Natural Product: NPC203020

Natural Product IDNPC203020
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Eugenol 4-O-Beta-D-(6-O-Galloyl)Glucopyranoside
IUPAC Name [(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-(2-methoxy-4-prop-2-enylphenoxy)oxan-2-yl]methyl 3,4,5-trihydroxybenzoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL495649
PubChem CID 44583693
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

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 MXIGGCCKAQLWPD-OXUVVOBNSA-N
Standard InCHI InChI=1S/C23H26O11/c1-3-4-11-5-6-15(16(7-11)31-2)33-23-21(29)20(28)19(27)17(34-23)10-32-22(30)12-8-13(24)18(26)14(25)9-12/h3,5-9,17,19-21,23-29H,1,4,10H2,2H3/t17-,19-,20+,21-,23-/m1/s1
SMILES C=CCc1ccc(c(c1)OC)O[C@@H]1O[C@H](COC(=O)c2cc(O)c(c(c2)O)O)[C@H]([C@@H]([C@H]1O)O)O

  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
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[10869193]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota Berries n.a. n.a. PMID[18314960]
NPO15339 Artemisia afra Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[34771106]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38256897]
NPO15339 Artemisia afra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8843 Epipactis palustris Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15050 Rumex obtusifolius Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15050 Rumex obtusifolius Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15050 Rumex obtusifolius Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15339 Artemisia afra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2373 Popillia japonica Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15050 Rumex obtusifolius Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8843 Epipactis palustris Species Orchidaceae 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

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 NPC203020 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
0.7429 Intermediate Similarity NPC160780
0.6957 Remote Similarity NPC166277
0.6857 Remote Similarity NPC472859
0.6528 Remote Similarity NPC25389
0.6528 Remote Similarity NPC1913
0.6429 Remote Similarity NPC484156
0.6184 Remote Similarity NPC327032
0.6184 Remote Similarity NPC197708
0.6164 Remote Similarity NPC111785
0.6029 Remote Similarity NPC270849
0.6026 Remote Similarity NPC102851
0.5976 Remote Similarity NPC33298
0.5949 Remote Similarity NPC5786
0.5875 Remote Similarity NPC472860
0.5875 Remote Similarity NPC289346
0.5875 Remote Similarity NPC484816
0.5854 Remote Similarity NPC479375
0.5789 Remote Similarity NPC119125
0.5769 Remote Similarity NPC311803
0.5632 Remote Similarity NPC479369
0.5595 Remote Similarity NPC658
0.5588 Remote Similarity NPC92117
0.5507 Remote Similarity NPC9912
0.5352 Remote Similarity NPC479769
0.5333 Remote Similarity NPC479768
0.5312 Remote Similarity NPC67629
0.5312 Remote Similarity NPC79736
0.5287 Remote Similarity NPC105591
0.527 Remote Similarity NPC65833
0.5258 Remote Similarity NPC267549
0.5256 Remote Similarity NPC140151
0.5238 Remote Similarity NPC10205
0.5213 Remote Similarity NPC486577
0.5208 Remote Similarity NPC316539
0.519 Remote Similarity NPC215811
0.5185 Remote Similarity NPC36130
0.5176 Remote Similarity NPC471405
0.5139 Remote Similarity NPC472024
0.5116 Remote Similarity NPC157816
0.506 Remote Similarity NPC137813

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC203020 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