CNP0264682.0

Cimicifugoside

Created on · Last update on

NPLikeness
NP Likeness Score: The likelihood of the compound to be a natural product, ranges from -5 (less likely) to 5 (very likely).
3.50
Annotation Level
★ ★ ★ ☆ ☆
Mol. Weight
674.36661
Mol. Formula
C37H54O11

Representations

Molecular details

COCONUT id
CNP0264682.0
Name
Cimicifugoside
IUPAC name
[2-hydroxy-1,4',6',12',17',17'-hexamethyl-18'-(3,4,5-trihydroxytetrahydropyran-2-yl)oxy-spiro[3,6-dioxabicyclo[3.1.0]hexane-4,8'-9-oxahexacyclo[11.9.0.0^{1,21}.0^{4,12}.0^{5,10}.0^{16,21}]docos-13-ene]-3'-yl] acetate
InChI
InChI=1S/C37H54O11/c1-17-12-37(29-34(7,47-29)30(42)48-37)46-20-13-32(5)22-9-8-21-31(3,4)23(45-28-27(41)26(40)19(39)15-43-28)10-11-35(21)16-36(22,35)14-24(44-18(2)38)33(32,6)25(17)20/h9,17,19-21,23-30,39-42H,8,10-16H2,1-7H3
InChIKey
XUJMHSCMPCZWOV-UHFFFAOYSA-N
Canonical SMILES (RDKit)
CC(=O)OC1CC23CC24CCC(OC2OCC(O)C(O)C2O)C(C)(C)C4CC=C3C2(C)CC3OC4(CC(C)C3C12C)OC(O)C1(C)OC41
Murcko Framework
O1CCCCC1OC2CCC34CC54C(=CCC3C2)C6CC7OC8(OCC9OC98)CCC7C6CC5
Synonyms
  • [2-Hydroxy-1,4',6',12',17',17'-hexamethyl-18'-(3,4,5-trihydroxyoxan-2-yl)oxyspiro[3,6-dioxabicyclo[3.1.0]hexane-4,8'-9-oxahexacyclo[11.9.0.01,21.04,12.05,10.016,21]docos-13-ene]-3'-yl] acetate
  • 66176-93-0
  • CID 441913
CAS
  • 66176-93-0

Chemical classification

NP Classification

References

Citations

No citations

Collections

KNApSaCK

KNApSAcK-3D is a database that expands on the original KNApSAcK metabolite database by incorporating 3D structural information. The 3D structures were meticulously generated using computational methods, ensuring their accuracy and potential for further research. These structures provide a valuable resource for researchers to investigate potential interactions between metabolites and proteins, estimate biological activities, and potentially uncover novel insights in various fields of study. The database is accessible through the KNApSAcK Family website.

10.71606/coconut.cnpc0023

UNPD (Universal Natural Products Database)

The Universal Natural Products Database provides a comprehensive collection of natural product structures, their reported biological activities, and virtual screening results. This database offers valuable insights into the chemical diversity and potential pharmaceutical applications of natural compounds. Analysis reveals significant overlap between natural products and FDA-approved drugs in chemical space, suggesting a wealth of potential lead compounds for drug discovery. The database also highlights the polypharmacology of natural products, with many compounds demonstrating interactions with multiple target proteins. To complement existing experimental data, high-throughput virtual screening was conducted against a wide range of target proteins associated with FDA-approved drugs. This approach enabled predictions of the most promising natural products for drug discovery and their potential therapeutic indications. Overall, the Natural Products Database demonstrates that natural compounds possess vast chemical diversity, favourable drug-like properties, and the ability to interact with multiple cellular targets, making them a rich source for pharmaceutical research and development. License: No Licensing information (Cite paper)

10.71606/coconut.cnpc0050

ChEBI NPs

ChEBI is a constantly growing database and ontology of chemical entities of biological interest. It has been expanding steadily in content and has added new features, such as incorporating all user-requested compounds and emphasizing immunology, natural products, and metabolites in various species. Additional data types, including reference citations, species, and components for metabolites, have been incorporated.

