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Nigericin

PubChem CID
34230
Structure
Nigericin_small.png
Molecular Formula
Synonyms
  • nigericin
  • Azalomycin M
  • 28380-24-7
  • Helixin C
  • Antibiotic X-464
Molecular Weight
725.0 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2005-06-24
  • Modify:
    2025-01-11
Description
Nigericin is a polyether antibiotic which affects ion transport and ATPase activity in mitochondria. It is produced by Streptomyces hygroscopicus. It has a role as an antimicrobial agent, an antibacterial agent, a potassium ionophore and a bacterial metabolite.
A polyether antibiotic which affects ion transport and ATPase activity in mitochondria. It is produced by Streptomyces hygroscopicus. (From Merck Index, 11th ed)
Nigericin has been reported in Streptomyces, Streptomyces violaceusniger, and Streptomyces hygroscopicus with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Nigericin.png

1.2 3D Status

Conformer generation is disallowed since too many atoms

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

(2R)-2-[(2R,3S,6R)-6-[[(2S,4R,5R,6R,7R,9R)-2-[(2R,5S)-5-[(2R,3S,5R)-5-[(2S,3S,5R,6R)-6-hydroxy-6-(hydroxymethyl)-3,5-dimethyloxan-2-yl]-3-methyloxolan-2-yl]-5-methyloxolan-2-yl]-7-methoxy-2,4,6-trimethyl-1,10-dioxaspiro[4.5]decan-9-yl]methyl]-3-methyloxan-2-yl]propanoic acid
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

2.1.2 InChI

InChI=1S/C40H68O11/c1-21-11-12-28(46-33(21)26(6)36(42)43)17-29-18-30(45-10)27(7)40(48-29)25(5)19-38(9,51-40)32-13-14-37(8,49-32)35-23(3)16-31(47-35)34-22(2)15-24(4)39(44,20-41)50-34/h21-35,41,44H,11-20H2,1-10H3,(H,42,43)/t21-,22-,23-,24+,25+,26+,27+,28+,29+,30+,31+,32+,33+,34-,35+,37-,38-,39-,40+/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.3 InChIKey

DANUORFCFTYTSZ-SJSJOXFOSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.4 SMILES

C[C@H]1CC[C@@H](O[C@H]1[C@@H](C)C(=O)O)C[C@@H]2C[C@H]([C@H]([C@@]3(O2)[C@@H](C[C@@](O3)(C)[C@H]4CC[C@@](O4)(C)[C@H]5[C@H](C[C@@H](O5)[C@@H]6[C@H](C[C@H]([C@@](O6)(CO)O)C)C)C)C)C)OC
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

2.2 Molecular Formula

C40H68O11
Computed by PubChem 2.2 (PubChem release 2021.10.14)

2.3 Other Identifiers

2.3.1 CAS

28643-80-3

2.3.2 European Community (EC) Number

2.3.3 UNII

2.3.4 ChEBI ID

2.3.5 ChEMBL ID

2.3.6 DrugBank ID

2.3.7 DSSTox Substance ID

2.3.8 KEGG ID

2.3.9 Metabolomics Workbench ID

2.3.10 Nikkaji Number

2.3.11 Wikidata

2.3.12 Wikipedia

2.4 Synonyms

2.4.1 MeSH Entry Terms

  • Epinigericin
  • Nigericin
  • Pandavir

2.4.2 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
725.0 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
5.5
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
3
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
11
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
9
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
724.47616298 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
724.47616298 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
142 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
51
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
1230
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
19
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 Chemical Classes

3.2.1 Drugs

Pharmaceuticals -> Antibiotics
S6 | ITNANTIBIOTIC | Antibiotic List from the ITN MSCA ANSWER | DOI:10.5281/zenodo.2621956

3.2.2 Pesticides

Biocide
S120 | DUSTCT2024 | Substances from Second NORMAN Collaborative Dust Trial | DOI:10.5281/zenodo.13835254

4 Spectral Information

4.1 1D NMR Spectra

4.1.1 13C NMR Spectra

Copyright
Copyright © 2016-2024 W. Robien, Inst. of Org. Chem., Univ. of Vienna. All Rights Reserved.
Thumbnail
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4.2 Mass Spectrometry

4.2.1 GC-MS

Source of Spectrum
Y5-56-584-4
Copyright
Copyright © 2020-2024 John Wiley & Sons, Inc. All Rights Reserved.
Thumbnail
Thumbnail

6 Chemical Vendors

7 Pharmacology and Biochemistry

7.1 MeSH Pharmacological Classification

Ionophores
Chemical agents that increase the permeability of biological or artificial lipid membranes to specific ions. Most ionophores are relatively small organic molecules that act as mobile carriers within membranes or coalesce to form ion permeable channels across membranes. Many are antibiotics, and many act as uncoupling agents by short-circuiting the proton gradient across mitochondrial membranes. (See all compounds classified as Ionophores.)
Anti-Bacterial Agents
Substances that inhibit the growth or reproduction of BACTERIA. (See all compounds classified as Anti-Bacterial Agents.)

