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Record Information
Version2.0
Created at2022-09-09 18:03:49 UTC
Updated at2022-09-09 18:03:49 UTC
NP-MRD IDNP0288384
Secondary Accession NumbersNone
Natural Product Identification
Common Namen-[(2r,9r,12r,19r,22r,29r)-5,15,25-trihydroxy-19,29-bis[(1-hydroxyethylidene)amino]-2,12,22-trimethyl-4,10,14,20,24,30-hexaoxo-1,11,21-trioxa-5,15,25-triazacyclotriacontan-9-yl]ethanimidic acid
DescriptionVicibactin belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides. n-[(2r,9r,12r,19r,22r,29r)-5,15,25-trihydroxy-19,29-bis[(1-hydroxyethylidene)amino]-2,12,22-trimethyl-4,10,14,20,24,30-hexaoxo-1,11,21-trioxa-5,15,25-triazacyclotriacontan-9-yl]ethanimidic acid is found in Rhizobium etli and Rhizobium leguminosarum. n-[(2r,9r,12r,19r,22r,29r)-5,15,25-trihydroxy-19,29-bis[(1-hydroxyethylidene)amino]-2,12,22-trimethyl-4,10,14,20,24,30-hexaoxo-1,11,21-trioxa-5,15,25-triazacyclotriacontan-9-yl]ethanimidic acid was first documented in 2003 (PMID: 12829293). Based on a literature review a small amount of articles have been published on Vicibactin (PMID: 26575143) (PMID: 23361163) (PMID: 19778043) (PMID: 15583159).
Structure
Thumb
SynonymsNot Available
Chemical FormulaC33H54N6O15
Average Mass774.8220 Da
Monoisotopic Mass774.36472 Da
IUPAC NameN-[(2R,9R,12R,19R,22R,29R)-5,15,25-trihydroxy-19,29-bis[(1-hydroxyethylidene)amino]-2,12,22-trimethyl-4,10,14,20,24,30-hexaoxo-1,11,21-trioxa-5,15,25-triazacyclotriacontan-9-yl]ethanimidic acid
Traditional NameN-[(2R,9R,12R,19R,22R,29R)-5,15,25-trihydroxy-19,29-bis[(1-hydroxyethylidene)amino]-2,12,22-trimethyl-4,10,14,20,24,30-hexaoxo-1,11,21-trioxa-5,15,25-triazacyclotriacontan-9-yl]ethanimidic acid
CAS Registry NumberNot Available
SMILES
C[C@@H]1CC(=O)N(O)CCC[C@@H](N=C(C)O)C(=O)O[C@H](C)CC(=O)N(O)CCC[C@@H](N=C(C)O)C(=O)O[C@H](C)CC(=O)N(O)CCC[C@@H](N=C(C)O)C(=O)O1
InChI Identifier
InChI=1S/C33H54N6O15/c1-19-16-28(43)37(49)13-8-11-26(35-23(5)41)32(47)53-21(3)18-30(45)39(51)15-9-12-27(36-24(6)42)33(48)54-20(2)17-29(44)38(50)14-7-10-25(31(46)52-19)34-22(4)40/h19-21,25-27,49-51H,7-18H2,1-6H3,(H,34,40)(H,35,41)(H,36,42)/t19-,20-,21-,25-,26-,27-/m1/s1
InChI KeyNEZSNYPOAQRZDV-ZXXBMJRBSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Rhizobium etliLOTUS Database
Rhizobium leguminosarumLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassMacrolactams
Sub ClassNot Available
Direct ParentMacrolactams
Alternative Parents
Substituents
  • Alpha-amino acid ester
  • Macrolactam
  • Macrolide
  • N-acyl-alpha amino acid or derivatives
  • Alpha-amino acid or derivatives
  • Tricarboxylic acid or derivatives
  • Acetamide
  • Carboxamide group
  • Carboxylic acid ester
  • Hydroxamic acid
  • Lactone
  • Secondary carboxylic acid amide
  • Oxacycle
  • Carboxylic acid derivative
  • Polyol
  • Azacycle
  • Organoheterocyclic compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.6ChemAxon
pKa (Strongest Acidic)5.17ChemAxon
pKa (Strongest Basic)1.61ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area298.29 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity185.13 m³·mol⁻¹ChemAxon
Polarizability79.1 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID59650540
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound101941096
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Zheng D, Burr TJ: Inhibition of Grape Crown Gall by Agrobacterium vitis F2/5 Requires Two Nonribosomal Peptide Synthetases and One Polyketide Synthase. Mol Plant Microbe Interact. 2016 Feb;29(2):109-18. doi: 10.1094/MPMI-07-15-0153-R. Epub 2016 Jan 15. [PubMed:26575143 ]
  2. Wright W, Little J, Liu F, Chakraborty R: Isolation and structural identification of the trihydroxamate siderophore vicibactin and its degradative products from Rhizobium leguminosarum ATCC 14479 bv. trifolii. Biometals. 2013 Apr;26(2):271-83. doi: 10.1007/s10534-013-9609-3. Epub 2013 Jan 30. [PubMed:23361163 ]
  3. Heemstra JR Jr, Walsh CT, Sattely ES: Enzymatic tailoring of ornithine in the biosynthesis of the Rhizobium cyclic trihydroxamate siderophore vicibactin. J Am Chem Soc. 2009 Oct 28;131(42):15317-29. doi: 10.1021/ja9056008. [PubMed:19778043 ]
  4. Yeoman KH, Curson AR, Todd JD, Sawers G, Johnston AW: Evidence that the Rhizobium regulatory protein RirA binds to cis-acting iron-responsive operators (IROs) at promoters of some Fe-regulated genes. Microbiology (Reading). 2004 Dec;150(Pt 12):4065-74. doi: 10.1099/mic.0.27419-0. [PubMed:15583159 ]
  5. Yeoman KH, Mitelheiser S, Sawers G, Johnston AW: The ECF sigma factor RpoI of R. leguminosarum initiates transcription of the vbsGSO and vbsADL siderophore biosynthetic genes in vitro. FEMS Microbiol Lett. 2003 Jun 27;223(2):239-44. doi: 10.1016/S0378-1097(03)00386-0. [PubMed:12829293 ]
  6. LOTUS database [Link]