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3''-deamino-3''-hydroxykanamycin B

PubChem CID
11784999
Structure
3''-deamino-3''-hydroxykanamycin B_small.png
3''-deamino-3''-hydroxykanamycin B_3D_Structure.png
Molecular Formula
Synonyms
  • Nebramycin III
  • Nebramycin factor 3
  • 31077-70-0
  • 3''-deamino-3''-hydroxykanamycin B
  • NK 1012-1
Molecular Weight
484.5 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2006-10-26
  • Modify:
    2025-01-18
Description
3''-deamino-3''-hydroxykanamycin B is a kanamycin that is kanamycin B in which the 3''-amino group has been replaced by a hydroxy group. It is functionally related to a kanamycin B. It is a conjugate base of a 3''-deamino-3''-hydroxykanamycin B(4+).

1 Structures

1.1 2D Structure

Chemical Structure Depiction
3''-deamino-3''-hydroxykanamycin B.png

1.2 3D Conformer

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

(2S,3R,4S,5S,6R)-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2R,3R,4R,5S,6R)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

2.1.2 InChI

InChI=1S/C18H36N4O11/c19-2-6-9(24)11(26)8(22)17(30-6)32-15-4(20)1-5(21)16(14(15)29)33-18-13(28)12(27)10(25)7(3-23)31-18/h4-18,23-29H,1-3,19-22H2/t4-,5+,6+,7+,8+,9+,10+,11+,12-,13+,14-,15+,16-,17+,18+/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.3 InChIKey

MOWMHIINUAQFMU-DNBVWFFRSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.4 SMILES

C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)N)N
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

2.2 Molecular Formula

C18H36N4O11
Computed by PubChem 2.2 (PubChem release 2021.10.14)

2.3 Other Identifiers

2.3.1 CAS

2.3.2 UNII

2.3.3 ChEBI ID

2.3.4 KEGG ID

2.3.5 Metabolomics Workbench ID

2.3.6 Nikkaji Number

2.3.7 Wikidata

2.4 Synonyms

2.4.1 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
484.5 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
-6.9
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
11
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
15
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
484.23805798 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
484.23805798 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
283 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
33
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
638
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Isotope Atom Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Atom Stereocenter Count
Property Value
15
Reference
Computed by PubChem
Property Name
Undefined Atom Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Undefined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Covalently-Bonded Unit Count
Property Value
1
Reference
Computed by PubChem
Property Name
Compound Is Canonicalized
Property Value
Yes
Reference
Computed by PubChem (release 2021.10.14)

5 Chemical Vendors

6 Toxicity

6.1 Toxicological Information

6.1.1 Acute Effects

7 Literature

7.1 Consolidated References

7.2 Springer Nature References

7.3 Nature Journal References

7.4 Chemical Co-Occurrences in Literature

8 Patents

8.1 Depositor-Supplied Patent Identifiers

8.2 Chemical Co-Occurrences in Patents

8.3 Chemical-Disease Co-Occurrences in Patents

8.4 Chemical-Gene Co-Occurrences in Patents

9 Interactions and Pathways

9.1 Protein Bound 3D Structures

9.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

10 Classification

10.1 ChEBI Ontology

10.2 ChemIDplus

10.3 MolGenie Organic Chemistry Ontology

11 Information Sources

  1. CAS Common Chemistry
    LICENSE
    The data from CAS Common Chemistry is provided under a CC-BY-NC 4.0 license, unless otherwise stated.
    https://creativecommons.org/licenses/by-nc/4.0/
    3′′-Deamino-3′′-hydroxykanamycin B
    https://commonchemistry.cas.org/detail?cas_rn=31077-70-0
  2. ChemIDplus
    ChemIDplus Chemical Information Classification
    https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
  3. FDA Global Substance Registration System (GSRS)
    LICENSE
    Unless otherwise noted, the contents of the FDA website (www.fda.gov), both text and graphics, are not copyrighted. They are in the public domain and may be republished, reprinted and otherwise used freely by anyone without the need to obtain permission from FDA. Credit to the U.S. Food and Drug Administration as the source is appreciated but not required.
    https://www.fda.gov/about-fda/about-website/website-policies#linking
  4. ChEBI
  5. Japan Chemical Substance Dictionary (Nikkaji)
  6. KEGG
    LICENSE
    Academic users may freely use the KEGG website. Non-academic use of KEGG generally requires a commercial license
    https://www.kegg.jp/kegg/legal.html
  7. Metabolomics Workbench
  8. Nature Chemical Biology
  9. Protein Data Bank in Europe (PDBe)
  10. RCSB Protein Data Bank (RCSB PDB)
    LICENSE
    Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data.
    https://www.rcsb.org/pages/policies
  11. Springer Nature
  12. Wikidata
  13. PubChem
  14. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
CONTENTS