Natural Product: NPC478998

Natural Product IDNPC478998
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
VDHXFGANCMGBFE-NHYVETCYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10393702
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002518] Annonaceous acetogenins

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 VDHXFGANCMGBFE-NHYVETCYSA-N
Standard InCHI InChI=1S/C35H62O7/c1-3-4-5-6-7-8-9-10-15-18-23-30(37)32-25-26-33(41-32)31(38)24-19-22-29(36)21-17-14-12-11-13-16-20-28-27-35(2,40)42-34(28)39/h27,30-33,37-38,40H,3-26H2,1-2H3/t30-,31-,32-,33-,35?/m1/s1
SMILES CCCCCCCCCCCC[C@H]([C@H]1CC[C@H]([C@@H](CCCC(=O)CCCCCCCCC2=CC(C)(O)OC2=O)O)O1)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
NPO26361 Annona cherimolia Species Annonaceae Eukaryota Seeds n.a. n.a. PMID[11325235]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota Seeds n.a. n.a. PMID[14575439]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26361 Annona cherimolia Species Annonaceae 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
- Artemia LC50 = 0.375 ug.mL-1 PMID[14575439]

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 NPC478998 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
0.8039 Intermediate Similarity NPC11456
0.7255 Intermediate Similarity NPC144415
0.7255 Intermediate Similarity NPC608157
0.6545 Remote Similarity NPC605396
0.625 Remote Similarity NPC477010
0.6167 Remote Similarity NPC477015
0.614 Remote Similarity NPC477012
0.6078 Remote Similarity NPC73310
0.6078 Remote Similarity NPC473529
0.6078 Remote Similarity NPC180363
0.6078 Remote Similarity NPC94875
0.6078 Remote Similarity NPC11332
0.6078 Remote Similarity NPC145914
0.6078 Remote Similarity NPC601174
0.6078 Remote Similarity NPC601403
0.6078 Remote Similarity NPC603568
0.6078 Remote Similarity NPC604330
0.6078 Remote Similarity NPC608300
0.6078 Remote Similarity NPC611200
0.6078 Remote Similarity NPC611571
0.6071 Remote Similarity NPC473687
0.6071 Remote Similarity NPC204686
0.6071 Remote Similarity NPC219498
0.6071 Remote Similarity NPC473904
0.6071 Remote Similarity NPC308412
0.6071 Remote Similarity NPC134885
0.6071 Remote Similarity NPC488247
0.6071 Remote Similarity NPC210218
0.6071 Remote Similarity NPC488248
0.6 Remote Similarity NPC280612
0.5965 Remote Similarity NPC134807
0.5862 Remote Similarity NPC139418
0.5741 Remote Similarity NPC329829
0.5741 Remote Similarity NPC475159
0.5741 Remote Similarity NPC131002
0.5741 Remote Similarity NPC473780
0.5741 Remote Similarity NPC604521
0.5536 Remote Similarity NPC156804
0.549 Remote Similarity NPC485062
0.549 Remote Similarity NPC485063
0.5455 Remote Similarity NPC25764
0.5455 Remote Similarity NPC235809
0.5455 Remote Similarity NPC39279
0.5455 Remote Similarity NPC39167
0.5455 Remote Similarity NPC292809
0.5455 Remote Similarity NPC202055
0.5455 Remote Similarity NPC606804
0.5455 Remote Similarity NPC607425
0.5455 Remote Similarity NPC608574
0.5439 Remote Similarity NPC163093
0.5439 Remote Similarity NPC607439
0.5385 Remote Similarity NPC477017
0.5385 Remote Similarity NPC477016
0.5345 Remote Similarity NPC241360
0.5345 Remote Similarity NPC293136
0.5179 Remote Similarity NPC100921
0.5179 Remote Similarity NPC477018
0.5172 Remote Similarity NPC473156
0.5172 Remote Similarity NPC282815
0.5172 Remote Similarity NPC600956
0.5167 Remote Similarity NPC329838
0.5085 Remote Similarity NPC473671
0.5085 Remote Similarity NPC219652
0.5085 Remote Similarity NPC475268
0.5085 Remote Similarity NPC473840
0.5085 Remote Similarity NPC470400
0.5085 Remote Similarity NPC77871
0.5085 Remote Similarity NPC9678
0.5085 Remote Similarity NPC319036
0.5085 Remote Similarity NPC605867

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC478998 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