10.71606/coconut.cnpc0008

CMAUP (cCollective molecular activities of useful plants)

CMAUP, the Collective Molecular Activities of Useful Plants database, provides comprehensive insights into the multi-target activities of diverse plant species. It details the collective landscapes of multiple targets, activity levels, and regulated biological pathways, processes, and diseases for over 5,000 plants. These landscapes are derived from extensive data on plant ingredients active against various targets. This freely accessible resource allows users to search and explore the complex interactions between plants and their biological effects, aiding mechanistic studies and expanding potential applications. License: If you use the database in your research, please cite: (https://bidd.group/CMAUP)

10.71606/coconut.cnpc0011

TCMDB-Taiwan (Traditional Chinese Medicine database)

TCM Database@Taiwan is a groundbreaking resource in the field of computer-aided drug design, focusing on traditional Chinese medicine. This free, web-based database addresses the previous lack of a comprehensive 3D small molecular structure database for TCM compounds. It contains a vast collection of pure compounds isolated from TCM ingredients, offering both 2D and 3D formats for download and virtual screening. The database features advanced search options, allowing users to query based on molecular properties, substructures, TCM ingredients, and classifications. Developed through extensive volunteer efforts over several years, TCM Database@Taiwan represents a significant step towards modernizing traditional Chinese medicine. It provides researchers worldwide with easy access to a wealth of TCM compound information, facilitating the discovery of novel lead compounds and advancing the integration of traditional Chinese medicine with modern pharmaceutical research methods. License: Traditional Chinese Medicine Database @ Taiwan Copyright © 2010 All Rights Reserved.

10.71606/coconut.cnpc0045

NPASS

The NPASS natural product activity and species source database has been updated with significant enhancements to support drug discovery, medicinal plant research, and microbial investigations. This update expands the database's coverage of natural products (NPs), their activities against specific targets, and their composition in various species. The database now includes new data on composition and concentration values of NPs in different species, as well as extended information on NP activities against various targets. NPASS has also broadened its species source data, incorporating new types such as co-cultured and engineered microbes. Additionally, the update introduces estimated activity profiles for NPs without experimental data, utilizing the Chemical Checker tool. To further aid researchers, the database now provides computed drug-likeness properties and ADMET (absorption, distribution, metabolism, excretion, and toxicity) information for all NPs. These comprehensive updates make NPASS an even more valuable resource for researchers in the fields of natural product discovery and medicinal research. The updated version of NPASS is freely accessible online, promoting open access to this crucial scientific data. License: No Licensing information (Cite paper)

10.71606/coconut.cnpc0030

NPEdia

RIKEN Natural Products Encyclopedia (RIKEN NPEdia) is a comprehensive natural products database developed as part of the RIKEN Natural Products Depository (RIKEN NPDepo) chemical resource bank. This database primarily catalogs secondary metabolites isolated from diverse organisms such as actinomycetes, fungi, and plants. Each entry in NPEdia provides detailed information including molecular structure, origin, and various properties of the compounds. The database offers functionality for searching compounds, registering new data, and facilitating a compound-order system. Future plans include integrating metabolites with metabolic pathway maps, protein-protein interaction maps, and chemical genomics maps. NPEdia aims to serve as a valuable resource for researchers across various fields, offering a user-friendly interface and comprehensive information. For the most up-to-date information and details about NPEdia, interested parties can visit the official website. License: No Licensing information (Cite paper)

10.71606/coconut.cnpc0033

Super Natural II

Super Natural II is a comprehensive natural product database that serves as a valuable resource for drug discovery and development. This updated version significantly expands upon its predecessor, offering a vast collection of natural compounds along with their structural and physicochemical properties. The database facilitates the exploration of topological pharmacophore patterns shared between natural products and commercial drugs, contributing to a deeper understanding of their potential therapeutic applications. Super Natural II provides users with advanced search capabilities, including template-based similarity searches and substructure queries. Additionally, it offers predicted toxicity information for many compounds and includes vendor details for easy sourcing. The database also integrates pathway information related to the synthesis and degradation of natural products, as well as insights into their mechanisms of action compared to structurally similar drugs and their target proteins. By consolidating this wealth of information into a freely accessible platform, Super Natural II addresses the challenges of scattered or restricted natural product data, supporting researchers in their quest for novel drug candidates inspired by nature. License: No Licensing information (Cite paper)

10.71606/coconut.cnpc0044

Stereochemical Variants

Molecular Properties

  • Mol. Formula : C37H54O11
  • Mol. Weight 674.36661
  • Total atom number : 102
  • Heavy atom number : 48
  • Aromatic Ring Count : 0
  • Rotatable Bond count : 3
  • Minimal number of rings : 9
  • Formal Charge : 102
  • Contains Sugar : True
  • Contains Ring Sugars : True
  • Contains Linear Sugars : False

Molecular Descriptors

  • NP-likeness scores : 3.50
  • Alogp : 2.95
  • TopoPSA : 156.67
  • Fsp3 : 0.92
  • Hydrogen Bond Acceptor Count : 11
  • Hydrogen Bond Donor Count : 4
  • Lipinski Hydrogen Bond Acceptor Count : 11
  • Lipinski Hydrogen Bond Donor Count : 4
  • Lipinski RO5 Violations : 2
2D
Cimicifugoside
3D Structure (by RDKit) Interactive JSmol molecular viewer 3D
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