Natural Product: NPC475436

Natural Product IDNPC475436
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
XASDQEOMZDFLDT-QGYWBVHWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL505676
PubChem CID 44559499
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides
          • [CHEMONTID:0002364] Steroidal 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 XASDQEOMZDFLDT-QGYWBVHWSA-N
Standard InCHI InChI=1S/C39H64O12/c1-17-7-12-39(46-16-17)18(2)28-27(51-39)15-24-22-14-26(25-13-21(40)8-10-37(25,5)23(22)9-11-38(24,28)6)49-36-33(45)34(30(42)20(4)48-36)50-35-32(44)31(43)29(41)19(3)47-35/h17-36,40-45H,7-16H2,1-6H3/t17-,18+,19-,20-,21+,22-,23+,24+,25-,26+,27+,28+,29-,30-,31+,32+,33-,34+,35+,36+,37-,38+,39-/m1/s1
SMILES CC1CCC2(C(C3C(O2)CC4C3(CCC5C4CC(C6C5(CCC(C6)O)C)OC7C(C(C(C(O7)C)O)OC8C(C(C(C(O8)C)O)O)O)O)C)C)OC1

  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
NPO4703 Solanum hispidum Species Solanaceae Eukaryota leaves n.a. n.a. PMID[15217270]
NPO4703 Solanum hispidum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4703 Solanum hispidum Species Solanaceae 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
NPT21 Organism Aspergillus niger Aspergillus niger MIC = 400.0 ug.mL-1 PMID[25176189]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes MIC = 200.0 ug.mL-1 PMID[18303847]
NPT329 Organism Trichophyton rubrum Trichophyton rubrum MIC = 50.0 ug.mL-1 PMID[22840694]
NPT20 Organism Candida albicans Candida albicans MIC = 200.0 ug.mL-1 DOI[10.6019/CHEMBL1201861]

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 NPC475436 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
1.0 High Similarity NPC131693
0.88 High Similarity NPC144790
0.88 High Similarity NPC149400
0.8537 High Similarity NPC312678
0.8537 High Similarity NPC253268
0.8072 Intermediate Similarity NPC179859
0.8072 Intermediate Similarity NPC473851
0.775 Intermediate Similarity NPC277715
0.7419 Intermediate Similarity NPC485603
0.7241 Intermediate Similarity NPC485591
0.7195 Intermediate Similarity NPC88962
0.7 Intermediate Similarity NPC291547
0.7 Intermediate Similarity NPC485593
0.7 Intermediate Similarity NPC174024
0.6848 Remote Similarity NPC485590
0.6705 Remote Similarity NPC485594
0.6327 Remote Similarity NPC485605
0.6224 Remote Similarity NPC14704
0.618 Remote Similarity NPC473774
0.618 Remote Similarity NPC481419
0.618 Remote Similarity NPC481417
0.6129 Remote Similarity NPC234352
0.6019 Remote Similarity NPC485604
0.59 Remote Similarity NPC485599
0.5824 Remote Similarity NPC481420
0.5824 Remote Similarity NPC481421
0.5802 Remote Similarity NPC296734
0.5679 Remote Similarity NPC248944
0.5679 Remote Similarity NPC7479
0.5679 Remote Similarity NPC257296
0.5631 Remote Similarity NPC485596
0.5567 Remote Similarity NPC477451
0.5556 Remote Similarity NPC306131
0.5556 Remote Similarity NPC200802
0.5545 Remote Similarity NPC480554
0.5545 Remote Similarity NPC485595
0.5534 Remote Similarity NPC485597
0.551 Remote Similarity NPC222731
0.5446 Remote Similarity NPC480553
0.5429 Remote Similarity NPC485598
0.5426 Remote Similarity NPC24960
0.54 Remote Similarity NPC19400
0.534 Remote Similarity NPC70204
0.5288 Remote Similarity NPC113044
0.5288 Remote Similarity NPC283829
0.5288 Remote Similarity NPC161676
0.5258 Remote Similarity NPC481424
0.5258 Remote Similarity NPC481422
0.5243 Remote Similarity NPC470432
0.5243 Remote Similarity NPC230507
0.5243 Remote Similarity NPC6295
0.5229 Remote Similarity NPC184617
0.5214 Remote Similarity NPC480556
0.5204 Remote Similarity NPC297348
0.5204 Remote Similarity NPC249204
0.5204 Remote Similarity NPC48339
0.5204 Remote Similarity NPC177834
0.5204 Remote Similarity NPC141769
0.5204 Remote Similarity NPC477547
0.5192 Remote Similarity NPC195297
0.5152 Remote Similarity NPC294686
0.514 Remote Similarity NPC470433
0.514 Remote Similarity NPC46190
0.514 Remote Similarity NPC171073
0.514 Remote Similarity NPC602423
0.5102 Remote Similarity NPC181845
0.5051 Remote Similarity NPC325828
0.5048 Remote Similarity NPC141433
0.5046 Remote Similarity NPC300557

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC475436 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
0.5679 Remote Similarity NPD6928 Phase 2
0.5051 Remote Similarity NPD8171 Phase 2

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