Natural Product: NPC140521

Natural Product IDNPC140521
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Oncostemonol B
IUPAC Name [3-[(Z)-16-(3,5-dihydroxyphenyl)hexadec-8-enyl]-5-hydroxyphenyl] acetate
Synonyms oncostemonol B
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL458522
PubChem CID 11755009
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002319] Phenol esters

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 CATXXSJNZBRPTC-IHWYPQMZSA-N
Standard InCHI InChI=1S/C30H42O5/c1-24(31)35-30-21-26(20-29(34)23-30)17-15-13-11-9-7-5-3-2-4-6-8-10-12-14-16-25-18-27(32)22-28(33)19-25/h2-3,18-23,32-34H,4-17H2,1H3/b3-2-
SMILES CC(=O)Oc1cc(CCCCCCC/C=CCCCCCCCc2cc(cc(c2)O)O)cc(c1)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
NPO33313 oncostemon bojerianum Species n.a. n.a. leaves Madagascar rainforest n.a. PMID[12444688]

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
NPT179 Cell line A2780 Homo sapiens IC50 = 10.2 ug.mL-1 PubChem BioAssay data set

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 NPC140521 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
0.9149 High Similarity NPC249836
0.8 Intermediate Similarity NPC127894
0.8 Intermediate Similarity NPC470759
0.7872 Intermediate Similarity NPC78446
0.72 Intermediate Similarity NPC219070
0.68 Remote Similarity NPC114064
0.6667 Remote Similarity NPC15860
0.6458 Remote Similarity NPC53051
0.6458 Remote Similarity NPC24404
0.6458 Remote Similarity NPC313030
0.6383 Remote Similarity NPC470700
0.6383 Remote Similarity NPC54844
0.6383 Remote Similarity NPC39097
0.6383 Remote Similarity NPC302681
0.6383 Remote Similarity NPC118286
0.6383 Remote Similarity NPC109691
0.6327 Remote Similarity NPC146798
0.6327 Remote Similarity NPC222522
0.6327 Remote Similarity NPC106396
0.6327 Remote Similarity NPC94351
0.6327 Remote Similarity NPC168303
0.6275 Remote Similarity NPC71002
0.6275 Remote Similarity NPC302219
0.6275 Remote Similarity NPC242342
0.6275 Remote Similarity NPC249828
0.6275 Remote Similarity NPC85479
0.6122 Remote Similarity NPC39664
0.5962 Remote Similarity NPC10588
0.5862 Remote Similarity NPC470699
0.5849 Remote Similarity NPC72947
0.5818 Remote Similarity NPC471498
0.5818 Remote Similarity NPC471503
0.5686 Remote Similarity NPC168657
0.5472 Remote Similarity NPC166761
0.541 Remote Similarity NPC123559
0.537 Remote Similarity NPC284011
0.5312 Remote Similarity NPC29577
0.5254 Remote Similarity NPC305603
0.5254 Remote Similarity NPC61033
0.5179 Remote Similarity NPC470161
0.5106 Remote Similarity NPC246056
0.5102 Remote Similarity NPC294186
0.5102 Remote Similarity NPC147310
0.5102 Remote Similarity NPC137415
0.5102 Remote Similarity NPC166313
0.5102 Remote Similarity NPC192032
0.5102 Remote Similarity NPC24407
0.5102 Remote Similarity NPC11280
0.5079 Remote Similarity NPC603370

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC140521 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