CNP0216017.0

beta-D-Glucopyranoside, 2-(3-hydroxy-4-methoxyphenyl)ethyl 3-O-(6-deoxy-alpha-L-mannopyranosyl)-, 4-[3-(4-hydroxy-3-methoxyphenyl)-2-propenoate], (E)-

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).
1.75
Annotation Level
★ ★ ☆ ☆ ☆
Mol. Weight
652.23672
Mol. Formula
C31H40O15

Representations

Molecular details

COCONUT id
CNP0216017.0
Name
beta-D-Glucopyranoside, 2-(3-hydroxy-4-methoxyphenyl)ethyl 3-O-(6-deoxy-alpha-L-mannopyranosyl)-, 4-[3-(4-hydroxy-3-methoxyphenyl)-2-propenoate], (E)-
IUPAC name
[5-hydroxy-6-[2-(3-hydroxy-4-methoxy-phenyl)ethoxy]-2-(hydroxymethyl)-4-(3,4,5-trihydroxy-6-methyl-tetrahydropyran-2-yl)oxy-tetrahydropyran-3-yl] 3-(4-hydroxy-3-methoxy-phenyl)prop-2-enoate
InChI
InChI=1S/C31H40O15/c1-15-24(36)25(37)26(38)31(43-15)46-29-27(39)30(42-11-10-17-5-8-20(40-2)19(34)12-17)44-22(14-32)28(29)45-23(35)9-6-16-4-7-18(33)21(13-16)41-3/h4-9,12-13,15,22,24-34,36-39H,10-11,14H2,1-3H3
InChIKey
WLWAYPFRKDSFCL-UHFFFAOYSA-N
Canonical SMILES (RDKit)
COC1=CC=C(CCOC2OC(CO)C(OC(=O)C=CC3=CC=C(O)C(OC)=C3)C(OC3OC(C)C(O)C(O)C3O)C2O)C=C1O
Murcko Framework
O(CCc1ccccc1)C2OCC(OCC=Cc3ccccc3)C(OC4OCCCC4)C2

Chemical classification

NP Classification

References

Citations

No citations

Collections

PubChem NPs

Natural Products subset of PubChem.

10.71606/coconut.cnpc0037

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

ZINC NP

Subset of Natural Products from ZINC 15 database.

10.71606/coconut.cnpc0052

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

ANPDB

The African Natural Products Database (ANPDB) is a comprehensive collection of natural products extracted from African flora. This database combines information from various regions of Africa, currently including the Northern African Natural Products Database and the Eastern African Natural Products Database. ANPDB stands as the largest repository of natural products isolated from native African organisms, covering a wide range of sources including plants, microorganisms, animals, and marine life. The database provides detailed information on each compound, including names, molecular structures, source organisms, references, biological activities, and modes of action when available. Users can access ANPDB through various search options, such as compound names, chemical structures, organisms, or keywords. Additionally, the database offers region-specific data access and allows for downloading of chemical structures for virtual screening experiments. ANPDB serves as a valuable resource for researchers exploring the potential of African natural products in drug discovery and development, and it is freely accessible to the public. License: This database is freely accessible. Terms and rights are at the sole discretion of the prospective user, and as agreed with the scientific author(s) or publishing house.

10.71606/coconut.cnpc0057

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

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

Australian natural products

The ongoing enhancement of the "Phytochemistry of Australian Plants" database, originally compiled by David Collins and Don McGilvery, represents a significant advancement in the field of natural product chemistry. This comprehensive resource now incorporates a wealth of information, including chemical structures, bibliographic references, and species names, all linked to persistent identifiers. These identifiers connect to the relevant scientific literature and the Atlas of Living Australia (ALA), providing users with access to detailed geographical distribution data. The current curation effort has substantially improved the database's utility and accessibility. Approximately 80% of the references now include DOIs, ISBNs, or ISSNs, ensuring easier location and verification of source materials. Furthermore, all species and genera entries are now associated with persistent identifiers linking to the ALA or other authoritative datasets. Notably, about 70% of the chemical structures have been validated and are presented in SMILES format, enhancing the database's value for computational chemistry and cheminformatics applications.

10.71606/coconut.cnpc0055

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

EMNPD

EMNPD, a comprehensive endophytic microorganism natural products database, has been developed to fill the gap in open-access resources for this field. It currently contains data on over 6,000 natural products from endophytic microorganisms, including their physico-chemical properties, bioactivity, and source organism information. EMNPD aims to be a valuable tool for drug discovery and research into bioactive substances by providing a free and accessible repository of knowledge. License: EMNPD aims to function as an open-access knowledge repository for the study of endophytic microorganisms and their natural products, thereby facilitating drug discovery research and exploration of bioactive substances. The database can be accessed at http://emnpd.idrblab.cn/ without the need for registration, enabling researchers to freely download the data.

