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Corynebactin

PubChem CID
125349
Structure
Corynebactin_small.png
Molecular Formula
Synonyms
  • Corynebactin
  • Bacillibactin
  • 95536-41-7
  • 36PG6K45CP
  • 95536-04-2
Molecular Weight
882.8 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2005-06-24
  • Modify:
    2025-01-18
Description
Corynebactin is a crown compound that is enterobactin in which the pro-R hydrogens at positions 2, 6 and 10 of the trilactone backbone are replaced by methyl groups, and in which a glycine spacer separates the trilactone backbone from each of the catecholamide arms. It is the endogenous siderophore of Bacillus subtilis, used for the acquisition of iron. It has a role as a metabolite and a bacterial metabolite. It is a crown compound, a member of catechols and a macrocyclic lactone.
Corynebactin has been reported in Bacillus subtilis, Corynebacterium glutamicum, and other organisms with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Corynebactin.png

1.2 3D Status

Conformer generation is disallowed since too many atoms, too flexible

2 Biologic Description

IUPAC Condensed
Bz(2,3-diOH)-Gly-Thr(1)-(3).Bz(2,3-diOH)-Gly-Thr(2)-(1).Bz(2,3-diOH)-Gly-Thr(3)-(2)

3 Names and Identifiers

3.1 Computed Descriptors

3.1.1 IUPAC Name

N-[2-[[(2R,3S,6R,7S,10R,11S)-7,11-bis[[2-[(2,3-dihydroxybenzoyl)amino]acetyl]amino]-2,6,10-trimethyl-4,8,12-trioxo-1,5,9-trioxacyclododec-3-yl]amino]-2-oxoethyl]-2,3-dihydroxybenzamide
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

3.1.2 InChI

InChI=1S/C39H42N6O18/c1-16-28(43-25(49)13-40-34(55)19-7-4-10-22(46)31(19)52)37(58)62-18(3)30(45-27(51)15-42-36(57)21-9-6-12-24(48)33(21)54)39(60)63-17(2)29(38(59)61-16)44-26(50)14-41-35(56)20-8-5-11-23(47)32(20)53/h4-12,16-18,28-30,46-48,52-54H,13-15H2,1-3H3,(H,40,55)(H,41,56)(H,42,57)(H,43,49)(H,44,50)(H,45,51)/t16-,17-,18-,28+,29+,30+/m1/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.3 InChIKey

RCQTVEFBFUNTGM-BDVHUIKKSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.4 SMILES

C[C@@H]1[C@@H](C(=O)O[C@@H]([C@@H](C(=O)O[C@@H]([C@@H](C(=O)O1)NC(=O)CNC(=O)C2=C(C(=CC=C2)O)O)C)NC(=O)CNC(=O)C3=C(C(=CC=C3)O)O)C)NC(=O)CNC(=O)C4=C(C(=CC=C4)O)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

3.2 Molecular Formula

C39H42N6O18
Computed by PubChem 2.2 (PubChem release 2021.10.14)

3.3 Other Identifiers

3.3.1 CAS

95536-04-2

3.3.2 UNII

3.3.3 ChEBI ID

3.3.4 DSSTox Substance ID

3.3.5 KEGG ID

3.3.6 Metabolomics Workbench ID

3.3.7 Nikkaji Number

3.3.8 Wikidata

3.3.9 Wikipedia

3.4 Synonyms

3.4.1 MeSH Entry Terms

corynebactin

3.4.2 Depositor-Supplied Synonyms

4 Chemical and Physical Properties

4.1 Computed Properties

Property Name
Molecular Weight
Property Value
882.8 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
1.6
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
12
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
18
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
12
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
882.25555851 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
882.25555851 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
375 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
63
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
1510
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
6
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 Spectral Information

5.1 Mass Spectrometry

5.1.1 LC-MS

MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
883.265
Instrument
qTof
Ionization Mode
positive
Top 5 Peaks

883.264893 100

690.226624 57.18

884.264343 43.89

691.224915 20.39

885.264282 15.57

Thumbnail
Thumbnail

7 Chemical Vendors

8 Pharmacology and Biochemistry

8.1 Biochemical Reactions

9 Literature

9.1 Consolidated References

9.2 NLM Curated PubMed Citations

9.3 Chemical Co-Occurrences in Literature

9.4 Chemical-Gene Co-Occurrences in Literature

9.5 Chemical-Disease Co-Occurrences in Literature

10 Patents

10.1 Depositor-Supplied Patent Identifiers

10.2 Chemical Co-Occurrences in Patents

10.3 Chemical-Disease Co-Occurrences in Patents

10.4 Chemical-Gene Co-Occurrences in Patents

11 Interactions and Pathways

11.1 Protein Bound 3D Structures

12 Taxonomy

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

13 Classification

13.1 MeSH Tree

13.2 ChEBI Ontology

13.3 ChemIDplus

13.4 EPA DSSTox Classification

13.5 The Natural Products Atlas Classification

13.6 LOTUS Tree

13.7 MolGenie Organic Chemistry Ontology

14 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. EPA DSSTox
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  4. 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
  5. ChEBI
  6. 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/
  7. Japan Chemical Substance Dictionary (Nikkaji)
  8. 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
  9. Natural Product Activity and Species Source (NPASS)
  10. 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/
  11. MassBank of North America (MoNA)
    LICENSE
    The content of the MoNA database is licensed under CC BY 4.0.
    https://mona.fiehnlab.ucdavis.edu/documentation/license
  12. Metabolomics Workbench
  13. Rhea - Annotated Reactions Database
    LICENSE
    Rhea has chosen to apply the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/). This means that you are free to copy, distribute, display and make commercial use of the database in all legislations, provided you credit (cite) Rhea.
    https://www.rhea-db.org/help/license-disclaimer
  14. Wikidata
  15. Wikipedia
  16. PubChem
  17. 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
  18. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  19. NCBI
CONTENTS