8 Safety and Hazards

8.1 Hazards Identification

8.1.1 GHS Classification

1 of 2
View All
Pictogram(s)
Acute Toxic
Irritant
Signal
Danger
GHS Hazard Statements

H301 (100%): Toxic if swallowed [Danger Acute toxicity, oral]

H315 (95.5%): Causes skin irritation [Warning Skin corrosion/irritation]

H319 (97.7%): Causes serious eye irritation [Warning Serious eye damage/eye irritation]

H335 (95.5%): May cause respiratory irritation [Warning Specific target organ toxicity, single exposure; Respiratory tract irritation]

Precautionary Statement Codes

P261, P264, P264+P265, P270, P271, P280, P301+P316, P302+P352, P304+P340, P305+P351+P338, P319, P321, P330, P332+P317, P337+P317, P362+P364, P403+P233, P405, and P501

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

ECHA C&L Notifications Summary

Aggregated GHS information provided per 44 reports by companies from 7 notifications to the ECHA C&L Inventory. Each notification may be associated with multiple companies.

Information may vary between notifications depending on impurities, additives, and other factors. The percentage value in parenthesis indicates the notified classification ratio from companies that provide hazard codes. Only hazard codes with percentage values above 10% are shown.

8.1.2 Hazard Classes and Categories

Acute Tox. 3 (100%)

Skin Irrit. 2 (95.5%)

Eye Irrit. 2 (97.7%)

STOT SE 3 (95.5%)

Acute Tox. 3 (100%)

Skin Irrit. 2 (99.3%)

Eye Irrit. 2 (99.3%)

STOT SE 3 (99.3%)

9 Toxicity

9.1 Toxicological Information

9.1.1 Acute Effects

10 Associated Disorders and Diseases

11 Literature

11.1 Consolidated References

11.2 NLM Curated PubMed Citations

11.3 Chemical Co-Occurrences in Literature

11.4 Chemical-Gene Co-Occurrences in Literature

11.5 Chemical-Disease Co-Occurrences in Literature

12 Patents

12.1 Depositor-Supplied Patent Identifiers

12.2 WIPO PATENTSCOPE

12.3 Chemical Co-Occurrences in Patents

12.4 Chemical-Disease Co-Occurrences in Patents

12.5 Chemical-Gene Co-Occurrences in Patents

13 Interactions and Pathways

13.1 Chemical-Target Interactions

13.2 Drug-Drug Interactions

14 Biological Test Results

14.1 BioAssay Results

15 Taxonomy

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

16 Classification

16.1 MeSH Tree

16.2 ChEBI Ontology

16.3 KEGG: Lipid

16.4 ChemIDplus

16.5 ChEMBL Target Tree

16.6 UN GHS Classification

16.7 NORMAN Suspect List Exchange Classification

16.8 EPA DSSTox Classification

16.9 The Natural Products Atlas Classification

16.10 LOTUS Tree

16.11 EPA Substance Registry Services Tree

16.12 MolGenie Organic Chemistry Ontology

17 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. ChEBI
  8. 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/
  9. 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
  10. Comparative Toxicogenomics Database (CTD)
    LICENSE
    It is to be used only for research and educational purposes. Any reproduction or use for commercial purpose is prohibited without the prior express written permission of NC State University.
    http://ctdbase.org/about/legal.jsp
  11. Japan Chemical Substance Dictionary (Nikkaji)
  12. 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
  13. Natural Product Activity and Species Source (NPASS)
  14. The Natural Products Atlas
    LICENSE
    The Natural Products Atlas is licensed under a Creative Commons Attribution 4.0 International License.
    https://www.npatlas.org/terms
    The Natural Products Atlas Classification
    https://www.npatlas.org/
  15. Metabolomics Workbench
  16. 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/
    Nigericin
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  17. SpectraBase
    Nigericin - "( as free acid" structure)
    https://spectrabase.com/spectrum/HpoCYAfIlBc
  18. Wikidata
  19. Wikipedia
  20. 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
  21. PubChem
  22. GHS Classification (UNECE)
  23. EPA Substance Registry Services
  24. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  25. PATENTSCOPE (WIPO)
  26. NCBI
CONTENTS