CNP0115962.0

A-90289 A

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).
1.24
Annotation Level
★ ★ ★ ★ ☆
Mol. Weight
1225.54108
Mol. Formula
C53H87N5O25S

Organisms (1)

Representations

Molecular details

COCONUT id
CNP0115962.0
Name
A-90289 A
IUPAC name
2-[[5-(aminomethyl)-3,4-dihydroxy-tetrahydrofuran-2-yl]oxy-[5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-4-sulfooxy-tetrahydrofuran-2-yl]methyl]-1,4-dimethyl-6-[3-[3-methyl-5-oxo-5-(3,4,5-trimethoxy-6-methyl-tetrahydropyran-2-yl)oxy-pentanoyl]oxyhexadecanoyloxy]-3-oxo-1,4-diazepane-5-carboxylic acid
InChI
InChI=1S/C53H87N5O25S/c1-9-10-11-12-13-14-15-16-17-18-19-20-30(77-34(60)23-28(2)24-35(61)80-52-47(75-8)46(74-7)42(73-6)29(3)76-52)25-36(62)78-32-27-56(4)38(48(66)57(5)37(32)50(67)68)43(82-51-40(64)39(63)31(26-54)79-51)44-41(65)45(83-84(70,71)72)49(81-44)58-22-21-33(59)55-53(58)69/h21-22,28-32,37-47,49,51-52,63-65H,9-20,23-27,54H2,1-8H3,(H,67,68)(H,55,59,69)(H,70,71,72)
InChIKey
QEIIFQMHVIQJFR-UHFFFAOYSA-N
Canonical SMILES (RDKit)
CCCCCCCCCCCCCC(CC(=O)OC1CN(C)C(C(OC2OC(CN)C(O)C2O)C2OC(N3C=CC(=O)NC3=O)C(OS(=O)(=O)O)C2O)C(=O)N(C)C1C(=O)O)OC(=O)CC(C)CC(=O)OC1OC(C)C(OC)C(OC)C1OC
Murcko Framework
O(CCCOC1CNCC(NC1)C(OC2OCCC2)C3OC(N4C=CCNC4)CC3)CCCCCOC5OCCCC5
Synonyms
  • CHEBI:199353
  • 2-[[5-(aminomethyl)-3,4-dihydroxyoxolan-2-yl]oxy-[5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-4-sulooxyoxolan-2-yl]methyl]-1,4-dimethyl-6-[3-[3-methyl-5-oxo-5-(3,4,5-trimethoxy-6-methyloxan-2-yl)oxypentanoyl]oxyhexadecanoyloxy]-3-oxo-1,4-diazepane-5-carboxylic acid
  • A-90289 A

Chemical classification

NP Classification

References

Citations

A-90289 A and B, new inhibitors of bacterial translocase I, produced by Streptomyces sp. SANK 60405.

Fujita Y, Kizuka M, Funabashi M, Ogawa Y, Ishikawa T, Nonaka K, Takatsu T.

DOI: 10.1038/ja.2011.38

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

StreptomeDB

StreptomeDB is a pioneering online database that facilitates interactive phylogenetic exploration of streptomycetes and their natural products (NPs). As the first and only public resource of its kind, it serves as a vital tool in the quest for novel antimicrobials to combat the growing threat of antimicrobial resistance. The database focuses on NPs isolated from or mutasynthesized by streptomycetes, soil bacteria that have been the source of many existing antibiotics. In its third release, StreptomeDB has undergone significant enhancements, particularly in terms of data content. The database now includes a wealth of newly annotated NPs, curated from recent scientific literature. To improve its utility and integration with other resources, entries in StreptomeDB have been linked to various spectral, biochemical, and chemical vendor databases, as well as a genome-based NP prediction server. Additionally, the database now provides predicted pharmacokinetic and toxicity profiles for the compounds. StreptomeDB's real-world applications in life sciences underscore its importance as a source of inspiration for the rational design of new antibiotics, potentially unlocking the vast, untapped reservoir of streptomycetes NPs. License: No license information (Cite Paper)

10.71606/coconut.cnpc0043

ChemSpider NPs

ChemSpider is a free, online chemical database offering access to physical and chemical properties, molecular structure, spectral data, synthetic methods, safety information, and nomenclature for almost 25 million unique chemical compounds sourced and linked to almost 400 separate data sources on the Web.

10.71606/coconut.cnpc0010

Stereochemical Variants

Molecular Properties

  • Mol. Formula : C53H87N5O25S
  • Mol. Weight 1225.54108
  • Total atom number : 171
  • Heavy atom number : 84
  • Aromatic Ring Count : 1
  • Rotatable Bond count : 33
  • Minimal number of rings : 5
  • Formal Charge : 171
  • Contains Sugar : True
  • Contains Ring Sugars : True
  • Contains Linear Sugars : False

Molecular Descriptors

  • NP-likeness scores : 1.24
  • Alogp : -0.34
  • TopoPSA : 409.53
  • Fsp3 : 0.83
  • Hydrogen Bond Acceptor Count : 26
  • Hydrogen Bond Donor Count : 7
  • Lipinski Hydrogen Bond Acceptor Count : 26
  • Lipinski Hydrogen Bond Donor Count : 7
  • Lipinski RO5 Violations : 3
2D
A-90289 A
3D Structure (by RDKit) Interactive JSmol molecular viewer 3D
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