Natural Product: NPC132153

Natural Product IDNPC132153
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PXHNTRFQGHWVGX-ZQQZZLNPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101945296
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 PXHNTRFQGHWVGX-ZQQZZLNPSA-N
Standard InCHI InChI=1S/C50H84O19/c1-23(2)11-10-15-50(9,69-44-41(62)38(59)35(56)28(21-52)65-44)25-12-17-49(8)33(25)26(54)19-31-47(6)16-14-32(46(4,5)30(47)13-18-48(31,49)7)67-45-42(39(60)36(57)29(66-45)22-63-24(3)53)68-43-40(61)37(58)34(55)27(20-51)64-43/h11,25-45,51-52,54-62H,10,12-22H2,1-9H3/t25-,26+,27+,28+,29+,30-,31+,32-,33-,34+,35+,36+,37-,38-,39-,40+,41+,42+,43-,44-,45-,47-,48+,49+,50-/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](COC(=O)C)O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)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
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[ 12877918]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Flower buds n.a. n.a. PMID[12880307]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Stems n.a. n.a. PMID[17663584]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Roots n.a. n.a. PMID[18186611]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota leaves and stems n.a. n.a. PMID[25442304]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Steamed Roots n.a. n.a. PMID[26200131]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14105.2 Panax pseudo-ginseng var. notoginseng Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14105.2 Panax pseudo-ginseng var. notoginseng Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21891 Panax notoginseng 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

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 NPC132153 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
0.8539 High Similarity NPC208650
0.8471 Intermediate Similarity NPC208477
0.8404 Intermediate Similarity NPC135369
0.8352 Intermediate Similarity NPC220427
0.8085 Intermediate Similarity NPC14946
0.8085 Intermediate Similarity NPC63368
0.8061 Intermediate Similarity NPC241381
0.7955 Intermediate Similarity NPC69737
0.79 Intermediate Similarity NPC146868
0.7895 Intermediate Similarity NPC159005
0.7738 Intermediate Similarity NPC31907
0.7647 Intermediate Similarity NPC488294
0.7579 Intermediate Similarity NPC65167
0.7391 Intermediate Similarity NPC269627
0.7363 Intermediate Similarity NPC181467
0.7113 Intermediate Similarity NPC472988
0.7113 Intermediate Similarity NPC38217
0.71 Intermediate Similarity NPC246124
0.7064 Intermediate Similarity NPC488291
0.7048 Intermediate Similarity NPC488292
0.6907 Remote Similarity NPC234160
0.6729 Remote Similarity NPC146652
0.6703 Remote Similarity NPC157659
0.6667 Remote Similarity NPC488293
0.6404 Remote Similarity NPC66654
0.6321 Remote Similarity NPC180183
0.6316 Remote Similarity NPC312553
0.6316 Remote Similarity NPC8039
0.6316 Remote Similarity NPC120123
0.6105 Remote Similarity NPC159036
0.61 Remote Similarity NPC127801
0.6075 Remote Similarity NPC472718
0.5941 Remote Similarity NPC152584
0.5865 Remote Similarity NPC208594
0.5849 Remote Similarity NPC160816
0.5789 Remote Similarity NPC160734
0.5784 Remote Similarity NPC194842
0.5758 Remote Similarity NPC472987
0.5743 Remote Similarity NPC213190
0.5727 Remote Similarity NPC6931
0.5714 Remote Similarity NPC472897
0.5714 Remote Similarity NPC472896
0.5676 Remote Similarity NPC472716
0.567 Remote Similarity NPC114874
0.5638 Remote Similarity NPC234287
0.5638 Remote Similarity NPC88000
0.5638 Remote Similarity NPC4831
0.5638 Remote Similarity NPC472023
0.5631 Remote Similarity NPC472715
0.5514 Remote Similarity NPC476360
0.5514 Remote Similarity NPC476361
0.5446 Remote Similarity NPC16573
0.5446 Remote Similarity NPC165033
0.5446 Remote Similarity NPC273879
0.5426 Remote Similarity NPC280825
0.5426 Remote Similarity NPC473198
0.5385 Remote Similarity NPC472719
0.5288 Remote Similarity NPC131479
0.5192 Remote Similarity NPC139271
0.5182 Remote Similarity NPC237071
0.5182 Remote Similarity NPC238796
0.51 Remote Similarity NPC309425
0.5098 Remote Similarity NPC252253
0.5049 Remote Similarity NPC45959
0.5047 Remote Similarity NPC276758
0.5047 Remote Similarity NPC304011
0.5043 Remote Similarity NPC470514
0.5043 Remote Similarity NPC610948

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC132153 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