Natural Product: NPC217738

Natural Product IDNPC217738
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XBGLCVZQMWKHFC-NMQALWILSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 75412556
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 XBGLCVZQMWKHFC-NMQALWILSA-N
Standard InCHI InChI=1S/C58H98O26/c1-24(2)10-9-14-58(8,84-51-46(74)41(69)40(68)31(80-51)23-77-49-44(72)36(64)27(62)21-75-49)25-11-16-57(7)35(25)26(61)18-33-55(5)15-13-34(54(3,4)32(55)12-17-56(33,57)6)81-52-47(42(70)38(66)29(19-59)78-52)83-53-48(43(71)39(67)30(20-60)79-53)82-50-45(73)37(65)28(63)22-76-50/h10,25-53,59-74H,9,11-23H2,1-8H3/t25-,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-,52-,53-,55-,56+,57+,58-/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](CO)O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)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](CO2)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
NPO28005 Panax japonicus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[12350149]
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]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Steamed Roots n.a. n.a. PMID[26200131]
NPO28005 Panax japonicus Species Araliaceae Eukaryota Roots n.a. n.a. PMID[28006911]
NPO28005 Panax japonicus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[28202328]
NPO28005 Panax japonicus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14105.1 Panax pseudo - ginseng var. japonicus Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14105.1 Panax pseudo - ginseng var. japonicus Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28005 Panax japonicus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28005 Panax japonicus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28005 Panax japonicus 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 NPC217738 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
0.9773 High Similarity NPC159005
0.9551 High Similarity NPC14946
0.9551 High Similarity NPC63368
0.8989 High Similarity NPC208650
0.8791 High Similarity NPC220427
0.8247 Intermediate Similarity NPC135369
0.8229 Intermediate Similarity NPC246124
0.809 Intermediate Similarity NPC208477
0.8 Intermediate Similarity NPC69737
0.7798 Intermediate Similarity NPC488293
0.7767 Intermediate Similarity NPC146868
0.7692 Intermediate Similarity NPC488294
0.7573 Intermediate Similarity NPC241381
0.7353 Intermediate Similarity NPC6931
0.7273 Intermediate Similarity NPC488291
0.7083 Intermediate Similarity NPC269627
0.7019 Intermediate Similarity NPC180183
0.701 Intermediate Similarity NPC194842
0.7 Intermediate Similarity NPC31907
0.6875 Remote Similarity NPC181467
0.6765 Remote Similarity NPC65167
0.6699 Remote Similarity NPC160816
0.6636 Remote Similarity NPC488292
0.6505 Remote Similarity NPC472988
0.6505 Remote Similarity NPC38217
0.6486 Remote Similarity NPC146652
0.6346 Remote Similarity NPC476360
0.6346 Remote Similarity NPC476361
0.6311 Remote Similarity NPC234160
0.63 Remote Similarity NPC131479
0.6224 Remote Similarity NPC312553
0.6147 Remote Similarity NPC472718
0.6082 Remote Similarity NPC157659
0.6061 Remote Similarity NPC8039
0.6061 Remote Similarity NPC120123
0.6036 Remote Similarity NPC472716
0.6019 Remote Similarity NPC152584
0.598 Remote Similarity NPC213190
0.5957 Remote Similarity NPC66654
0.5865 Remote Similarity NPC127801
0.5859 Remote Similarity NPC159036
0.5648 Remote Similarity NPC208594
0.5534 Remote Similarity NPC472987
0.549 Remote Similarity NPC472897
0.549 Remote Similarity NPC472896
0.5446 Remote Similarity NPC305418
0.5421 Remote Similarity NPC472715
0.5385 Remote Similarity NPC610948
0.5327 Remote Similarity NPC472719
0.5253 Remote Similarity NPC234287
0.5248 Remote Similarity NPC160734
0.5238 Remote Similarity NPC16573
0.5229 Remote Similarity NPC472717
0.5229 Remote Similarity NPC210759
0.5146 Remote Similarity NPC114874
0.513 Remote Similarity NPC323231
0.5122 Remote Similarity NPC606950
0.51 Remote Similarity NPC88000
0.51 Remote Similarity NPC4831
0.51 Remote Similarity NPC472023
0.5094 Remote Similarity NPC165033
0.5094 Remote Similarity NPC273879
0.5088 Remote Similarity NPC469946
0.5043 Remote Similarity NPC607354

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC217738 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