Natural Product: NPC204901

Natural Product IDNPC204901
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 2-Methyl-5-{8(Z),11(Z),14-Pentadecatrienyl}Resorcinol
IUPAC Name 2-methyl-5-[(8Z,11Z)-pentadeca-8,11,14-trienyl]benzene-1,3-diol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL470345
PubChem CID 13732723
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000134] Phenols
        • [CHEMONTID:0001286] Benzenediols
          • [CHEMONTID:0000137] Resorcinols

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 UKMBKJYRCZVQFL-AFJQJTPPSA-N
Standard InCHI InChI=1S/C22H32O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-20-17-21(23)19(2)22(24)18-20/h3,5-6,8-9,17-18,23-24H,1,4,7,10-16H2,2H3/b6-5-,9-8-
SMILES C=CC/C=CC/C=CCCCCCCCc1cc(O)c(c(c1)O)C

  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
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Fruits n.a. n.a. PMID[8021657]
NPO13016 Viscaria viscosa Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12510 Aronia arbutifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13070 Clibadium mexiae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1744 Discaria serratifolia Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11636 Ideopsis similis Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO998 Justicia hayatai Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3469 Pteris dactylina Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9180 Pyrostegia venusta Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3580 Rana amurensis Species Ranidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3469 Pteris dactylina Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3580 Rana amurensis Species Ranidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3580 Rana amurensis Species Ranidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13070 Clibadium mexiae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12510 Aronia arbutifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3469 Pteris dactylina Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11636 Ideopsis similis Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13016 Viscaria viscosa Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3580 Rana amurensis Species Ranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO998 Justicia hayatai Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9180 Pyrostegia venusta Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1744 Discaria serratifolia Species Rhamnaceae 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
NPT43 Individual protein Tyrosinase Agaricus bisporus Inhibition = 16.0 % PMID[8021657]

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 NPC204901 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
0.85 High Similarity NPC158253
0.775 Intermediate Similarity NPC232523
0.7381 Intermediate Similarity NPC10588
0.6818 Remote Similarity NPC72947
0.6522 Remote Similarity NPC192
0.6222 Remote Similarity NPC71002
0.6222 Remote Similarity NPC302219
0.6222 Remote Similarity NPC242342
0.6222 Remote Similarity NPC249828
0.6222 Remote Similarity NPC85479
0.5952 Remote Similarity NPC470700
0.5952 Remote Similarity NPC54844
0.5952 Remote Similarity NPC39097
0.5952 Remote Similarity NPC302681
0.5952 Remote Similarity NPC118286
0.5952 Remote Similarity NPC109691
0.5682 Remote Similarity NPC53051
0.5682 Remote Similarity NPC24404
0.5682 Remote Similarity NPC313030
0.5682 Remote Similarity NPC39664
0.5556 Remote Similarity NPC146798
0.5556 Remote Similarity NPC222522
0.5556 Remote Similarity NPC106396
0.5556 Remote Similarity NPC94351
0.5556 Remote Similarity NPC168303
0.5532 Remote Similarity NPC284011
0.551 Remote Similarity NPC210497
0.5319 Remote Similarity NPC488413
0.5319 Remote Similarity NPC166761
0.5319 Remote Similarity NPC488412
0.5294 Remote Similarity NPC112596
0.52 Remote Similarity NPC48730

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC204901 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