Natural Product: NPC113628

Natural Product IDNPC113628
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ONCLDGVLVUPPIN-BHPKHCPMSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 14475468
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

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 ONCLDGVLVUPPIN-BHPKHCPMSA-N
Standard InCHI InChI=1S/C15H22O/c1-10-13-5-4-12(9-16)15(13)7-6-11(8-15)14(10,2)3/h9,11-13H,1,4-8H2,2-3H3/t11-,12-,13-,15+/m1/s1
SMILES C=C1[C@H]2CC[C@H](C=O)[C@]32CC[C@H](C3)C1(C)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
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[14510614]
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. stem n.a. PMID[21443171]
NPO24110 Lippia alba Species Verbenaceae Eukaryota n.a. n.a. n.a. PMID[37631258]
NPO24110 Lippia alba Species Verbenaceae Eukaryota n.a. n.a. n.a. PMID[38897034]
NPO24684 Eremanthus crotonoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23737 Allium turcomanicum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19677 Cephalaria transsylvanica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25027 Cynoglossum creticum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2617 Dracocephalum multicaule Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21168 Erylus lendenfeldi Species Geodiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24110 Lippia alba Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22352 Lysimachia heterogenea Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23423 Phellopterus littoralis n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO12731 Porodaedalea pini Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24716 Pulvinula constellatio Species Pyronemataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22021 Teucrium spinosum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23283 Triptilion benaventei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14889 Vachellia farnesiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23283 Triptilion benaventei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22021 Teucrium spinosum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22352 Lysimachia heterogenea Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23737 Allium turcomanicum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24110 Lippia alba Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12731 Porodaedalea pini Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24684 Eremanthus crotonoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2617 Dracocephalum multicaule Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14889 Vachellia farnesiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23423 Phellopterus littoralis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24716 Pulvinula constellatio Species Pyronemataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19677 Cephalaria transsylvanica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25027 Cynoglossum creticum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21168 Erylus lendenfeldi Species Geodiidae 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 NPC113628 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
0.6053 Remote Similarity NPC147524

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC113628 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