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Gentamicin C1A

PubChem CID
72396
Structure
Gentamicin C1A_small.png
Gentamicin C1A_3D_Structure.png
Molecular Formula
Synonyms
  • Gentamicin C1a
  • 26098-04-4
  • Gentamycin C1A
  • Gentamycin C12
  • Gentamicin Cla
Molecular Weight
449.5 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2004-09-16
  • Modify:
    2025-01-18
Description
Gentamycin C1a is a gentamycin C. It is a conjugate base of a gentamycin C1a(5+).
Gentamicin C1a has been reported in Cordyceps farinosa, Serratia plymuthica, and other organisms with data available.
Gentamicin C1a is one of the major components of the gentamicin complex. Gentamicin C1a lacks methyl groups on the 2-amino-hexose ring and has a free amine at the 6' position.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Gentamicin C1A.png

1.2 3D Conformer

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

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

2.1.2 InChI

InChI=1S/C19H39N5O7/c1-19(27)7-28-18(13(26)16(19)24-2)31-15-11(23)5-10(22)14(12(15)25)30-17-9(21)4-3-8(6-20)29-17/h8-18,24-27H,3-7,20-23H2,1-2H3/t8-,9+,10-,11+,12-,13+,14+,15-,16+,17+,18+,19-/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.3 InChIKey

VEGXETMJINRLTH-BOZYPMBZSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.4 SMILES

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

2.2 Molecular Formula

C19H39N5O7
Computed by PubChem 2.2 (PubChem release 2021.10.14)

2.3 Other Identifiers

2.3.1 CAS

2.3.2 Deprecated CAS

58207-27-5

2.3.3 European Community (EC) Number

2.3.4 UNII

2.3.5 ChEBI ID

2.3.6 ChEMBL ID

2.3.7 DrugBank ID

2.3.8 DSSTox Substance ID

2.3.9 KEGG ID

2.3.10 Metabolomics Workbench ID

2.3.11 NCI Thesaurus Code

2.3.12 Nikkaji Number

2.3.13 Wikidata

2.4 Synonyms

2.4.1 MeSH Entry Terms

  • gentamicin C
  • gentamicin C sulfate
  • gentamicin C1
  • gentamicin C1 sulfate
  • gentamicin C1 sulfate (5:2)
  • gentamicin C1a
  • gentamicin C2
  • gentamicin C2a
  • Sch 13706

2.4.2 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
449.5 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
-5
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
8
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
12
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
449.28494860 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
449.28494860 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
214 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
31
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
592
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
12
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)

3.2 Experimental Properties

3.2.1 Collision Cross Section

212.3 Ų [M+Na]+ [CCS Type: TW; Method: calibrated with Waters Major Mix]

212.1 Ų [M+H]+ [CCS Type: TW; Method: calibrated with Waters Major Mix]

3.3 Chemical Classes

3.3.1 Drugs

Pharmaceuticals -> Antibiotics
S6 | ITNANTIBIOTIC | Antibiotic List from the ITN MSCA ANSWER | DOI:10.5281/zenodo.2621956
Pharmaceuticals -> Listed in ZINC15
S55 | ZINC15PHARMA | Pharmaceuticals from ZINC15 | DOI:10.5281/zenodo.3247749

4 Spectral Information

4.1 1D NMR Spectra

4.1.1 13C NMR Spectra

1 of 2
Instrument Name
Bruker WH-90
Copyright
Copyright © 2002-2024 Wiley-VCH Verlag GmbH & Co. KGaA. All Rights Reserved.
Thumbnail
Thumbnail
2 of 2
Instrument Name
Bruker WH-90
Copyright
Copyright © 2002-2024 Wiley-VCH Verlag GmbH & Co. KGaA. All Rights Reserved.
Thumbnail
Thumbnail

6 Chemical Vendors

7 Safety and Hazards

7.1 Hazards Identification

7.1.1 GHS Classification

Pictogram(s)
Health Hazard
Environmental Hazard
Signal
Danger
GHS Hazard Statements

H317 (100%): May cause an allergic skin reaction [Warning Sensitization, Skin]

H334 (100%): May cause allergy or asthma symptoms or breathing difficulties if inhaled [Danger Sensitization, respiratory]

H360D (100%): May damage the unborn child [Danger Reproductive toxicity]

H400 (100%): Very toxic to aquatic life [Warning Hazardous to the aquatic environment, acute hazard]

H410 (100%): Very toxic to aquatic life with long lasting effects [Warning Hazardous to the aquatic environment, long-term hazard]

Precautionary Statement Codes

P203, P233, P260, P261, P271, P272, P273, P280, P284, P302+P352, P304+P340, P318, P321, P333+P317, P342+P316, P362+P364, P391, P403, P405, and P501

(The corresponding statement to each P-code can be found at the GHS Classification page.)

