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Record Information
Version1.0
Created at2021-01-06 06:20:39 UTC
Updated at2021-07-15 17:35:17 UTC
NP-MRD IDNP0021040
Secondary Accession NumbersNone
Natural Product Identification
Common NameLysobactin
Provided ByNPAtlasNPAtlas Logo
Description Lysobactin is found in Cytophaga sp. PBJ-5356, Lysobacter and Lysobacter sp. SC 14067 (ATCC 53042). It was first documented in 1988 (PMID: 3209465). Based on a literature review very few articles have been published on (2S)-2-{[(2R)-2-amino-1-hydroxy-4-methylpentylidene]amino}-N-[(3S,6S,12S,15S,18R,21S,24S,27S,28R)-15-[(2S)-butan-2-yl]-18-(3-carbamimidamidopropyl)-5,8,11,14,17,20,23,26-octahydroxy-6-[(S)-hydroxy(C-hydroxycarbonimidoyl)methyl]-24-[(1R)-1-hydroxy-2-methylpropyl]-12-[(1S)-1-hydroxyethyl]-3-(hydroxymethyl)-21-(2-methylpropyl)-2-oxo-28-phenyl-1-oxa-4,7,10,13,16,19,22,25-octaazacyclooctacosa-4,7,10,13,16,19,22,25-octaen-27-yl]-4-methylpentanimidic acid.
Structure
Thumb
Synonyms
ValueSource
(2S)-2-{[(2R)-2-amino-1-hydroxy-4-methylpentylidene]amino}-N-[(3S,6S,12S,15S,18R,21S,24S,27S,28R)-15-[(2S)-butan-2-yl]-18-(3-carbamimidamidopropyl)-5,8,11,14,17,20,23,26-octahydroxy-6-[(S)-hydroxy(C-hydroxycarbonimidoyl)methyl]-24-[(1R)-1-hydroxy-2-methylpropyl]-12-[(1S)-1-hydroxyethyl]-3-(hydroxymethyl)-21-(2-methylpropyl)-2-oxo-28-phenyl-1-oxa-4,7,10,13,16,19,22,25-octaazacyclooctacosa-4,7,10,13,16,19,22,25-octaen-27-yl]-4-methylpentanimidateGenerator
Chemical FormulaC58H97N15O17
Average Mass1276.5020 Da
Monoisotopic Mass1275.71869 Da
IUPAC Name(2S)-2-[(2R)-2-amino-4-methylpentanamido]-N-[(3S,6S,12S,15S,18R,21S,24S,27S,28R)-15-[(2S)-butan-2-yl]-6-[(S)-carbamoyl(hydroxy)methyl]-18-{3-[(diaminomethylidene)amino]propyl}-24-[(1R)-1-hydroxy-2-methylpropyl]-12-[(1S)-1-hydroxyethyl]-3-(hydroxymethyl)-21-(2-methylpropyl)-2,5,8,11,14,17,20,23,26-nonaoxo-28-phenyl-1-oxa-4,7,10,13,16,19,22,25-octaazacyclooctacosan-27-yl]-4-methylpentanamide
Traditional Name(2S)-2-[(2R)-2-amino-4-methylpentanamido]-N-[(3S,6S,12S,15S,18R,21S,24S,27S,28R)-15-[(2S)-butan-2-yl]-6-[(S)-carbamoyl(hydroxy)methyl]-18-{3-[(diaminomethylidene)amino]propyl}-24-[(1R)-1-hydroxy-2-methylpropyl]-12-[(1S)-1-hydroxyethyl]-3-(hydroxymethyl)-21-(2-methylpropyl)-2,5,8,11,14,17,20,23,26-nonaoxo-28-phenyl-1-oxa-4,7,10,13,16,19,22,25-octaazacyclooctacosan-27-yl]-4-methylpentanamide
CAS Registry NumberNot Available
SMILES
CC[C@H](C)[C@@H]1NC(=O)[C@@H](CCCN=C(N)N)NC(=O)[C@H](CC(C)C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@H](N)CC(C)C)[C@H](OC(=O)[C@H](CO)NC(=O)[C@@H](NC(=O)CNC(=O)[C@@H](NC1=O)[C@H](C)O)[C@H](O)C(N)=O)C1=CC=CC=C1)[C@H](O)C(C)C
InChI Identifier
InChI=1S/C58H97N15O17/c1-12-30(10)39-53(85)71-40(31(11)75)52(84)64-24-38(76)69-42(45(78)47(60)79)55(87)68-37(25-74)57(89)90-46(32-17-14-13-15-18-32)43(73-51(83)36(23-28(6)7)66-48(80)33(59)21-26(2)3)56(88)72-41(44(77)29(8)9)54(86)67-35(22-27(4)5)50(82)65-34(49(81)70-39)19-16-20-63-58(61)62/h13-15,17-18,26-31,33-37,39-46,74-75,77-78H,12,16,19-25,59H2,1-11H3,(H2,60,79)(H,64,84)(H,65,82)(H,66,80)(H,67,86)(H,68,87)(H,69,76)(H,70,81)(H,71,85)(H,72,88)(H,73,83)(H4,61,62,63)/t30-,31-,33+,34+,35-,36-,37-,39-,40-,41-,42-,43-,44+,45-,46+/m0/s1
InChI KeyKQMKBWMQSNKASI-AVSFGBOWSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Cytophaga sp. PBJ-5356Bacteria
LysobacterNPAtlas
Lysobacter sp. SC 14067 (ATCC 53042)Bacteria
Chemical Taxonomy
ClassificationNot classified
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-0.18ALOGPS
logP-5ChemAxon
logS-4.2ALOGPS
pKa (Strongest Acidic)10.59ChemAxon
pKa (Strongest Basic)11.1ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count20ChemAxon
Hydrogen Donor Count18ChemAxon
Polar Surface Area531.73 ŲChemAxon
Rotatable Bond Count23ChemAxon
Refractivity320.72 m³·mol⁻¹ChemAxon
Polarizability134.85 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
NPAtlas IDNPA017094
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID9868564
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11693839
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. O'Sullivan J, McCullough JE, Tymiak AA, Kirsch DR, Trejo WH, Principe PA: Lysobactin, a novel antibacterial agent produced by Lysobacter sp. I. Taxonomy, isolation and partial characterization. J Antibiot (Tokyo). 1988 Dec;41(12):1740-4. doi: 10.7164/antibiotics.41.1740. [PubMed:3209465 ]