Natural Product: NPC29989

Natural Product IDNPC29989
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.
 Platyphyllenone
IUPAC Name (E)-1,7-bis(4-hydroxyphenyl)hept-4-en-3-one
Synonyms Platyphyllenone
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL330645
PubChem CID 23786382
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002650] Diarylheptanoids
        • [CHEMONTID:0002651] Linear diarylheptanoids

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 GIKJADRKBZHVCY-DUXPYHPUSA-N
Standard InCHI InChI=1S/C19H20O3/c20-17(10-7-16-8-13-19(22)14-9-16)4-2-1-3-15-5-11-18(21)12-6-15/h2,4-6,8-9,11-14,21-22H,1,3,7,10H2/b4-2+
SMILES C(/C=C/C(=O)CCc1ccc(cc1)O)Cc1ccc(cc1)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
NPO4138.1 Betula platyphylla var. japonica Varieties Betulaceae Eukaryota floral spikes n.a. n.a. PMID[17346076]
NPO15361 Alnus japonica Species Betulaceae Eukaryota bark n.a. n.a. PMID[20045319]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota bark n.a. n.a. PMID[20363129]
NPO4971 Alnus firma Species Betulaceae Eukaryota n.a. n.a. n.a. PMID[21504848]
NPO32876 alnus hirsuta f. sibirica Species Betulaceae Eukaryota n.a. n.a. n.a. PMID[23465614]
NPO15361 Alnus japonica Species Betulaceae Eukaryota n.a. n.a. n.a. PMID[26341132]
NPO4138.1 Betula platyphylla var. japonica Varieties Betulaceae Eukaryota bark n.a. n.a. PMID[9873651]
NPO32876 alnus hirsuta f. sibirica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4138.1 Betula platyphylla var. japonica Varieties Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15361 Alnus japonica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4971 Alnus firma Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4138.1 Betula platyphylla var. japonica Varieties Betulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15361 Alnus japonica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4138.1 Betula platyphylla var. japonica Varieties Betulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15361 Alnus japonica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15361 Alnus japonica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15361 Alnus japonica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4971 Alnus firma Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4138 Betula platyphylla Species Betulaceae 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
NPT31 Individual protein Cyclooxygenase-2 Homo sapiens Inhibition = 98.39 % PMID[31255927]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT71 Cell line HEK293 Homo sapiens EC50 = 45000.0 nM PMID[7853002]
NPT521 Cell line RBL-2H3 Rattus norvegicus Inhibition = 14.4 % DrugMatrix in vitro pharmacology data
NPT521 Cell line RBL-2H3 Rattus norvegicus Inhibition = 18.8 % PMID[19191549]
NPT520 Cell line 3T3-L1 Mus musculus Activity = 39.4 % PMID[19514743]
NPT520 Cell line 3T3-L1 Mus musculus Activity = 82.8 % PMID[20491440]
NPT520 Cell line 3T3-L1 Mus musculus Activity = 101.7 % PMID[17323995]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 30700.0 nM PMID[33422907]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 6900.0 nM PMID[33422907]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 15900.0 nM PMID[33422907]
NPT28833 No target No relevant target n.a. IC50 = 101200.0 nM PMID[33422907]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 34700.0 nM PMID[21504848]
NPT742 Organism Influenza A virus Influenza A virus EC50 = 282800.0 nM PMID[10425121]
NPT2 Others Unspecified n.a. Ratio > 3.0 n.a. PMID[26287401]
NPT471 Organism Trypanosoma brucei brucei Trypanosoma brucei brucei EC50 = 2600.0 nM PMID[15711537]
NPT471 Organism Trypanosoma brucei brucei Trypanosoma brucei brucei EC50 = 1900.0 nM PMID[20056545]
NPT471 Organism Trypanosoma brucei brucei Trypanosoma brucei brucei EC50 = 120.0 nM PMID[10585207]
NPT841 Organism Leishmania major Leishmania major EC50 = 9900.0 nM PMID[11325244]
NPT842 Organism Leishmania mexicana Leishmania mexicana EC50 = 21000.0 nM PMID[19423348]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 58.6 % PMID[26475519]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 90.9 % PMID[26475519]





 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 NPC29989 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
0.8919 High Similarity NPC49529
0.7632 Intermediate Similarity NPC61062
0.75 Intermediate Similarity NPC123228
0.75 Intermediate Similarity NPC123722
0.7073 Intermediate Similarity NPC602856
0.6857 Remote Similarity NPC260000
0.6757 Remote Similarity NPC151405
0.6591 Remote Similarity NPC5018
0.625 Remote Similarity NPC179777
0.6136 Remote Similarity NPC69332
0.6053 Remote Similarity NPC188677
0.575 Remote Similarity NPC113460
0.5745 Remote Similarity NPC95178
0.5625 Remote Similarity NPC277394
0.54 Remote Similarity NPC19290
0.5349 Remote Similarity NPC280347
0.5349 Remote Similarity NPC261573
0.5319 Remote Similarity NPC88141
0.5208 Remote Similarity NPC70843
0.5192 Remote Similarity NPC485985
0.5111 Remote Similarity NPC177576
0.5102 Remote Similarity NPC114298

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC29989 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