Natural Product: NPC146868

Natural Product IDNPC146868
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
NTYAVUNEPXGZQJ-KXJMYDKTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101835367
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene saponins

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 NTYAVUNEPXGZQJ-KXJMYDKTSA-N
Standard InCHI InChI=1S/C57H94O26/c1-24(2)10-9-14-57(8,83-51-47(74)43(70)40(67)30(80-51)23-76-49-45(72)41(68)37(64)27(20-58)77-49)25-11-16-56(7)36(25)26(60)18-32-54(5)15-13-33(53(3,4)31(54)12-17-55(32,56)6)81-52-48(44(71)38(65)28(21-59)78-52)82-50-46(73)42(69)39(66)29(79-50)22-75-35(63)19-34(61)62/h10,25-33,36-52,58-60,64-74H,9,11-23H2,1-8H3,(H,61,62)/t25-,26+,27+,28+,29+,30+,31-,32+,33-,36-,37+,38+,39+,40+,41-,42-,43-,44-,45+,46+,47+,48+,49+,50-,51-,52-,54-,55+,56+,57-/m0/s1
SMILES CC(=CCC[C@@](C)([C@H]1CC[C@]2(C)[C@@H]1[C@@H](C[C@@H]1[C@@]3(C)CC[C@@H](C(C)(C)[C@@H]3CC[C@@]21C)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](COC(=O)CC(=O)O)O1)O)O)O)O)O[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)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
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29141 Panax ginseng Species Araliaceae 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
NPT23107 Protein complex AMPK alpha2/beta1/gamma1 Homo sapiens EC50 = 16.8 nM PMID[28345906]
NPT23107 Protein complex AMPK alpha2/beta1/gamma1 Homo sapiens FC = 1.7 n.a. PMID[28345906]

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 NPC146868 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
0.9792 High Similarity NPC241381
0.9694 High Similarity NPC488294
0.8774 High Similarity NPC488291
0.8542 High Similarity NPC208650
0.8416 Intermediate Similarity NPC135369
0.8367 Intermediate Similarity NPC220427
0.8125 Intermediate Similarity NPC488293
0.8113 Intermediate Similarity NPC488292
0.7941 Intermediate Similarity NPC14946
0.7941 Intermediate Similarity NPC159005
0.7941 Intermediate Similarity NPC63368
0.7708 Intermediate Similarity NPC208477
0.7629 Intermediate Similarity NPC69737
0.7037 Intermediate Similarity NPC246124
0.6981 Remote Similarity NPC65167
0.6796 Remote Similarity NPC269627
0.6765 Remote Similarity NPC181467
0.6701 Remote Similarity NPC31907
0.6574 Remote Similarity NPC472988
0.6574 Remote Similarity NPC38217
0.6389 Remote Similarity NPC234160
0.6228 Remote Similarity NPC472718
0.6034 Remote Similarity NPC180183
0.6 Remote Similarity NPC312553
0.6 Remote Similarity NPC146652
0.5897 Remote Similarity NPC6931
0.5865 Remote Similarity NPC157659
0.5849 Remote Similarity NPC8039
0.5849 Remote Similarity NPC120123
0.5847 Remote Similarity NPC472716
0.5818 Remote Similarity NPC152584
0.5676 Remote Similarity NPC127801
0.566 Remote Similarity NPC159036
0.5636 Remote Similarity NPC213190
0.5603 Remote Similarity NPC160816
0.5588 Remote Similarity NPC66654
0.5536 Remote Similarity NPC194842
0.5478 Remote Similarity NPC208594
0.5431 Remote Similarity NPC476360
0.5431 Remote Similarity NPC476361
0.5364 Remote Similarity NPC472987
0.5321 Remote Similarity NPC472897
0.5321 Remote Similarity NPC472896
0.531 Remote Similarity NPC472719
0.5263 Remote Similarity NPC472715
0.5225 Remote Similarity NPC16573
0.513 Remote Similarity NPC236753
0.5094 Remote Similarity NPC234287
0.5093 Remote Similarity NPC160734
0.5089 Remote Similarity NPC165033
0.5089 Remote Similarity NPC273879
0.5088 Remote Similarity NPC131479

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC146868 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