Natural Product: NPC292042

Natural Product IDNPC292042
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 NVUZRGZISKJWEE-HALXFFPSSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
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 NVUZRGZISKJWEE-HALXFFPSSA-N
Standard InCHI InChI=1S/C46H74O18/c1-19-9-14-46(64-40(19)56-6)20(2)30-27(63-46)16-26-24-8-7-22-15-23(10-12-44(22,4)25(24)11-13-45(26,30)5)58-43-39(62-41-35(53)33(51)31(49)21(3)57-41)37(55)38(29(18-48)60-43)61-42-36(54)34(52)32(50)28(17-47)59-42/h7,19-21,23-43,47-55H,8-18H2,1-6H3/t19-,20+,21+,23+,24-,25+,26+,27+,28-,29-,30+,31+,32-,33-,34+,35-,36-,37+,38-,39-,40+,41+,42+,43-,44+,45+,46+/m1/s1
SMILES C[C@@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC=C6C[C@H](CC[C@]6(C)[C@H]5CC[C@]34C)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O)O[C@H]3[C@@H]([C@@H]([C@H]([C@H](C)O3)O)O)O)O2)O[C@@H]1OC

  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
NPO14775 Eupenicillium javanicum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17711347]
NPO14775 Eupenicillium javanicum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[18771240]
NPO9062 Lilium longiflorum Thunb. Strain Liliaceae Eukaryota n.a. n.a. n.a. PMID[21524113]
NPO3457 Streptomyces diastaticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[8904845]
NPO14775 Eupenicillium javanicum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3457 Streptomyces diastaticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO7703 Xanthorrhoea preissii Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16807 Cyclamen purpurascens Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5811 Pityrodia lepidota Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20448 Trifolium caucasicum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9062 Lilium longiflorum Thunb. Strain Liliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8173 Lupinus multiflorus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6023 Neurolaena venturana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9062 Lilium longiflorum Thunb. Strain Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16807 Cyclamen purpurascens Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9062 Lilium longiflorum Thunb. Strain Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20448 Trifolium caucasicum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6023 Neurolaena venturana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8173 Lupinus multiflorus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5811 Pityrodia lepidota Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14775 Eupenicillium javanicum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16807 Cyclamen purpurascens Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9062 Lilium longiflorum Thunb. Strain Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10340 Crepis rubra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5425 Polygala nyikensis Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2383 Mimosa acacioides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7703 Xanthorrhoea preissii Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3457 Streptomyces diastaticus Species Streptomycetaceae Bacteria 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 NPC292042 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
0.82 Intermediate Similarity NPC480555
0.82 Intermediate Similarity NPC150372
0.8155 Intermediate Similarity NPC194207
0.8155 Intermediate Similarity NPC22779
0.79 Intermediate Similarity NPC470433
0.79 Intermediate Similarity NPC46190
0.79 Intermediate Similarity NPC171073
0.7822 Intermediate Similarity NPC248746
0.7778 Intermediate Similarity NPC232054
0.7745 Intermediate Similarity NPC42171
0.7593 Intermediate Similarity NPC480553
0.7453 Intermediate Similarity NPC269297
0.7453 Intermediate Similarity NPC222202
0.7407 Intermediate Similarity NPC480554
0.7383 Intermediate Similarity NPC475333
0.7383 Intermediate Similarity NPC224098
0.7383 Intermediate Similarity NPC208383
0.7228 Intermediate Similarity NPC94272
0.6957 Remote Similarity NPC480556
0.6923 Remote Similarity NPC113044
0.6923 Remote Similarity NPC283829
0.6923 Remote Similarity NPC161676
0.6759 Remote Similarity NPC300557
0.6757 Remote Similarity NPC309278
0.6752 Remote Similarity NPC224314
0.6636 Remote Similarity NPC73243
0.6636 Remote Similarity NPC244086
0.6636 Remote Similarity NPC84956
0.6606 Remote Similarity NPC6806
0.6574 Remote Similarity NPC602423
0.6571 Remote Similarity NPC470432
0.6571 Remote Similarity NPC230507
0.6545 Remote Similarity NPC475182
0.6518 Remote Similarity NPC247037
0.6514 Remote Similarity NPC122819
0.6514 Remote Similarity NPC477809
0.646 Remote Similarity NPC32361
0.646 Remote Similarity NPC13193
0.6415 Remote Similarity NPC6295
0.64 Remote Similarity NPC165439
0.6348 Remote Similarity NPC249265
0.6337 Remote Similarity NPC181845
0.6296 Remote Similarity NPC305423
0.6293 Remote Similarity NPC23808
0.6293 Remote Similarity NPC87998
0.6281 Remote Similarity NPC477808
0.6228 Remote Similarity NPC475550
0.6147 Remote Similarity NPC14704
0.6132 Remote Similarity NPC19400
0.605 Remote Similarity NPC308140
0.6018 Remote Similarity NPC124677
0.5963 Remote Similarity NPC485595
0.5917 Remote Similarity NPC287885
0.5841 Remote Similarity NPC265275
0.5833 Remote Similarity NPC477811
0.5766 Remote Similarity NPC195297
0.5678 Remote Similarity NPC486386
0.5625 Remote Similarity NPC141433
0.5614 Remote Similarity NPC98696
0.5583 Remote Similarity NPC254255
0.5556 Remote Similarity NPC150057
0.5556 Remote Similarity NPC147753
0.5508 Remote Similarity NPC102016
0.5508 Remote Similarity NPC95051
0.5431 Remote Similarity NPC475643
0.5398 Remote Similarity NPC15249
0.5398 Remote Similarity NPC25455
0.5304 Remote Similarity NPC160426
0.5285 Remote Similarity NPC218571
0.5285 Remote Similarity NPC487615
0.5273 Remote Similarity NPC477451
0.5214 Remote Similarity NPC40440
0.521 Remote Similarity NPC249553
0.521 Remote Similarity NPC471464
0.5159 Remote Similarity NPC31896
0.5133 Remote Similarity NPC306131
0.5133 Remote Similarity NPC200802
0.5093 Remote Similarity NPC486114
0.5091 Remote Similarity NPC297348
0.5091 Remote Similarity NPC249204
0.5091 Remote Similarity NPC48339
0.5091 Remote Similarity NPC141769
0.5091 Remote Similarity NPC477547
0.5085 Remote Similarity NPC486388
0.5046 Remote Similarity NPC485594
0.5043 Remote Similarity NPC470748
0.5043 Remote Similarity NPC107962
0.5043 Remote Similarity NPC295980
0.5043 Remote Similarity NPC600116
0.5041 Remote Similarity NPC128572

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC292042 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
0.6514 Remote Similarity NPD8449 Approved
0.5556 Remote Similarity NPD8450 Suspended

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