10.71606/coconut.cnpc0056

SANCDB

SANCDB is a pioneering South African natural compound database, representing a significant advancement in natural products research within the country. This curated and fully-referenced resource contains detailed information on natural products extracted from indigenous sources, compiled from various academic publications. The database features a user-friendly web interface that facilitates easy searching and browsing of compounds. Each entry in SANCDB is meticulously linked to its original source, ensuring transparency and credibility. Additionally, the platform incorporates a submission system, enabling researchers to contribute their own findings, thus fostering collaborative growth of the database. As the first of its kind in Africa, SANCDB aims to bolster in silico screening of South African natural products for drug discovery purposes. This freely accessible resource marks a crucial step towards establishing a community-driven platform to enhance natural products research in South Africa, with potential to significantly impact the field of drug discovery.

10.71606/coconut.cnpc0039

NANPDB (Natural Products from Northern African Sources)

NANPDB, the Northern African Natural Products Database, is a comprehensive online repository of natural products sourced from Northern Africa. This extensive library encompasses compounds derived from plants, animals, fungi, and bacteria. The database was meticulously compiled by gathering information from a wide range of sources, including prominent natural product journals, local African publications, and doctoral theses found in university libraries. NANPDB covers an extensive period, showcasing the rich diversity of natural products in the region. The database primarily focuses on plant-derived compounds but also includes contributions from endophytes, animals (such as corals), fungi, and bacteria. To enhance its utility for researchers, NANPDB incorporates computed physicochemical properties for each compound, which are valuable for predicting drug metabolism and pharmacokinetics. This feature makes NANPDB an invaluable resource for scientists exploring potential new drugs and other applications of natural products from Northern Africa. License: This database is freely accessible. Terms and rights are at the sole discretion of the prospective user, and as agreed with the scientific author(s) or publishing house.

10.71606/coconut.cnpc0027

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

VietHerb

VIETHERB is a comprehensive database of Vietnamese traditional medicinal herbs. It aims to organize and digitize information that was previously scattered across handwritten records and text-based systems. The database provides detailed data on various herb species, including their metabolites, therapeutic effects, morphological characteristics, and geographical distributions. VIETHERB serves as a valuable resource for researchers, practitioners, and others interested in traditional Vietnamese medicine. Users can easily search for specific herbs using scientific names or explore connections between different species based on shared attributes. This centralized repository of herbal knowledge supports efforts to modernize traditional medicine, aids in drug discovery research, and contributes to the conservation of plant biodiversity. By making this wealth of information readily accessible, VIETHERB facilitates the study, evaluation, and potential integration of Vietnamese herbal remedies with modern medical practices. License: No Licensing information (Cite paper)

10.71606/coconut.cnpc0051

NPACT

The Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database (NPACT) is a comprehensive resource for biomedical researchers and pharmaceutical companies interested in plant-derived molecules for drug development. This centralized database, accessible at crdd.osdd.net/raghava/npact/, compiles information on experimentally validated plant-based compounds with anti-cancer properties. NPACT offers detailed records for each compound, including structural data, curated experimental results from both in vitro and in vivo studies, and references for further investigation. The database provides a wealth of information on the compounds' properties, their effects on various cancer types and cell lines, identified protein targets, and commercial availability. To enhance its utility, NPACT features user-friendly browsing and querying options, as well as an online similarity tool. The database is also interconnected with other relevant resources in the field, facilitating broader access to related information and supporting comprehensive research in plant-derived anti-cancer compounds. License: No Licensing information (Cite paper)

10.71606/coconut.cnpc0029

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

ConMedNP

ConMedNP evaluates the medicinal potential and "drug-likeness" of roughly 3200 natural compounds and their hemisynthetic derivatives from the Central African flora. The research focuses on 376 medicinal plant species across 79 families, using literature data and 3D structure analysis to assess oral availability based on Lipinski's "Rule of Five." The compounds were categorized into "drug-like," "lead-like," and "fragment-like" subsets and compared with existing databases like CamMedNP and the Dictionary of Natural products. A diversity analysis was also performed against the ChemBridge DIVERSet™ Database. The findings suggest that Central African flora holds promise for drug discovery, and the available 3D structures could be valuable resources for virtual screening and natural product lead generation.

10.71606/coconut.cnpc0012

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 : C31H40O15
  • Mol. Weight 652.23672
  • Total atom number : 86
  • Heavy atom number : 46
  • Aromatic Ring Count : 2
  • Rotatable Bond count : 12
  • Minimal number of rings : 4
  • Formal Charge : 86
  • Contains Sugar : True
  • Contains Ring Sugars : True
  • Contains Linear Sugars : False

Molecular Descriptors

  • NP-likeness scores : 1.75
  • Alogp : -0.41
  • TopoPSA : 223.29
  • Fsp3 : 0.52
  • Hydrogen Bond Acceptor Count : 15
  • Hydrogen Bond Donor Count : 7
  • Lipinski Hydrogen Bond Acceptor Count : 15
  • Lipinski Hydrogen Bond Donor Count : 7
  • Lipinski RO5 Violations : 3
2D
beta-D-Glucopyranoside, 2-(3-hydroxy-4-methoxyphenyl)ethyl 3-O-(6-deoxy-alpha-L-mannopyranosyl)-, 4-[3-(4-hydroxy-3-methoxyphenyl)-2-propenoate], (E)-
3D Structure (by RDKit) Interactive JSmol molecular viewer 3D
Report this compound
Request changes to this page

This website requires cookies, and the limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our Privacy Notice and Terms of Use.