Natural Product: NPC231566

Natural Product IDNPC231566
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
GKUDQPRHGFTRHK-LYKFGKFTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2442985
PubChem CID 25147100
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 GKUDQPRHGFTRHK-LYKFGKFTSA-N
Standard InCHI InChI=1S/C58H94O26/c1-24-34(64)39(69)42(72)48(77-24)82-44-37(67)27(19-60)79-51(46(44)84-47-41(71)35(65)25(62)20-74-47)80-28-21-75-50(45(38(28)68)83-49-43(73)40(70)36(66)26(18-59)78-49)81-33-10-11-54(5)29(52(33,2)3)8-12-55(6)30(54)9-13-58-31-16-53(4,22-61)14-15-57(31,23-76-58)32(63)17-56(55,58)7/h22,24-51,59-60,62-73H,8-21,23H2,1-7H3/t24-,25+,26+,27+,28-,29-,30+,31+,32+,33-,34-,35-,36+,37+,38-,39+,40-,41+,42+,43+,44-,45+,46+,47-,48-,49-,50-,51-,53-,54-,55+,56-,57+,58-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@H]1[C@@H]([C@@H](CO)O[C@H]([C@@H]1O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O[C@H]1CO[C@H]([C@@H]([C@H]1O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC[C@]24[C@@H]5C[C@](C)(CC[C@]5(CO4)[C@@H](C[C@@]32C)O)C=O)C1(C)C)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
NPO32586 ardisia gigantifolia stapf. Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[24095094]
NPO32586 ardisia gigantifolia stapf. Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT65 Cell line HepG2 Homo sapiens IC50 = 1900.0 nM PMID[24571273]
NPT3508 Cell line EJ Homo sapiens IC50 = 2000.0 nM PMID[24571273]
NPT165 Cell line HeLa Homo sapiens IC50 = 1800.0 nM PMID[23368966]
NPT180 Cell line HCT-8 Homo sapiens IC50 > 100000.0 nM PMID[22472691]
NPT181 Cell line Bel-7402 Homo sapiens IC50 = 1580.0 nM PMID[17315965]
NPT81 Cell line A549 Homo sapiens IC50 > 100000.0 nM PMID[25136754]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 2100.0 nM PMID[24095094]

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 NPC231566 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
0.9619 High Similarity NPC262567
0.9279 High Similarity NPC471431
0.9167 High Similarity NPC471425
0.9 High Similarity NPC471429
0.8929 High Similarity NPC471427
0.8772 High Similarity NPC471626
0.8636 High Similarity NPC205129
0.8596 High Similarity NPC471426
0.8519 High Similarity NPC138219
0.8519 High Similarity NPC475234
0.8407 Intermediate Similarity NPC189575
0.8333 Intermediate Similarity NPC40716
0.8273 Intermediate Similarity NPC473688
0.819 Intermediate Similarity NPC106701
0.812 Intermediate Similarity NPC471424
0.7925 Intermediate Similarity NPC158051
0.7857 Intermediate Similarity NPC475630
0.7851 Intermediate Similarity NPC471428
0.7748 Intermediate Similarity NPC77717
0.7658 Intermediate Similarity NPC253611
0.7658 Intermediate Similarity NPC488782
0.7521 Intermediate Similarity NPC471430
0.7434 Intermediate Similarity NPC267238
0.7345 Intermediate Similarity NPC158367
0.7265 Intermediate Similarity NPC209798
0.7257 Intermediate Similarity NPC119628
0.7248 Intermediate Similarity NPC18724
0.7107 Intermediate Similarity NPC66513
0.7069 Intermediate Similarity NPC157571
0.7027 Intermediate Similarity NPC224003
0.7016 Intermediate Similarity NPC22709
0.6975 Remote Similarity NPC51579
0.6923 Remote Similarity NPC148593
0.6923 Remote Similarity NPC471373
0.6891 Remote Similarity NPC471375
0.6721 Remote Similarity NPC126753
0.6638 Remote Similarity NPC171741
0.6552 Remote Similarity NPC323231
0.6417 Remote Similarity NPC207693
0.6417 Remote Similarity NPC470623
0.6393 Remote Similarity NPC273189
0.6341 Remote Similarity NPC471374
0.6311 Remote Similarity NPC184805
0.5968 Remote Similarity NPC87393
0.5846 Remote Similarity NPC470622
0.5188 Remote Similarity NPC185466
0.5185 Remote Similarity NPC477465
0.5149 Remote Similarity NPC607904
0.5115 Remote Similarity NPC606145
0.5039 Remote Similarity NPC157474
0.5038 Remote Similarity NPC609281

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC231566 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