CNP0251500.0

1-[2-hydroxy-4,6-bis[[3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy]phenyl]-3-(4-hydroxyphenyl)prop-2-en-1-one

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).
1.31
Annotation Level
★ ☆ ☆ ☆ ☆
Mol. Weight
596.17412
Mol. Formula
C27H32O15

Representations

Molecular details

COCONUT id
CNP0251500.0
Name
-
IUPAC name
1-[2-hydroxy-4,6-bis[[3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy]phenyl]-3-(4-hydroxyphenyl)prop-2-en-1-one
InChI
InChI=1S/C27H32O15/c28-9-17-20(33)22(35)24(37)26(41-17)39-13-7-15(32)19(14(31)6-3-11-1-4-12(30)5-2-11)16(8-13)40-27-25(38)23(36)21(34)18(10-29)42-27/h1-8,17-18,20-30,32-38H,9-10H2
InChIKey
QTLVRDBUJNNTDS-UHFFFAOYSA-N
Canonical SMILES (RDKit)
O=C(C=CC1=CC=C(O)C=C1)C1=C(O)C=C(OC2OC(CO)C(O)C(O)C2O)C=C1OC1OC(CO)C(O)C(O)C1O
Murcko Framework
O(c1ccc(c(OC2OCCCC2)c1)CC=Cc3ccccc3)C4OCCCC4

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

TIPdb (database of Taiwan indigenous plants)

TIPdb-3D is a comprehensive three-dimensional chemical structure database derived from the original TIPdb, which catalogs bioactive phytochemicals found in Taiwan's indigenous plants. This new database enhances the potential for discovering novel pharmacologically active compounds by providing 3D structures of the phytochemicals. These structures were generated using the Merck Molecular Force Field, a widely-respected method in computational chemistry. The 3D format offers significant advantages for researchers, enabling more sophisticated analyses of structure-activity relationships and facilitating the exploration of chemical space. Additionally, it allows for more accurate protein-ligand docking simulations, a crucial step in identifying potential drug candidates. By leveraging Taiwan's rich biodiversity and the wealth of indigenous and endemic plant species, TIPdb-3D serves as a valuable resource for researchers in the fields of pharmacology, natural product chemistry, and drug discovery. License: No Licensing information (Cite paper).

10.71606/coconut.cnpc0047

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

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

Latin America dataset

The number of databases of natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several Latin American countries, herein we introduce the first version of the Latin American Natural Products Database (LANaPDB), a public compound collection that gathers the chemical information of NPs contained in diverse databases from this geographical region. The current version of LANaPDB unifies the information from six countries and contains 12,959 chemical structures. The structural classification showed that the most abundant compounds are the terpenoids (63.2%), phenylpropanoids (18%) and alkaloids (11.8%). From the analysis of the distribution of properties of pharmaceutical interest, it was observed that many LANaPDB compounds satisfy some drug-like rules of thumb for physicochemical properties. The concept of the chemical multiverse was employed to generate multiple chemical spaces from two different fingerprints and two dimensionality reduction techniques. Comparing LANaPDB with FDA-approved drugs and the major open-access repository of NPs, COCONUT, it was concluded that the chemical space covered by LANaPDB completely overlaps with COCONUT and, in some regions, with FDA-approved drugs. LANaPDB will be updated, adding more compounds from each database, plus the addition of databases from other Latin American countries. License: Data available on GitHub no license provided.

10.71606/coconut.cnpc0061

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 : C27H32O15
  • Mol. Weight 596.17412
  • Total atom number : 74
  • Heavy atom number : 42
  • Aromatic Ring Count : 2
  • Rotatable Bond count : 9
  • Minimal number of rings : 4
  • Formal Charge : 74
  • Contains Sugar : True
  • Contains Ring Sugars : True
  • Contains Linear Sugars : False

Molecular Descriptors

  • NP-likeness scores : 1.31
  • Alogp : -2.65
  • TopoPSA : 256.29
  • Fsp3 : 0.44
  • Hydrogen Bond Acceptor Count : 15
  • Hydrogen Bond Donor Count : 10
  • Lipinski Hydrogen Bond Acceptor Count : 15
  • Lipinski Hydrogen Bond Donor Count : 10
  • Lipinski RO5 Violations : 3
2D
3D Structure (by RDKit) Interactive JSmol molecular viewer 3D
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