ECHA C&L Notifications Summary
The GHS information provided by 1 company from 1 notification to the ECHA C&L Inventory.

7.1.2 Hazard Classes and Categories

Skin Sens. 1B (100%)

Resp. Sens. 1B (100%)

Repr. 1B (100%)

Aquatic Acute 1 (100%)

Aquatic Chronic 1 (100%)

8 Toxicity

8.1 Toxicological Information

8.1.1 Acute Effects

9 Literature

9.1 Consolidated References

9.2 NLM Curated PubMed Citations

9.3 Springer Nature References

9.4 Nature Journal References

9.5 Chemical Co-Occurrences in Literature

9.6 Chemical-Gene Co-Occurrences in Literature

9.7 Chemical-Disease Co-Occurrences in Literature

10 Patents

10.1 Depositor-Supplied Patent Identifiers

10.2 WIPO PATENTSCOPE

10.3 Chemical Co-Occurrences in Patents

10.4 Chemical-Disease Co-Occurrences in Patents

10.5 Chemical-Gene Co-Occurrences in Patents

11 Interactions and Pathways

11.1 Protein Bound 3D Structures

11.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Conformer

11.2 Chemical-Target Interactions

11.3 Drug-Drug Interactions

12 Biological Test Results

12.1 BioAssay Results

13 Taxonomy

The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata) | DOI:10.5281/zenodo.5794106

14 Classification

14.1 MeSH Tree

14.2 NCI Thesaurus Tree

14.3 ChEBI Ontology

14.4 ChemIDplus

14.5 ChEMBL Target Tree

14.6 UN GHS Classification

14.7 NORMAN Suspect List Exchange Classification

14.8 CCSBase Classification

14.9 EPA DSSTox Classification

14.10 LOTUS Tree

14.11 MolGenie Organic Chemistry Ontology

15 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/
  2. ChemIDplus
    ChemIDplus Chemical Information Classification
    https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
  3. DrugBank
    LICENSE
    Creative Common's Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/legalcode)
    https://www.drugbank.ca/legal/terms_of_use
  4. EPA DSSTox
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  5. European Chemicals Agency (ECHA)
    LICENSE
    Use of the information, documents and data from the ECHA website is subject to the terms and conditions of this Legal Notice, and subject to other binding limitations provided for under applicable law, the information, documents and data made available on the ECHA website may be reproduced, distributed and/or used, totally or in part, for non-commercial purposes provided that ECHA is acknowledged as the source: "Source: European Chemicals Agency, http://echa.europa.eu/". Such acknowledgement must be included in each copy of the material. ECHA permits and encourages organisations and individuals to create links to the ECHA website under the following cumulative conditions: Links can only be made to webpages that provide a link to the Legal Notice page.
    https://echa.europa.eu/web/guest/legal-notice
  6. 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
  7. CCSbase
    CCSbase Classification
    https://ccsbase.net/
  8. ChEBI
  9. LOTUS - the natural products occurrence database
    LICENSE
    The code for LOTUS is released under the GNU General Public License v3.0.
    https://lotus.nprod.net/
  10. NCI Thesaurus (NCIt)
    LICENSE
    Unless otherwise indicated, all text within NCI products is free of copyright and may be reused without our permission. Credit the National Cancer Institute as the source.
    https://www.cancer.gov/policies/copyright-reuse
  11. ChEMBL
    LICENSE
    Access to the web interface of ChEMBL is made under the EBI's Terms of Use (http://www.ebi.ac.uk/Information/termsofuse.html). The ChEMBL data is made available on a Creative Commons Attribution-Share Alike 3.0 Unported License (http://creativecommons.org/licenses/by-sa/3.0/).
    http://www.ebi.ac.uk/Information/termsofuse.html
  12. Japan Chemical Substance Dictionary (Nikkaji)
  13. 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
  14. Natural Product Activity and Species Source (NPASS)
  15. Metabolomics Workbench
  16. Nature Chemical Biology
  17. NORMAN Suspect List Exchange
    LICENSE
    Data: CC-BY 4.0; Code (hosted by ECI, LCSB): Artistic-2.0
    https://creativecommons.org/licenses/by/4.0/
    Gentamicin C1a
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  18. Protein Data Bank in Europe (PDBe)
  19. 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
  20. SpectraBase
  21. Springer Nature
  22. Wikidata
  23. PubChem
  24. Medical Subject Headings (MeSH)
    LICENSE
    Works produced by the U.S. government are not subject to copyright protection in the United States. Any such works found on National Library of Medicine (NLM) Web sites may be freely used or reproduced without permission in the U.S.
    https://www.nlm.nih.gov/copyright.html
  25. GHS Classification (UNECE)
  26. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  27. PATENTSCOPE (WIPO)
CONTENTS