Natural Product: NPC21046

Natural Product IDNPC21046
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Rosmadial
IUPAC Name (1'S,3R)-7-hydroxy-2',2'-dimethyl-2-oxo-6-propan-2-ylspiro[1-benzofuran-3,6'-cyclohexane]-1',4-dicarbaldehyde
Synonyms Rosmadial
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL494864
PubChem CID 15801061
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000301] Benzofurans

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 JBWRHBJFAVSAMJ-VBKZILBWSA-N
Standard InCHI InChI=1S/C20H24O5/c1-11(2)13-8-12(9-21)15-17(16(13)23)25-18(24)20(15)7-5-6-19(3,4)14(20)10-22/h8-11,14,23H,5-7H2,1-4H3/t14-,20+/m0/s1
SMILES CC(C)c1cc(C=O)c2c(c1O)OC(=O)[C@]12CCCC(C)(C)[C@@H]1C=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
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[12880325]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[1567426]
NPO20067 Salvia pachyphylla Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17190465]
NPO2794 Salvia clevelandii Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17190465]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[17217287]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[26020634]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[37570961]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. leaf n.a. PMID[8229021]
NPO23960 Artemisia siversiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28257 Dioscorea communis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO415 Deguelia hatschbachii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25212 Ritterella rubra n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22016 Notholaena dealbata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4009 Allochromatium minutissimum Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO20067 Salvia pachyphylla Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27437 Camptothecium lutescens Species Brachytheciaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26223 Cladonia bellidiflora Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25868 Decachaeta ovatifolia n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO12476 Delphinium cyphoplectrum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26087 Euphorbia retusa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10497 Hydrolithon reinboldii Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26054 Palmaria palmata Species Palmariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6346 Phallusia fumigata Species Ascidiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26316 Pleurophycus gardneri Species Alariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23417 Rhabdia lycioides n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO10155 Stauntonia obovatifoliola Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25974 Streptomyces lateritius Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO24740 Uvaria klaineana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24988 Viburnum sieboldi Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24740 Uvaria klaineana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28257 Dioscorea communis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25974 Streptomyces lateritius Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO415 Deguelia hatschbachii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6346 Phallusia fumigata Species Ascidiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24988 Viburnum sieboldi Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26223 Cladonia bellidiflora Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4009 Allochromatium minutissimum Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO23417 Rhabdia lycioides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO22016 Notholaena dealbata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26054 Palmaria palmata Species Palmariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24740 Uvaria klaineana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25868 Decachaeta ovatifolia n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26087 Euphorbia retusa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28257 Dioscorea communis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12476 Delphinium cyphoplectrum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10497 Hydrolithon reinboldii Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2794 Salvia clevelandii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23960 Artemisia siversiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27437 Camptothecium lutescens Species Brachytheciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25212 Ritterella rubra n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10155 Stauntonia obovatifoliola Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26316 Pleurophycus gardneri Species Alariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25779 Vicia sativa Species Fabaceae 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
NPT179 Cell line A2780 Homo sapiens GI50 = 36000.0 nM PMID[17190465]
NPT1577 Cell line SW1573 Homo sapiens GI50 = 32000.0 nM PMID[17190465]
NPT1183 Cell line WiDr Homo sapiens GI50 = 59000.0 nM PMID[17190465]
NPT396 Cell line T47D Homo sapiens GI50 = 48000.0 nM PMID[17190465]
NPT1723 Cell line HBL-100 Homo sapiens GI50 = 26000.0 nM PMID[17190465]

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 NPC21046 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
0.5538 Remote Similarity NPC610125
0.5079 Remote Similarity NPC3009

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC21046 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