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Record Information
Version2.0
Created at2021-01-05 21:28:46 UTC
Updated at2021-07-15 17:10:25 UTC
NP-MRD IDNP0011952
Secondary Accession NumbersNone
Natural Product Identification
Common NamePradimicin E
Provided ByNPAtlasNPAtlas Logo
Description Pradimicin E is found in Actinomadura and Actinomadura hibisca. Pradimicin E was first documented in 1990 (PMID: 2387770). Based on a literature review very few articles have been published on Pradimicin E.
Structure
Thumb
Synonyms
ValueSource
Des-N-methyl-pradimicin DMeSH
2-({[(10S,11S)-10-{[(2S,3R,4S,5S,6R)-5-amino-3-hydroxy-6-methyl-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-2,5,11,17-tetrahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0,.0,.0,]docosa-1(14),2,4(9),5,7,12,16(21),17,19-nonaen-6-yl](hydroxy)methylidene}amino)acetateGenerator
Chemical FormulaC38H40N2O18
Average Mass812.7340 Da
Monoisotopic Mass812.22761 Da
IUPAC Name2-{[(10S,11S)-10-{[(2S,3R,4S,5S,6R)-5-amino-3-hydroxy-6-methyl-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-2,5,11,17-tetrahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1(14),2,4(9),5,7,12,16,18,20-nonaen-6-yl]formamido}acetic acid
Traditional Name{[(10S,11S)-10-{[(2S,3R,4S,5S,6R)-5-amino-3-hydroxy-6-methyl-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-2,5,11,17-tetrahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1(14),2,4(9),5,7,12,16,18,20-nonaen-6-yl]formamido}acetic acid
CAS Registry NumberNot Available
SMILES
COC1=CC(O)=C2C(=O)C3=CC4=C(C(O)=C3C(=O)C2=C1)C1=C(O)C(C(=O)NCC(O)=O)=C(C)C=C1[C@H](O[C@@H]1O[C@H](C)[C@H](N)[C@H](O[C@@H]2OC[C@@H](O)[C@H](O)[C@H]2O)[C@H]1O)[C@H]4O
InChI Identifier
InChI=1S/C38H40N2O18/c1-10-4-16-23(30(49)20(10)36(53)40-8-19(43)44)22-14(7-15-24(31(22)50)27(46)13-5-12(54-3)6-17(41)21(13)26(15)45)28(47)34(16)57-38-33(52)35(25(39)11(2)56-38)58-37-32(51)29(48)18(42)9-55-37/h4-7,11,18,25,28-29,32-35,37-38,41-42,47-52H,8-9,39H2,1-3H3,(H,40,53)(H,43,44)/t11-,18-,25+,28+,29+,32-,33-,34+,35+,37+,38+/m1/s1
InChI KeyHELMFNXPQUQJFY-FPDYCEOPSA-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
ActinomaduraNPAtlas
Actinomadura hibiscaLOTUS Database
Species Where Detected
Species NameSourceReference
Actinomadura hibisca P157-2 (ATCC 53557)KNApSAcK 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
logP0.7ALOGPS
logP-1.3ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)2.7ChemAxon
pKa (Strongest Basic)8.91ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area334.55 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity193.78 m³·mol⁻¹ChemAxon
Polarizability82.05 ųChemAxon
Number of Rings7ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA020694
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00017597
Chemspider ID401868
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound456406
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Sawada Y, Nishio M, Yamamoto H, Hatori M, Miyaki T, Konishi M, Oki T: New antifungal antibiotics, pradimicins D and E. Glycine analogs of pradimicins A and C. J Antibiot (Tokyo). 1990 Jul;43(7):771-7. doi: 10.7164/antibiotics.43.771. [PubMed:2387770 ]