Natural Product: NPC192066

Natural Product IDNPC192066
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
(2R)-2-Hydroxy-N-[(2S,3R,4E,8E)-3-Hydroxy-9-Methyl-1-[(2R,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-(Hydroxymethyl)Oxan-2-Yl]Oxyoctadeca-4,8-Dien-2-Yl]Hexadecanamide
IUPAC Name (2R)-2-hydroxy-N-[(2S,3R,4E,8E)-3-hydroxy-9-methyl-1-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoctadeca-4,8-dien-2-yl]hexadecanamide
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL538217
PubChem CID 11498616
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000257] Sphingolipids
        • [CHEMONTID:0003258] Glycosphingolipids
          • [CHEMONTID:0001419] Neutral glycosphingolipids
            • [CHEMONTID:0001428] Simple glycosylceramides
              • [CHEMONTID:0004305] Glycosyl-N-acylsphingosines

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 YBSQGNFRWZKFMJ-FRJHFHMPSA-N
Standard InCHI InChI=1S/C41H77NO9/c1-4-6-8-10-12-13-14-15-16-18-20-24-29-35(45)40(49)42-33(31-50-41-39(48)38(47)37(46)36(30-43)51-41)34(44)28-25-21-23-27-32(3)26-22-19-17-11-9-7-5-2/h25,27-28,33-39,41,43-48H,4-24,26,29-31H2,1-3H3,(H,42,49)/b28-25+,32-27+/t33-,34+,35+,36+,37+,38-,39+,41+/m0/s1
SMILES CCCCCCCCCCCCCC[C@H](C(=N[C@H]([C@@H](/C=C/CC/C=C(/CCCCCCCCC)C)O)CO[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)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
NPO15453 Sarcophyton ehrenbergi Species Alcyoniidae Eukaryota n.a. n.a. n.a. DOI[10.1038/s41598-017-00527-8]
NPO15453 Sarcophyton ehrenbergi Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[19006372]
NPO15453 Sarcophyton ehrenbergi Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[20099902]
NPO15453 Sarcophyton ehrenbergi Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[25075977]
NPO15453 Sarcophyton ehrenbergi Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15453 Sarcophyton ehrenbergi Species Alcyoniidae 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
NPT113 Cell line RAW264.7 Mus musculus Activity = 20.3 % PubChem BioAssay data set
NPT113 Cell line RAW264.7 Mus musculus Activity = 64.3 % 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 NPC192066 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
1.0 High Similarity NPC3568
1.0 High Similarity NPC17290
1.0 High Similarity NPC256570
0.8529 High Similarity NPC23454
0.8529 High Similarity NPC70323
0.8529 High Similarity NPC262312
0.8529 High Similarity NPC35269
0.8308 Intermediate Similarity NPC263545
0.8308 Intermediate Similarity NPC473950
0.8308 Intermediate Similarity NPC111567
0.8308 Intermediate Similarity NPC186840
0.8308 Intermediate Similarity NPC144916
0.8308 Intermediate Similarity NPC486421
0.8308 Intermediate Similarity NPC309898
0.8308 Intermediate Similarity NPC273493
0.8308 Intermediate Similarity NPC475125
0.8308 Intermediate Similarity NPC486419
0.8308 Intermediate Similarity NPC15851
0.8308 Intermediate Similarity NPC115448
0.8308 Intermediate Similarity NPC20819
0.8308 Intermediate Similarity NPC486418
0.8308 Intermediate Similarity NPC473604
0.8308 Intermediate Similarity NPC486420
0.8308 Intermediate Similarity NPC479188
0.8308 Intermediate Similarity NPC81468
0.806 Intermediate Similarity NPC156782
0.806 Intermediate Similarity NPC54961
0.8028 Intermediate Similarity NPC8098
0.8028 Intermediate Similarity NPC183449
0.8028 Intermediate Similarity NPC197294
0.7941 Intermediate Similarity NPC158445
0.7941 Intermediate Similarity NPC157353
0.7941 Intermediate Similarity NPC282088
0.7246 Intermediate Similarity NPC282705
0.7246 Intermediate Similarity NPC182632
0.7162 Intermediate Similarity NPC45313
0.6761 Remote Similarity NPC242503
0.6714 Remote Similarity NPC43074
0.6714 Remote Similarity NPC139782
0.6714 Remote Similarity NPC74672
0.6714 Remote Similarity NPC61894
0.6714 Remote Similarity NPC209047
0.6714 Remote Similarity NPC297079
0.6456 Remote Similarity NPC201128
0.6282 Remote Similarity NPC604736

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC192066 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
0.6714 Remote Similarity NPD8522 Clinical (unspecified phase)

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