Natural Product: NPC470862

Natural Product IDNPC470862
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
O-Methylcapsicoside A
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2271371
PubChem CID 76334189
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 QKQPATPXWFRSQO-VYIDYXGMSA-N
Standard InCHI InChI=1S/C64H108O35/c1-22(21-87-56-47(81)43(77)38(72)31(15-65)89-56)8-11-64(86-5)23(2)37-30(99-64)13-27-25-7-6-24-12-29(28(71)14-63(24,4)26(25)9-10-62(27,37)3)88-57-50(84)46(80)52(36(20-70)94-57)95-61-55(54(42(76)35(19-69)93-61)97-59-49(83)45(79)40(74)33(17-67)91-59)98-60-51(85)53(41(75)34(18-68)92-60)96-58-48(82)44(78)39(73)32(16-66)90-58/h22-61,65-85H,6-21H2,1-5H3/t22-,23+,24+,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-,52+,53+,54+,55-,56-,57-,58+,59+,60+,61+,62+,63+,64?/m1/s1
SMILES OC[C@H]1O[C@@H](O[C@@H]2C[C@@H]3CC[C@@H]4[C@@H]([C@]3(C[C@H]2O)C)CC[C@]2([C@H]4C[C@H]3[C@@H]2[C@@H](C(O3)(OC)CC[C@H](CO[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O)C)C)C)[C@@H]([C@H]([C@H]1O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)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
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. DOI[10.1007/BF00232372]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. Granola: the 1999 growing season DOI[10.1016/S0956-7135(03)00077-X]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. seeds n.a. n.a. PMID[12105963]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. PMID[2831703]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. Database[FooDB]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. Database[Phenol-Explorer]

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
NPT4127 Organism Pseudomonas stutzeri Pseudomonas stutzeri MIC > 1000.0 ug.mL-1 PMID[19487444]
NPT729 Organism Micrococcus luteus Micrococcus luteus MIC > 1000.0 ug.mL-1 PMID[19487444]
NPT21 Organism Aspergillus niger Aspergillus niger MIC > 1000.0 ug.mL-1 PMID[12039561]
NPT1825 Organism Lactobacillus plantarum Lactobacillus plantarum MIC = 1000.0 ug.mL-1 PMID[19487444]
NPT4130 Organism Lactobacillus rhamnosus Lactobacillus rhamnosus MIC = 1000.0 ug.mL-1 PMID[19487444]
NPT4131 Organism Bacillus licheniformis DSM 13=ATCC 14580 Bacillus licheniformis DSM 13=ATCC 14580 MIC > 1000.0 ug.mL-1 PMID[12039561]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC > 1000.0 ug.mL-1 PMID[12039561]
NPT6635 Organism Hanseniaspora guilliermondii Hanseniaspora guilliermondii MIC = 25.0 ug.mL-1 PMID[19114678]
NPT20 Organism Candida albicans Candida albicans MIC = 50.0 ug.mL-1 PMID[1279126]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC = 50.0 ug.mL-1 PMID[19114678]
NPT19 Organism Escherichia coli Escherichia coli MIC > 1000.0 ug.mL-1 PMID[23398362]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 1000.0 ug.mL-1 PMID[19487444]
NPT4128 Organism Lactobacillus fermentum Lactobacillus fermentum MIC = 1000.0 ug.mL-1 PMID[19487444]
NPT4129 Organism Lactobacillus casei Lactobacillus casei MIC = 1000.0 ug.mL-1 PMID[19487444]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC > 1000.0 ug.mL-1 PMID[19487444]
NPT2922 Organism Staphylococcus aureus subsp. aureus Staphylococcus aureus subsp. aureus MIC > 1000.0 ug.mL-1 PMID[19487444]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MIC > 1000.0 ug.mL-1 PMID[12039561]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MIC > 1000.0 ug.mL-1 PMID[12039561]
NPT185 Organism Aspergillus flavus Aspergillus flavus MIC > 1000.0 ug.mL-1 PMID[12039561]
NPT2567 Organism Trichoderma viride Hypocrea rufa MIC = 250.0 ug.mL-1 PMID[12039561]
NPT923 Organism Rhizopus oryzae Rhizopus oryzae MIC = 125.0 ug.mL-1 PMID[12039561]
NPT4132 Organism Setophoma terrestris Setophoma terrestris MIC = 125.0 ug.mL-1 PMID[10999467]
NPT3086 Organism Penicillium expansum Penicillium expansum MIC = 1000.0 ug.mL-1 PMID[12061876]
NPT5427 Organism Hanseniaspora uvarum Hanseniaspora uvarum MIC = 25.0 ug.mL-1 PMID[20801038]
NPT5427 Organism Hanseniaspora uvarum Hanseniaspora uvarum MIC = 50.0 ug.mL-1 PMID[19114678]
NPT765 Organism Schizosaccharomyces pombe Schizosaccharomyces pombe MIC = 50.0 ug.mL-1 PMID[19114678]
NPT6379 Organism Saccharomycodes ludwigii Saccharomycodes ludwigii MIC = 50.0 ug.mL-1 PubChem BioAssay data set
NPT314 Organism Bacillus cereus Bacillus cereus MIC = 1000.0 ug.mL-1 PMID[19487444]
NPT6533 Organism Hanseniaspora vineae Hanseniaspora vineae MIC = 25.0 ug.mL-1 PMID[19114678]
NPT6538 Organism Hanseniaspora osmophila Hanseniaspora osmophila MIC = 50.0 ug.mL-1 PMID[19114678]

