CNP0186002.0

2-[2-[4,5-dihydroxy-2-(hydroxymethyl)-6-(5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-tetrahydropyran]-16-yl)oxy-tetrahydropyran-3-yl]oxy-5-hydroxy-6-(hydroxymethyl)-3-[3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-tetrahydropyran-4-yl]oxy-6-(hydroxymethyl)tetrahydropyran-3,4,5-triol

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).
1.86
Annotation Level
★ ☆ ☆ ☆ ☆
Mol. Weight
1064.54034
Mol. Formula
C51H84O23

Representations

Molecular details

COCONUT id
CNP0186002.0
Name
-
IUPAC name
2-[2-[4,5-dihydroxy-2-(hydroxymethyl)-6-(5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-tetrahydropyran]-16-yl)oxy-tetrahydropyran-3-yl]oxy-5-hydroxy-6-(hydroxymethyl)-3-[3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-tetrahydropyran-4-yl]oxy-6-(hydroxymethyl)tetrahydropyran-3,4,5-triol
InChI
InChI=1S/C51H84O23/c1-20-7-12-51(65-19-20)21(2)32-27(74-51)14-26-24-6-5-22-13-23(8-10-49(22,3)25(24)9-11-50(26,32)4)66-45-41(64)38(61)42(31(18-55)70-45)71-48-44(73-47-40(63)37(60)34(57)29(16-53)68-47)43(35(58)30(17-54)69-48)72-46-39(62)36(59)33(56)28(15-52)67-46/h20-48,52-64H,5-19H2,1-4H3
InChIKey
HMQLHCKDYUUVRG-UHFFFAOYSA-N
Canonical SMILES (RDKit)
CC1CCC2(OC1)OC1CC3C4CCC5CC(OC6OC(CO)C(OC7OC(CO)C(O)C(OC8OC(CO)C(O)C(O)C8O)C7OC7OC(CO)C(O)C(O)C7O)C(O)C6O)CCC5(C)C4CCC3(C)C1C2C
Murcko Framework
O1CCCCC1OC2CCOC(OC3COC(OC4CCC5C(CCC6C5CCC7C8CC9(OCCCC9)OC8CC67)C4)CC3)C2OC%10OCCCC%10

Chemical classification

NP Classification

References

Citations

No citations

Collections

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

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

HIT (Herbal Ingredients Targets)

The Herb Ingredients' Targets (HIT) database is a comprehensive and curated resource detailing the protein targets of herbal active ingredients. The database includes information on 586 herbal compounds from over 1300 reputable Chinese herbs, affecting 1301 known protein targets. Among these, 221 are direct targets. The dataset is derived from more than 3250 literatures and provides 5208 entries, overlapping with 280 therapeutic targets from the Therapeutic Targets Database (TTD) and 445 protein targets from DrugBank, corresponding to 1488 drug agents. HIT includes data on proteins directly or indirectly activated or inhibited by herbal compounds, as well as protein binders and enzymes that interact with these compounds. Additionally, the dataset features information on up/down-regulated genes in response to individual ingredients, along with experimental conditions, observed bioactivity, and various references. Crosslinks to other databases such as TTD, DrugBank, KEGG, PDB, Uniprot, Pfam, NCBI, and TCM-ID are also provided for extensive research opportunities. License: HIT is strictly for academic use only. Any commercial application should contact us at zwcao@tongji.edu.cn

10.71606/coconut.cnpc0018

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

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 : C51H84O23
  • Mol. Weight 1064.54034
  • Total atom number : 158
  • Heavy atom number : 74
  • Aromatic Ring Count : 0
  • Rotatable Bond count : 12
  • Minimal number of rings : 10
  • Formal Charge : 158
  • Contains Sugar : True
  • Contains Ring Sugars : True
  • Contains Linear Sugars : False

Molecular Descriptors

  • NP-likeness scores : 1.86
  • Alogp : -2.91
  • TopoPSA : 355.29
  • Fsp3 : 1.00
  • Hydrogen Bond Acceptor Count : 23
  • Hydrogen Bond Donor Count : 13
  • Lipinski Hydrogen Bond Acceptor Count : 23
  • Lipinski Hydrogen Bond Donor Count : 13
  • Lipinski RO5 Violations : 3
2D
3D Structure (by RDKit) Interactive JSmol molecular viewer 3D
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