Natural Product: NPC607158

Natural Product IDNPC607158
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 FOSYZKSOJUQLTD-NHPMXQBPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL4285863
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0002875] Tigliane and ingenane diterpenoids

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 FOSYZKSOJUQLTD-NHPMXQBPSA-N
Standard InCHI InChI=1S/C20H28O4/c1-9-6-12-14-13(18(14,4)5)7-11(3)19(17(12)23)8-10(2)16(22)20(19,24)15(9)21/h6,8,11-16,21-22,24H,7H2,1-5H3/t11-,12+,13-,14+,15-,16+,19+,20+/m1/s1
SMILES CC1=C[C@@H]2C(=O)[C@]3(C=C(C)[C@H](O)[C@@]3(O)[C@@H]1O)[C@H](C)C[C@@H]1[C@H]2C1(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
NPO28219 Euphorbia peplus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[21612217]
NPO28219 Euphorbia peplus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[27203291]
NPO54938 Euphorbia virgata Waldst. & Kit. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO61604 Euphorbia verrucosa L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO51080 Euphorbia stricta L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO59767 Euphorbia seguieriana Neck. s.str. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO55616 Euphorbia segetalis L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO51675 Euphorbia prostrata Aiton Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO58983 Euphorbia platyphyllos L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO58319 Euphorbia peplus L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO51668 Euphorbia palustris L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO47465 Euphorbia nutans Lag. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO56450 Euphorbia myrsinites L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO64224 Euphorbia marginata Pursh Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44063 Euphorbia maculata L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO59932 Euphorbia lathyris L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO47729 Euphorbia humifusa Willd. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO50868 Euphorbia exigua L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO61733 Euphorbia dulcis L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO60653 Euphorbia carniolica Jacq. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44604 Euphorbia amygdaloides L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO42915 Euphorbia falcata L. Genus Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28219 Euphorbia peplus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28219 Euphorbia peplus Species Euphorbiaceae 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
NPT25 Cell line MT4 Homo sapiens CC50 > 12000.0 nM PMID[30031972]
NPT28438 Unchecked Unchecked n.a. Ratio CC50/EC50 > 10.0 n.a. PMID[30031972]
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 EC50 > 12000.0 nM PMID[30031972]

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 NPC607158 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
0.8222 Intermediate Similarity NPC261341
0.7255 Intermediate Similarity NPC604048
0.6491 Remote Similarity NPC92898
0.6491 Remote Similarity NPC31883
0.6491 Remote Similarity NPC179891
0.5932 Remote Similarity NPC473488
0.5873 Remote Similarity NPC123855
0.5873 Remote Similarity NPC76550
0.5789 Remote Similarity NPC600642
0.569 Remote Similarity NPC482234
0.569 Remote Similarity NPC303053
0.541 Remote Similarity NPC267734
0.541 Remote Similarity NPC482241
0.5077 Remote Similarity NPC609657

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC607158 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