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Record Information
Version2.0
Created at2022-09-08 14:18:41 UTC
Updated at2022-09-08 14:18:41 UTC
NP-MRD IDNP0269002
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-hydroxy-3-[(hydroxymethylidene)amino]-n-[(6s,7s)-7,10,10-trimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]benzenecarboximidic acid
DescriptionJBIR-06, also known as JBIR 06, belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. 2-hydroxy-3-[(hydroxymethylidene)amino]-n-[(6s,7s)-7,10,10-trimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]benzenecarboximidic acid was first documented in 2008 (PMID: 18503204). Based on a literature review a small amount of articles have been published on JBIR-06 (PMID: 30166552) (PMID: 30698439).
Structure
Thumb
Synonyms
ValueSource
JBIR 06MeSH
Chemical FormulaC28H38N2O10
Average Mass562.6160 Da
Monoisotopic Mass562.25265 Da
IUPAC NameN-[(6S,7S)-3-(butan-2-yl)-7,10,10-trimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-1,4,8-trioxacyclododecan-6-yl]-2-hydroxy-3-[(hydroxymethylidene)amino]benzene-1-carboximidic acid
Traditional Name2-hydroxy-3-[(hydroxymethylidene)amino]-N-[(6S,7S)-7,10,10-trimethyl-12-(2-methylpropyl)-2,5,9,11-tetraoxo-3-(sec-butyl)-1,4,8-trioxacyclododecan-6-yl]benzenecarboximidic acid
CAS Registry NumberNot Available
SMILES
CCC(C)C1OC(=O)[C@@H](N=C(O)C2=CC=CC(N=CO)=C2O)[C@H](C)OC(=O)C(C)(C)C(=O)C(CC(C)C)OC1=O
InChI Identifier
InChI=1S/C28H38N2O10/c1-8-15(4)22-26(36)39-19(12-14(2)3)23(33)28(6,7)27(37)38-16(5)20(25(35)40-22)30-24(34)17-10-9-11-18(21(17)32)29-13-31/h9-11,13-16,19-20,22,32H,8,12H2,1-7H3,(H,29,31)(H,30,34)/t15?,16-,19?,20-,22?/m0/s1
InChI KeyDGUFUEHCXSEKMT-GBCVEWGJSA-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 OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassPeptidomimetics
Sub ClassDepsipeptides
Direct ParentCyclic depsipeptides
Alternative Parents
Substituents
  • Cyclic depsipeptide
  • N-acyl-alpha amino acid or derivatives
  • Macrolide
  • Macrolactam
  • Alpha-amino acid ester
  • Acylaminobenzoic acid or derivatives
  • Salicylic acid or derivatives
  • Salicylamide
  • Alpha-amino acid or derivatives
  • Benzoic acid or derivatives
  • Anilide
  • Tricarboxylic acid or derivatives
  • Benzamide
  • Benzoyl
  • N-arylamide
  • Phenol
  • Alpha-acyloxy ketone
  • 1-hydroxy-4-unsubstituted benzenoid
  • Benzenoid
  • Monocyclic benzene moiety
  • Vinylogous acid
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Cyclic ketone
  • Carboxylic acid ester
  • Lactone
  • Ketone
  • Oxacycle
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Organonitrogen compound
  • Carbonyl group
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic 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
logP7.15ChemAxon
pKa (Strongest Acidic)3.29ChemAxon
pKa (Strongest Basic)0.051ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area181.38 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity143.65 m³·mol⁻¹ChemAxon
Polarizability58.9 ųChemAxon
Number of Rings2ChemAxon
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 ID28285294
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound25022865
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Ueda JY, Nagai A, Izumikawa M, Chijiwa S, Takagi M, Shin-ya K: A novel antimycin-like compound, JBIR-06, from Streptomyces sp. ML55. J Antibiot (Tokyo). 2008 Apr;61(4):241-4. doi: 10.1038/ja.2008.35. [PubMed:18503204 ]
  2. Awakawa T, Fujioka T, Zhang L, Hoshino S, Hu Z, Hashimoto J, Kozone I, Ikeda H, Shin-Ya K, Liu W, Abe I: Reprogramming of the antimycin NRPS-PKS assembly lines inspired by gene evolution. Nat Commun. 2018 Aug 30;9(1):3534. doi: 10.1038/s41467-018-05877-z. [PubMed:30166552 ]
  3. Hamada C, Usuki Y, Takeuchi D, Ogawa H, Abe R, Satoh T: Total Syntheses and Configuration Assignments of JBIR-06 and Related Depsipeptides. Org Lett. 2019 Feb 15;21(4):965-968. doi: 10.1021/acs.orglett.8b03944. Epub 2019 Jan 30. [PubMed:30698439 ]
  4. LOTUS database [Link]