CNP0123784.0

2-[[3-[3-amino-6-(aminomethyl)-4,5-dihydroxy-tetrahydropyran-2-yl]oxy-5-[3,5-diamino-2-[3-amino-6-(aminomethyl)-4,5-dihydroxy-tetrahydropyran-2-yl]oxy-6-hydroxy-cyclohexoxy]-4-hydroxy-tetrahydrofuran-2-yl]methoxy]-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).
1.17
Annotation Level
★ ★ ☆ ☆ ☆
Mol. Weight
776.36511
Mol. Formula
C29H56N6O18

Representations

Molecular details

COCONUT id
CNP0123784.0
Name
-
IUPAC name
2-[[3-[3-amino-6-(aminomethyl)-4,5-dihydroxy-tetrahydropyran-2-yl]oxy-5-[3,5-diamino-2-[3-amino-6-(aminomethyl)-4,5-dihydroxy-tetrahydropyran-2-yl]oxy-6-hydroxy-cyclohexoxy]-4-hydroxy-tetrahydrofuran-2-yl]methoxy]-6-(hydroxymethyl)tetrahydropyran-3,4,5-triol
InChI
InChI=1S/C29H56N6O18/c30-2-8-15(38)18(41)12(34)26(47-8)51-23-7(33)1-6(32)14(37)25(23)53-29-22(45)24(52-27-13(35)19(42)16(39)9(3-31)48-27)11(50-29)5-46-28-21(44)20(43)17(40)10(4-36)49-28/h6-29,36-45H,1-5,30-35H2
InChIKey
RFQNNKVMXDYKTI-UHFFFAOYSA-N
Canonical SMILES (RDKit)
NCC1OC(OC2C(COC3OC(CO)C(O)C(O)C3O)OC(OC3C(O)C(N)CC(N)C3OC3OC(CN)C(O)C(O)C3N)C2O)C(N)C(O)C1O
Murcko Framework
O1CCCCC1OCC2OC(OC3CCCCC3OC4OCCCC4)CC2OC5OCCCC5
Synonyms
  • Neomycin-B-glucoside

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

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 : C29H56N6O18
  • Mol. Weight 776.36511
  • Total atom number : 109
  • Heavy atom number : 53
  • Aromatic Ring Count : 0
  • Rotatable Bond count : 12
  • Minimal number of rings : 5
  • Formal Charge : 109
  • Contains Sugar : True
  • Contains Ring Sugars : True
  • Contains Linear Sugars : False

Molecular Descriptors

  • NP-likeness scores : 1.17
  • Alogp : -11.07
  • TopoPSA : 432.26
  • Fsp3 : 1.00
  • Hydrogen Bond Acceptor Count : 24
  • Hydrogen Bond Donor Count : 16
  • Lipinski Hydrogen Bond Acceptor Count : 24
  • Lipinski Hydrogen Bond Donor Count : 16
  • Lipinski RO5 Violations : 3
2D
3D Structure (by RDKit) Interactive JSmol molecular viewer 3D

Contributors

1
COCONUT Curator
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