Natural Product: NPC142742

Natural Product IDNPC142742
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YVLOWIIIBDVWOW-GOHHXVKMSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 129316160
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000175] Glycerolipids
        • [CHEMONTID:0000637] Glycosylglycerols
          • [CHEMONTID:0003344] 3-O-beta-D-digalactosyl-sn-glycerols

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 YVLOWIIIBDVWOW-GOHHXVKMSA-N
Standard InCHI InChI=1S/C45H84O15/c1-3-5-7-9-11-13-15-16-18-19-21-23-25-27-36(47)55-30-33(58-37(48)28-26-24-22-20-17-14-12-10-8-6-4-2)31-56-44-43(54)41(52)39(50)35(60-44)32-57-45-42(53)40(51)38(49)34(29-46)59-45/h33-35,38-46,49-54H,3-32H2,1-2H3/t33-,34-,35-,38+,39+,40+,41+,42-,43-,44-,45+/m1/s1
SMILES CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C@H]([C@H]([C@@H](CO[C@@H]2[C@@H]([C@H]([C@H]([C@@H](CO)O2)O)O)O)O1)O)O)O)OC(=O)CCCCCCCCCCCCC

  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
NPO15967 Penicillium urticae Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[836020]
NPO14701 Monodora angolensis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8155 Lepidonia jonesii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15967 Penicillium urticae Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14701 Monodora angolensis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15967 Penicillium urticae Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8155 Lepidonia jonesii Species Asteraceae 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 NPC142742 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
0.902 High Similarity NPC488690
0.8947 High Similarity NPC156089
0.8226 Intermediate Similarity NPC470313
0.8226 Intermediate Similarity NPC473500
0.8226 Intermediate Similarity NPC611497
0.807 Intermediate Similarity NPC488689
0.7903 Intermediate Similarity NPC38295
0.7667 Intermediate Similarity NPC21693
0.7455 Intermediate Similarity NPC285003
0.7273 Intermediate Similarity NPC12040
0.7101 Intermediate Similarity NPC22558
0.7097 Intermediate Similarity NPC236649
0.7 Intermediate Similarity NPC476611
0.6949 Remote Similarity NPC83839
0.6875 Remote Similarity NPC110813
0.6613 Remote Similarity NPC488693
0.6508 Remote Similarity NPC331437
0.6364 Remote Similarity NPC133377
0.6316 Remote Similarity NPC206601
0.629 Remote Similarity NPC163812
0.6286 Remote Similarity NPC476612
0.6286 Remote Similarity NPC476613
0.6129 Remote Similarity NPC250619
0.6038 Remote Similarity NPC145112
0.6029 Remote Similarity NPC488694
0.5775 Remote Similarity NPC488692
0.569 Remote Similarity NPC147292
0.5574 Remote Similarity NPC241265
0.5541 Remote Similarity NPC475425
0.5469 Remote Similarity NPC143446
0.541 Remote Similarity NPC76881
0.5357 Remote Similarity NPC606861
0.5357 Remote Similarity NPC607126
0.5294 Remote Similarity NPC55678

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC142742 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
0.5294 Remote Similarity NPD6125 Phase 4
0.5082 Remote Similarity NPD3181 Phase 3

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