.5085 Remote Similarity NPC274327
0.5085 Remote Similarity NPC266960
0.5085 Remote Similarity NPC156222
0.5082 Remote Similarity NPC69394
0.5082 Remote Similarity NPC83508

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC607196 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