Natural Product: NPC108113

Natural Product IDNPC108113
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Eugenitol
IUPAC Name 5,7-dihydroxy-2,6-dimethylchromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3039487
PubChem CID 5036604
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0000144] Chromones

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 HMAUJNAGOIPKDG-UHFFFAOYSA-N
Standard InCHI InChI=1S/C11H10O4/c1-5-3-8(13)10-9(15-5)4-7(12)6(2)11(10)14/h3-4,12,14H,1-2H3
SMILES Cc1cc(=O)c2c(cc(c(C)c2O)O)o1

  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
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[1402962]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Flower Buds n.a. n.a. PMID[26977531]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota Fruits n.a. n.a. PMID[31301930]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[34770801]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[36985392]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37836118]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[39684253]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[39699537]
NPO6783 Avrainvillea rawsonii Species Udoteaceae Eukaryota n.a. n.a. n.a. PMID[7964790]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[8904847]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1032 Piper attenuatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5834 Pellicularia sasakii n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO1456 Bersama abyssinica Species Melianthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2395 Siphonaria australis Species Siphonariidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO1032 Piper attenuatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1934 Strychnos triplinervia Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7626 Damnacanthus major Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1934 Strychnos triplinervia Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO577 Lactifluus subvellereus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1032 Piper attenuatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7626 Damnacanthus major Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6072 Andinobates bombetes Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12409 Artemisia jacutica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5834 Pellicularia sasakii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO173 Aconitum sajanense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2395 Siphonaria australis Species Siphonariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6041 Lithocolletis coryli n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO9456 Rubus sanctus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6783 Avrainvillea rawsonii Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15735 Galeocerdo arcticus Species Carcharhinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1456 Bersama abyssinica Species Melianthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7383 Puccinia lagenophorae Species Pucciniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1032 Piper attenuatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1934 Strychnos triplinervia Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4504 Cassia jahnii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9718 Cyphelium chrysocephalum Species Caliciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7626 Damnacanthus major Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO577 Lactifluus subvellereus Species Russulaceae 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
NPT72 Individual protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 88.28 % PMID[23571415]
NPT73 Individual protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 77.61 % PMID[23571415]

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 NPC108113 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
0.6458 Remote Similarity NPC602367
0.6279 Remote Similarity NPC270369
0.6136 Remote Similarity NPC55925
0.587 Remote Similarity NPC55557
0.587 Remote Similarity NPC125920
0.5714 Remote Similarity NPC608958
0.5682 Remote Similarity NPC229613
0.5536 Remote Similarity NPC10097
0.5435 Remote Similarity NPC93756
0.5294 Remote Similarity NPC201395
0.5217 Remote Similarity NPC242712
0.5192 Remote Similarity NPC60667
0.5102 Remote Similarity NPC30647
0.5102 Remote Similarity NPC31872
0.5102 Remote Similarity NPC61871

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC108113 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