Natural Product: NPC45438

Natural Product IDNPC45438
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.
 2',4',6-Trihydroxychalcone
IUPAC Name (E)-3-phenyl-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one
Synonyms 2',4',6'-Trihydroxychalcone
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL129371
PubChem CID 6474295
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0003467] Linear 1,3-diarylpropanoids
        • [CHEMONTID:0001630] Chalcones and dihydrochalcones
          • [CHEMONTID:0003472] 2'-Hydroxychalcones

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 LOYXTWZXLWHMBX-VOTSOKGWSA-N
Standard InCHI InChI=1S/C15H12O4/c16-11-8-13(18)15(14(19)9-11)12(17)7-6-10-4-2-1-3-5-10/h1-9,16,18-19H/b7-6+
SMILES Oc1cc(O)c(c(c1)O)C(=O)/C=C/c1ccccc1

  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
NPO31438 Piper lanceaefolium Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[11809068]
NPO31438 Piper lanceaefolium Species Piperaceae Eukaryota n.a. leaf n.a. PMID[11809068]
NPO16668 Lonas annua Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36054828]
NPO16340 Heterostemma brownii Species Apocynaceae Eukaryota Stems n.a. n.a. PMID[9358639]
NPO16262 Bacillus mojavensis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO29601 Abrus fruticulosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16340 Heterostemma brownii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16152 Phlebia radiata Species Meruliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14970 Vitex polygama Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29601 Abrus fruticulosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29601 Abrus fruticulosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16152 Phlebia radiata Species Meruliaceae Eukaryota n.a. n.a. n.a. Database[Title]
NPO9557 Rumex bequaertii Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14970 Vitex polygama Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16262 Bacillus mojavensis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16152 Phlebia radiata Species Meruliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13843 Peronema canescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16340 Heterostemma brownii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29601 Abrus fruticulosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2736 Penstemon diffusus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16668 Lonas annua Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12242 Lactuca tatarica Species Asteraceae 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
NPT183 Individual protein Arachidonate 5-lipoxygenase Rattus norvegicus IC50 = 140000.0 nM DOI[10.1007/s00044-013-0745-7]
NPT1559 Protein family Cyclooxygenase Rattus norvegicus IC50 = 140000.0 nM DOI[10.1007/s00044-013-0745-7]
NPT1476 Protein family Cyclooxygenase Homo sapiens Inhibition = 6.9 % PMID[8254620]
NPT641 Individual protein Sodium/glucose cotransporter 2 Homo sapiens IC50 = 33300.0 nM PMID[28098449]
NPT43 Individual protein Tyrosinase Agaricus bisporus IC50 = 120000.0 nM PMID[17267225]
NPT640 Individual protein Sodium/glucose cotransporter 1 Homo sapiens IC50 = 25400.0 nM PMID[28098449]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Fmax = 87.8 % PMID[9767651]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 250.0 ug.mL-1 PMID[17112640]
NPT2 Others Unspecified n.a. Kd = 4600.0 nM PMID[9767651]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Activity = 14.23 % DOI[10.1007/s00044-011-9640-2]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 9.0 % PMID[8254620]





 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 NPC45438 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
0.7838 Intermediate Similarity NPC73532
0.7 Intermediate Similarity NPC297186
0.6905 Remote Similarity NPC482123
0.6829 Remote Similarity NPC212631
0.6829 Remote Similarity NPC608685
0.6818 Remote Similarity NPC87231
0.587 Remote Similarity NPC188646
0.5778 Remote Similarity NPC64359
0.5714 Remote Similarity NPC19174
0.5714 Remote Similarity NPC115159
0.5676 Remote Similarity NPC71664
0.5676 Remote Similarity NPC608893
0.5556 Remote Similarity NPC13238
0.5532 Remote Similarity NPC308037
0.5417 Remote Similarity NPC56031
0.5417 Remote Similarity NPC129132
0.5306 Remote Similarity NPC150399
0.5122 Remote Similarity NPC17525
0.5111 Remote Similarity NPC224273
0.5098 Remote Similarity NPC98254

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC45438 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