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Record Information
Version1.0
Created at2021-01-05 19:47:35 UTC
Updated at2021-07-15 17:05:23 UTC
NP-MRD IDNP0010184
Secondary Accession NumbersNone
Natural Product Identification
Common NamePadanamide B
Provided ByNPAtlasNPAtlas Logo
Description Padanamide B is found in Streptomyces sp. It was first documented in 2011 (PMID: 21749075). Based on a literature review very few articles have been published on (2S,3S,4S)-3-hydroxy-N-[(3S)-6-hydroxy-2-oxo-2,3,4,5-tetrahydropyridin-3-yl]-4-({hydroxy[(3S)-2-[(2R,3R)-3-hydroxy-2-[(1-hydroxy-2-methoxyethylidene)amino]-4-methylpentanoyl]-1,2-diazinan-3-yl]methylidene}amino)-2-methyl-5-phenylpentanimidic acid.
Structure
Data?1621576265
Synonyms
ValueSource
(2S,3S,4S)-3-Hydroxy-N-[(3S)-6-hydroxy-2-oxo-2,3,4,5-tetrahydropyridin-3-yl]-4-({hydroxy[(3S)-2-[(2R,3R)-3-hydroxy-2-[(1-hydroxy-2-methoxyethylidene)amino]-4-methylpentanoyl]-1,2-diazinan-3-yl]methylidene}amino)-2-methyl-5-phenylpentanimidateGenerator
Chemical FormulaC31H46N6O9
Average Mass646.7420 Da
Monoisotopic Mass646.33263 Da
IUPAC Name(2S,3S,4S)-N-[(3S)-2,6-dioxopiperidin-3-yl]-3-hydroxy-4-{[(3S)-2-[(2R,3R)-3-hydroxy-2-(2-methoxyacetamido)-4-methylpentanoyl]-1,2-diazinan-3-yl]formamido}-2-methyl-5-phenylpentanamide
Traditional Name(2S,3S,4S)-N-[(3S)-2,6-dioxopiperidin-3-yl]-3-hydroxy-4-{[(3S)-2-[(2R,3R)-3-hydroxy-2-(2-methoxyacetamido)-4-methylpentanoyl]-1,2-diazinan-3-yl]formamido}-2-methyl-5-phenylpentanamide
CAS Registry NumberNot Available
SMILES
COCC(=O)N[C@H]([C@H](O)C(C)C)C(=O)N1NCCC[C@H]1C(=O)N[C@@H](CC1=CC=CC=C1)[C@@H](O)[C@H](C)C(=O)N[C@H]1CCC(=O)NC1=O
InChI Identifier
InChI=1S/C31H46N6O9/c1-17(2)26(40)25(35-24(39)16-46-4)31(45)37-22(11-8-14-32-37)30(44)34-21(15-19-9-6-5-7-10-19)27(41)18(3)28(42)33-20-12-13-23(38)36-29(20)43/h5-7,9-10,17-18,20-22,25-27,32,40-41H,8,11-16H2,1-4H3,(H,33,42)(H,34,44)(H,35,39)(H,36,38,43)/t18-,20-,21-,22-,25+,26+,27-/m0/s1
InChI KeyHVEJTNNFGWKHNS-GYNFZRGZSA-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
Streptomyces sp.NPAtlas
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-0.22ALOGPS
logP-1.6ChemAxon
logS-3.2ALOGPS
pKa (Strongest Acidic)11.39ChemAxon
pKa (Strongest Basic)3.86ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area215.5 ŲChemAxon
Rotatable Bond Count14ChemAxon
Refractivity174.16 m³·mol⁻¹ChemAxon
Polarizability67.79 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA020068
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID28185040
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53483404
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Williams DE, Dalisay DS, Patrick BO, Matainaho T, Andrusiak K, Deshpande R, Myers CL, Piotrowski JS, Boone C, Yoshida M, Andersen RJ: Padanamides A and B, highly modified linear tetrapeptides produced in culture by a Streptomyces sp. isolated from a marine sediment. Org Lett. 2011 Aug 5;13(15):3936-9. doi: 10.1021/ol2014494. Epub 2011 Jul 12. [PubMed:21749075 ]