Natural Product: NPC289653

Natural Product IDNPC289653
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XKZKQTCECFWKBN-SREVYHEPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5312351
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0003086] Medium-chain fatty acids

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 XKZKQTCECFWKBN-SREVYHEPSA-N
Standard InCHI InChI=1S/C10H18O2/c1-2-3-4-5-6-7-8-9-10(11)12/h6-7H,2-5,8-9H2,1H3,(H,11,12)/b7-6-
SMILES CCCCC/C=CCCC(=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
NPO27883 Bursera simaruba Species Burseraceae Eukaryota Resin n.a. n.a. PMID[1294696]
NPO28935 Ericameria laricifolia Species Asteraceae Eukaryota n.a. Sonoran Desert n.a. PMID[15043404]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. aerial part n.a. PMID[18991207]
NPO27883 Bursera simaruba Species Burseraceae Eukaryota n.a. bark n.a. PMID[19329133]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota essential oil Tibet n.a. PMID[20944522]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota Twigs n.a. n.a. PMID[28541690]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[36552598]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[37746728]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[39013008]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[39395223]
NPO27903 Delphinium denudatum Species Ranunculaceae Eukaryota n.a. root n.a. PMID[9170290]
NPO16079 Cephalaria leucantha Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29411 Streptomyces nigrescens Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27883 Bursera simaruba Species Burseraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29377 Callistemon speciosus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29144 Ormosia fordiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1079 Vachellia karroo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27256 Solanum boerhaavii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29218 Ramalina farinacea Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26549 Polanisia trachysperma Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO862 Podocarpus elatus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28959 Cissus quadrangularis Species Vitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28549 Mentha incana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29307 Loranthus longiflorus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10654 Lindera obtusiloba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26851 Eupatorium rebaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28935 Ericameria laricifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18780 Diplacus aurantiacus Species Phrymaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27903 Delphinium denudatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27562 Coleus wulfenioides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27903 Delphinium denudatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26851 Eupatorium rebaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10654 Lindera obtusiloba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1079 Vachellia karroo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27903 Delphinium denudatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26851 Eupatorium rebaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10654 Lindera obtusiloba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18780 Diplacus aurantiacus Species Phrymaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10654 Lindera obtusiloba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10654 Lindera obtusiloba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29377 Callistemon speciosus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26851 Eupatorium rebaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28959 Cissus quadrangularis Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26549 Polanisia trachysperma Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29218 Ramalina farinacea Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29144 Ormosia fordiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28935 Ericameria laricifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27903 Delphinium denudatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29411 Streptomyces nigrescens Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO862 Podocarpus elatus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29307 Loranthus longiflorus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16079 Cephalaria leucantha Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27883 Bursera simaruba Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1079 Vachellia karroo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18780 Diplacus aurantiacus Species Phrymaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28549 Mentha incana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27256 Solanum boerhaavii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27562 Coleus wulfenioides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10654 Lindera obtusiloba Species Lauraceae 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 NPC289653 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
0.7 Intermediate Similarity NPC424
0.7 Intermediate Similarity NPC36061
0.7 Intermediate Similarity NPC69510
0.7 Intermediate Similarity NPC77272
0.7 Intermediate Similarity NPC290563
0.7 Intermediate Similarity NPC139029
0.7 Intermediate Similarity NPC281972
0.7 Intermediate Similarity NPC92114
0.7 Intermediate Similarity NPC261831
0.7 Intermediate Similarity NPC87564
0.6667 Remote Similarity NPC281245
0.6562 Remote Similarity NPC321062
0.6562 Remote Similarity NPC91495
0.6562 Remote Similarity NPC5413
0.6364 Remote Similarity NPC154245
0.6364 Remote Similarity NPC85813
0.6364 Remote Similarity NPC223697
0.6364 Remote Similarity NPC59051
0.6364 Remote Similarity NPC6095
0.625 Remote Similarity NPC95145
0.625 Remote Similarity NPC325642
0.625 Remote Similarity NPC65174
0.6 Remote Similarity NPC270796
0.5833 Remote Similarity NPC137538
0.5676 Remote Similarity NPC52264
0.5588 Remote Similarity NPC70387
0.5429 Remote Similarity NPC52955
0.5429 Remote Similarity NPC88966
0.5429 Remote Similarity NPC25417
0.5429 Remote Similarity NPC1813
0.5385 Remote Similarity NPC477201
0.5294 Remote Similarity NPC149821
0.5263 Remote Similarity NPC487561
0.5172 Remote Similarity NPC155263
0.5143 Remote Similarity NPC48162
0.5135 Remote Similarity NPC178586
0.5122 Remote Similarity NPC323597
0.5122 Remote Similarity NPC211752
0.5122 Remote Similarity NPC243532
0.5122 Remote Similarity NPC323498
0.5122 Remote Similarity NPC473863

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC289653 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
0.7 Intermediate Similarity NPD3195 Phase 2
0.7 Intermediate Similarity NPD3196 Approved
0.6579 Remote Similarity NPD39 Phase 4
0.6562 Remote Similarity NPD3173 Phase 4
0.6364 Remote Similarity NPD4266 Phase 2
0.6 Remote Similarity NPD5326 Phase 3
0.5676 Remote Similarity NPD3194 Phase 4
0.5429 Remote Similarity NPD3172 Approved
0.5143 Remote Similarity NPD3197 Phase 1

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