CNP0181691.0

SU-3

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).
1.67
Annotation Level
★ ★ ★ ★ ☆
Mol. Weight
464.28461
Mol. Formula
C20H40N4O8

Organisms (1)

Representations

Molecular details

COCONUT id
CNP0181691.0
Name
SU-3
IUPAC name
2-[4-amino-3-[3-amino-6-(methylaminomethyl)tetrahydropyran-2-yl]oxy-2,6-dihydroxy-cyclohexoxy]-5-methyl-4-(methylamino)tetrahydropyran-3,5-diol
InChI
InChI=1S/C20H40N4O8/c1-20(28)8-29-19(14(27)17(20)24-3)32-16-12(25)6-11(22)15(13(16)26)31-18-10(21)5-4-9(30-18)7-23-2/h9-19,23-28H,4-8,21-22H2,1-3H3
InChIKey
RNBRFANQNIXKOX-UHFFFAOYSA-N
Canonical SMILES (RDKit)
CNCC1CCC(N)C(OC2C(N)CC(O)C(OC3OCC(C)(O)C(NC)C3O)C2O)O1
Murcko Framework
O1CCCCC1OC2CCCC(OC3OCCCC3)C2
Synonyms
  • 72614-86-9
  • CHEBI:223311
  • (2R,3R,4R,5R)-2-[(1S,2S,3R,4S,6R)-4-amino-3-[(2R,3R,6S)-3-amino-6-(methylaminomethyl)oxan-2-yl]oxy-2,6-dihydroxycyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol
  • 2-[4-amino-3-[3-amino-6-(methylaminomethyl)oxan-2-yl]oxy-2,6-dihydroxycyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol
  • 6-O-(4-C-Methyl-3-methylamino-3-deoxy-beta-L-arabinopyranosyl)-4-O-(2-amino-6-methylamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)-3-amino-2,3-dideoxy-D-myo-inositol
  • SU-3
  • 1-Deamino-1-hydroxysagamicin
CAS
  • 72614-86-9

Chemical classification

NP Classification

References

Citations

Production of antibiotic SU-2 complex by a 2-deoxystreptamine idiotroph of Micromonospora sagamiensis.

Kase H, Kitamura S, Nakayama K.

DOI: 10.7164/antibiotics.35.385

Lens.org

Collections

NPAtlas

The Natural Products Atlas (www.npatlas.org) is an open-access database of microbial natural product structures. It addresses the lack of a comprehensive, freely available resource for these compounds, which has hindered the development of new technologies in natural products science. The database was created through manual curation and automated data mining of scientific literature and patents, overcoming challenges such as non-standardized formats and non-digitized texts. It provides referenced data on structures, names, source organisms, isolation references, total syntheses, and structural reassignments. The accompanying web portal offers interactive tools for searching, visualizing chemical space, and exploring discovery timelines. Developed under FAIR principles, the Natural Products Atlas integrates with other databases like MIBiG and GNPS. As a community-supported resource, it aims to accelerate natural products discovery and structural characterization processes.

10.71606/coconut.cnpc0031

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

Molecular Properties

  • Mol. Formula : C20H40N4O8
  • Mol. Weight 464.28461
  • Total atom number : 72
  • Heavy atom number : 32
  • Aromatic Ring Count : 0
  • Rotatable Bond count : 7
  • Minimal number of rings : 3
  • Formal Charge : 72
  • Contains Sugar : True
  • Contains Ring Sugars : True
  • Contains Linear Sugars : False

Molecular Descriptors

  • NP-likeness scores : 1.67
  • Alogp : -3.68
  • TopoPSA : 193.94
  • Fsp3 : 1.00
  • Hydrogen Bond Acceptor Count : 12
  • Hydrogen Bond Donor Count : 8
  • Lipinski Hydrogen Bond Acceptor Count : 12
  • Lipinski Hydrogen Bond Donor Count : 8
  • Lipinski RO5 Violations : 2
2D
SU-3
3D Structure (by RDKit) Interactive JSmol molecular viewer 3D
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