Natural Product: NPC532272

Natural Product IDNPC532272
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 OCTADECA-6,9-DIENEDIOIC ACID
IUPAC Name octadeca-6,9-dienedioic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 UANZCTRZDQLPDX-UHFFFAOYSA-N
Standard InCHI InChI=1S/C18H30O4/c19-17(20)15-13-11-9-7-5-3-1-2-4-6-8-10-12-14-16-18(21)22/h1-2,5,7H,3-4,6,8-16H2,(H,19,20)(H,21,22)
SMILES O=C(O)CCCCC=CCC=CCCCCCCCC(=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
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0014-5793(03)00033-4]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/ac991142i]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1034/j.1399-3054.2003.00030.x]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1046/j.1365-3040.2001.00686.x]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1074/jbc.274.1.397]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1074/jbc.M302362200]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1074/jbc.M314195200]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1074/jbc.M411109200]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1104/pp.103.022368]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[10952545]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. leaf n.a. PMID[10952545]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[11005203]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[12637544]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[12805618]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[14745019]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15280363]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15820655]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15834012]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota aerial parts n.a. n.a. PMID[15844959]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[1684022]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[17611796]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[18057039]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[18235971]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[18318836]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. leaf n.a. PMID[19521717]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[21193570]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[21194489]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[21395888]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[21800258]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[23370715]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[23950498]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. root n.a. PMID[24163311]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[24285094]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. root n.a. PMID[25457500]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. root n.a. PMID[27363486]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[27432888]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[8278506]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. root n.a. Database[MetaboLights]
NPO19866 Arabidopsis thaliana Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO19866 Arabidopsis thaliana Species Brassicaceae 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 NPC532272 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
0.8667 High Similarity NPC52955
0.8667 High Similarity NPC88966
0.8667 High Similarity NPC25417
0.8667 High Similarity NPC1813
0.8667 High Similarity NPC154245
0.8667 High Similarity NPC85813
0.8667 High Similarity NPC223697
0.8667 High Similarity NPC6095
0.8333 Intermediate Similarity NPC321062
0.8333 Intermediate Similarity NPC5413
0.8333 Intermediate Similarity NPC70387
0.8 Intermediate Similarity NPC149821
0.8 Intermediate Similarity NPC207292
0.7931 Intermediate Similarity NPC281245
0.7667 Intermediate Similarity NPC424
0.7667 Intermediate Similarity NPC36061
0.7667 Intermediate Similarity NPC69510
0.7667 Intermediate Similarity NPC77272
0.7667 Intermediate Similarity NPC290563
0.7667 Intermediate Similarity NPC139029
0.7667 Intermediate Similarity NPC281972
0.7667 Intermediate Similarity NPC92114
0.7667 Intermediate Similarity NPC261831
0.7667 Intermediate Similarity NPC87564
0.75 Intermediate Similarity NPC59051
0.7188 Intermediate Similarity NPC91495
0.6875 Remote Similarity NPC95145
0.6875 Remote Similarity NPC325642
0.6875 Remote Similarity NPC65174
0.6667 Remote Similarity NPC180534
0.6667 Remote Similarity NPC611531
0.6296 Remote Similarity NPC214610
0.6296 Remote Similarity NPC118968
0.6296 Remote Similarity NPC183424
0.6296 Remote Similarity NPC294085
0.625 Remote Similarity NPC34416
0.625 Remote Similarity NPC117572
0.6216 Remote Similarity NPC606120
0.5926 Remote Similarity NPC268826
0.5897 Remote Similarity NPC477201
0.5789 Remote Similarity NPC225929
0.5714 Remote Similarity NPC320642
0.5714 Remote Similarity NPC329550
0.5667 Remote Similarity NPC171736
0.5667 Remote Similarity NPC301585
0.5667 Remote Similarity NPC261080
0.5667 Remote Similarity NPC132565
0.5667 Remote Similarity NPC209970
0.5667 Remote Similarity NPC216630
0.5667 Remote Similarity NPC201844
0.5667 Remote Similarity NPC301696
0.5667 Remote Similarity NPC196924
0.5667 Remote Similarity NPC307783
0.5667 Remote Similarity NPC154186
0.5667 Remote Similarity NPC149184
0.5667 Remote Similarity NPC279026
0.5667 Remote Similarity NPC113928
0.5667 Remote Similarity NPC14227
0.561 Remote Similarity NPC323597
0.561 Remote Similarity NPC211752
0.561 Remote Similarity NPC243532
0.561 Remote Similarity NPC323498
0.5581 Remote Similarity NPC323045
0.5581 Remote Similarity NPC317881
0.5556 Remote Similarity NPC174560
0.5556 Remote Similarity NPC125312
0.55 Remote Similarity NPC106851
0.55 Remote Similarity NPC282788
0.55 Remote Similarity NPC274927
0.5484 Remote Similarity NPC604140
0.5476 Remote Similarity NPC317583
0.5476 Remote Similarity NPC68343
0.5476 Remote Similarity NPC328089
0.5455 Remote Similarity NPC322461
0.5366 Remote Similarity NPC179764
0.5357 Remote Similarity NPC134782
0.5333 Remote Similarity NPC155263
0.5333 Remote Similarity NPC605544
0.5333 Remote Similarity NPC607260
0.5278 Remote Similarity NPC294548
0.5278 Remote Similarity NPC48162
0.5278 Remote Similarity NPC224227
0.5238 Remote Similarity NPC251042
0.5238 Remote Similarity NPC255863
0.5238 Remote Similarity NPC473863
0.5238 Remote Similarity NPC174447
0.5238 Remote Similarity NPC136164
0.5238 Remote Similarity NPC122521
0.5238 Remote Similarity NPC245947
0.5217 Remote Similarity NPC329249
0.5217 Remote Similarity NPC92558
0.5152 Remote Similarity NPC55023
0.5152 Remote Similarity NPC21844
0.5116 Remote Similarity NPC318420
0.5116 Remote Similarity NPC323477
0.5116 Remote Similarity NPC326268

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC532272 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
0.8667 High Similarity NPD3172 Approved
0.8667 High Similarity NPD4266 Phase 2
0.8333 Intermediate Similarity NPD3173 Phase 4
0.7667 Intermediate Similarity NPD3195 Phase 2
0.7667 Intermediate Similarity NPD3196 Approved
0.7105 Intermediate Similarity NPD39 Phase 4
0.6667 Remote Similarity NPD622 Pre-clinical
0.6296 Remote Similarity NPD9655 Phase 4
0.625 Remote Similarity NPD4222 Phase 3
0.6216 Remote Similarity NPD3194 Phase 4
0.5667 Remote Similarity NPD2270 Pre-clinical
0.5667 Remote Similarity NPD633 Phase 3
0.5667 Remote Similarity NPD9448 Phase 2

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