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 NPC470862 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
0.8824 High Similarity NPC232611
0.8558 High Similarity NPC470864
0.8505 High Similarity NPC470867
0.8165 Intermediate Similarity NPC470866
0.8 Intermediate Similarity NPC115165
0.7798 Intermediate Similarity NPC83137
0.7685 Intermediate Similarity NPC470861
0.7607 Intermediate Similarity NPC263359
0.757 Intermediate Similarity NPC184617
0.7523 Intermediate Similarity NPC116756
0.7411 Intermediate Similarity NPC132080
0.7387 Intermediate Similarity NPC92710
0.7355 Intermediate Similarity NPC481190
0.7264 Intermediate Similarity NPC473601
0.7143 Intermediate Similarity NPC232037
0.7054 Intermediate Similarity NPC473518
0.7016 Intermediate Similarity NPC330026
0.6917 Remote Similarity NPC210569
0.6786 Remote Similarity NPC97700
0.6786 Remote Similarity NPC30856
0.6726 Remote Similarity NPC51520
0.6726 Remote Similarity NPC303069
0.6581 Remote Similarity NPC476112
0.6581 Remote Similarity NPC307534
0.6549 Remote Similarity NPC151134
0.6522 Remote Similarity NPC470863
0.6423 Remote Similarity NPC220836
0.6355 Remote Similarity NPC206003
0.6355 Remote Similarity NPC473610
0.6333 Remote Similarity NPC31896
0.6325 Remote Similarity NPC475625
0.625 Remote Similarity NPC475351
0.625 Remote Similarity NPC84111
0.625 Remote Similarity NPC287483
0.625 Remote Similarity NPC470865
0.6241 Remote Similarity NPC329820
0.6226 Remote Similarity NPC294686
0.622 Remote Similarity NPC244431
0.6216 Remote Similarity NPC195297
0.6186 Remote Similarity NPC309278
0.6179 Remote Similarity NPC94086
0.6179 Remote Similarity NPC473817
0.6075 Remote Similarity NPC234352
0.5984 Remote Similarity NPC79900
0.5981 Remote Similarity NPC325828
0.5963 Remote Similarity NPC222731
0.5893 Remote Similarity NPC107962
0.5873 Remote Similarity NPC248202
0.5862 Remote Similarity NPC475643
0.5854 Remote Similarity NPC233433
0.5766 Remote Similarity NPC121453
0.5726 Remote Similarity NPC477811
0.5725 Remote Similarity NPC481189
0.5702 Remote Similarity NPC125324
0.5692 Remote Similarity NPC208832
0.5683 Remote Similarity NPC329727
0.5667 Remote Similarity NPC98018
0.5667 Remote Similarity NPC284104
0.5667 Remote Similarity NPC103616
0.563 Remote Similarity NPC51172
0.563 Remote Similarity NPC49032
0.562 Remote Similarity NPC329807
0.5606 Remote Similarity NPC305771
0.5606 Remote Similarity NPC94072
0.5606 Remote Similarity NPC169816
0.56 Remote Similarity NPC256983
0.5581 Remote Similarity NPC473505
0.5575 Remote Similarity NPC54619
0.5538 Remote Similarity NPC273002
0.5536 Remote Similarity NPC250393
0.5462 Remote Similarity NPC485603
0.5462 Remote Similarity NPC477807
0.5455 Remote Similarity NPC32707
0.5439 Remote Similarity NPC107188
0.5379 Remote Similarity NPC15918
0.5372 Remote Similarity NPC300557
0.5366 Remote Similarity NPC475319
0.536 Remote Similarity NPC194207
0.536 Remote Similarity NPC22779
0.5349 Remote Similarity NPC262050
0.5328 Remote Similarity NPC485604
0.5308 Remote Similarity NPC190939
0.5299 Remote Similarity NPC6295
0.5268 Remote Similarity NPC297348
0.5268 Remote Similarity NPC249204
0.5268 Remote Similarity NPC48339
0.5268 Remote Similarity NPC141769
0.5268 Remote Similarity NPC477547
0.5234 Remote Similarity NPC480553
0.521 Remote Similarity NPC160426
0.5207 Remote Similarity NPC602423
0.5172 Remote Similarity NPC211354
0.5167 Remote Similarity NPC485605
0.5161 Remote Similarity NPC308459
0.5154 Remote Similarity NPC232054
0.5078 Remote Similarity NPC480554
0.5075 Remote Similarity NPC477808
0.5043 Remote Similarity NPC19400
0.5043 Remote Similarity NPC477451
0.5041 Remote Similarity NPC92890
0.5041 Remote Similarity NPC477809
0.5038 Remote Similarity NPC480556

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC470862 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
0.5981 Remote Similarity NPD8171 Phase 2
0.5299 Remote Similarity NPD8170 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