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Record Information
Version1.0
Created at2021-01-06 07:23:02 UTC
Updated at2021-07-15 17:38:17 UTC
NP-MRD IDNP0022160
Secondary Accession NumbersNone
Natural Product Identification
Common NameHerbicolin A
Provided ByNPAtlasNPAtlas Logo
Description Herbicolin A is found in Erwinia and Pantoea agglomerans. It was first documented in 1980 (PMID: 7410203). Based on a literature review very few articles have been published on (3R)-N-[(1Z)-1-{[(3S,6R,12R,18S,21R,24R,25S)-3-(3-carbamimidamidopropyl)-5,11,14,17,20,23-hexahydroxy-12-[2-(C-hydroxycarbonimidoyl)ethyl]-6-[(1R)-1-hydroxyethyl]-21-[(1S)-1-hydroxyethyl]-7,25-dimethyl-18-(2-methylpropyl)-2,8-dioxo-1-oxa-4,7,10,13,16,19,22-heptaazacyclopentacosa-4,10,13,16,19,22-hexaen-24-yl]-C-hydroxycarbonimidoyl}prop-1-en-1-yl]-3-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetradecanimidic acid.
Structure
Thumb
Synonyms
ValueSource
(3R)-N-[(1Z)-1-{[(3S,6R,12R,18S,21R,24R,25S)-3-(3-carbamimidamidopropyl)-5,11,14,17,20,23-hexahydroxy-12-[2-(C-hydroxycarbonimidoyl)ethyl]-6-[(1R)-1-hydroxyethyl]-21-[(1S)-1-hydroxyethyl]-7,25-dimethyl-18-(2-methylpropyl)-2,8-dioxo-1-oxa-4,7,10,13,16,19,22-heptaazacyclopentacosa-4,10,13,16,19,22-hexaen-24-yl]-C-hydroxycarbonimidoyl}prop-1-en-1-yl]-3-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetradecanimidateGenerator
Chemical FormulaC58H101N13O20
Average Mass1300.5170 Da
Monoisotopic Mass1299.72858 Da
IUPAC Name(3R)-N-[(1Z)-1-{[(3S,6R,12R,18S,21R,24R,25S)-12-(2-carbamoylethyl)-3-{3-[(diaminomethylidene)amino]propyl}-6-[(1R)-1-hydroxyethyl]-21-[(1S)-1-hydroxyethyl]-7,25-dimethyl-18-(2-methylpropyl)-2,5,8,11,14,17,20,23-octaoxo-1-oxa-4,7,10,13,16,19,22-heptaazacyclopentacosan-24-yl]carbamoyl}prop-1-en-1-yl]-3-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetradecanamide
Traditional Name(3R)-N-[(1Z)-1-{[(3S,6R,12R,18S,21R,24R,25S)-12-(2-carbamoylethyl)-3-{3-[(diaminomethylidene)amino]propyl}-6-[(1R)-1-hydroxyethyl]-21-[(1S)-1-hydroxyethyl]-7,25-dimethyl-18-(2-methylpropyl)-2,5,8,11,14,17,20,23-octaoxo-1-oxa-4,7,10,13,16,19,22-heptaazacyclopentacosan-24-yl]carbamoyl}prop-1-en-1-yl]-3-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetradecanamide
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCC[C@H](CC(=O)N\C(=C/C)C(=O)N[C@@H]1[C@H](C)OC(=O)[C@H](CCCN=C(N)N)NC(=O)[C@@H]([C@@H](C)O)N(C)C(=O)CNC(=O)[C@@H](CCC(N)=O)NC(=O)CNC(=O)[C@H](CC(C)C)NC(=O)[C@H](NC1=O)[C@H](C)O)O[C@@H]1O[C@@H](CO)[C@H](O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C58H101N13O20/c1-9-11-12-13-14-15-16-17-18-20-34(90-57-49(81)48(80)47(79)39(29-72)91-57)26-41(76)65-35(10-2)52(84)70-45-33(7)89-56(88)37(21-19-24-62-58(60)61)67-55(87)46(32(6)74)71(8)43(78)28-64-50(82)36(22-23-40(59)75)66-42(77)27-63-51(83)38(25-30(3)4)68-53(85)44(31(5)73)69-54(45)86/h10,30-34,36-39,44-49,57,72-74,79-81H,9,11-29H2,1-8H3,(H2,59,75)(H,63,83)(H,64,82)(H,65,76)(H,66,77)(H,67,87)(H,68,85)(H,69,86)(H,70,84)(H4,60,61,62)/b35-10-/t31-,32+,33-,34+,36+,37-,38-,39-,44+,45+,46+,47-,48-,49-,57+/m0/s1
InChI KeyGMKUYPOKOFFZTR-LCYRERJWSA-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
ErwiniaNPAtlas
Pantoea agglomeransLOTUS Database
Species Where Detected
Species NameSourceReference
Erwinia herbicola A 111KNApSAcK Database
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
logP0.37ALOGPS
logP-5.6ChemAxon
logS-4.3ALOGPS
pKa (Strongest Acidic)10.86ChemAxon
pKa (Strongest Basic)11.35ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count22ChemAxon
Hydrogen Donor Count17ChemAxon
Polar Surface Area526.74 ŲChemAxon
Rotatable Bond Count29ChemAxon
Refractivity323.3 m³·mol⁻¹ChemAxon
Polarizability136.77 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
NPAtlas IDNPA021059
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78443106
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound139589112
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Winkelmann G, Lupp R, Jung G: Herbicolins--New peptide antibiotics from Erwinia herbicola. J Antibiot (Tokyo). 1980 Apr;33(4):353-8. doi: 10.7164/antibiotics.33.353. [PubMed:7410203 ]