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Record Information
Version2.0
Created at2021-01-06 08:06:09 UTC
Updated at2021-07-15 17:40:27 UTC
NP-MRD IDNP0022957
Secondary Accession NumbersNone
Natural Product Identification
Common NamePradimicin FL
Provided ByNPAtlasNPAtlas Logo
Description Pradimicin FL is found in Actinomadura, Actinomadura verrucosospora and Actinomadura verrucosospora subsp. neohibisca subsp. nov.. Pradimicin FL was first documented in 1993 (PMID: 8478257). Based on a literature review very few articles have been published on (2S)-3-hydroxy-2-({hydroxy[(10S,11S)-2,5,11,17-tetrahydroxy-10-{[(2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0³,¹².0⁴,⁹.0¹⁶,²¹]Docosa-1(14),2,4(9),5,7,12,16(21),17,19-nonaen-6-yl]methylidene}amino)propanoic acid.
Structure
Thumb
Synonyms
ValueSource
(2S)-3-Hydroxy-2-({hydroxy[(10S,11S)-2,5,11,17-tetrahydroxy-10-{[(2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-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]methylidene}amino)propanoateGenerator
N-((5-O-(4,6-Dideoxy-4-methylamino-3-O-(beta-D-glucopyranosyl)-beta-D-galactopyranosyl)-5,6,8,13-tetrahydro-1,5,6,9,14-pentahydroxy-11-methoxy-3-methyl-8,13-dioxobenzo(a)naphthacene-2-yl)carbonyl)-D-serineMeSH
Chemical FormulaC41H46N2O20
Average Mass886.8130 Da
Monoisotopic Mass886.26439 Da
IUPAC Name(2S)-3-hydroxy-2-{[(10S,11S)-2,5,11,17-tetrahydroxy-10-{[(2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1,3(12),4,6,8,13,16,18,20-nonaen-6-yl]formamido}propanoic acid
Traditional Name(2S)-3-hydroxy-2-{[(10S,11S)-2,5,11,17-tetrahydroxy-10-{[(2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1,3(12),4,6,8,13,16,18,20-nonaen-6-yl]formamido}propanoic acid
CAS Registry NumberNot Available
SMILES
CN[C@H]1[C@@H](C)O[C@@H](O[C@@H]2[C@@H](O)C3=C(C(O)=C4C(=O)C5=CC(OC)=CC(O)=C5C(=O)C4=C3)C3=C(O)C(C(=O)N[C@@H](CO)C(O)=O)=C(C)C=C23)[C@H](O)[C@H]1O[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O
InChI Identifier
InChI=1S/C41H46N2O20/c1-11-5-17-24(31(51)21(11)38(56)43-18(9-44)39(57)58)23-15(8-16-25(32(23)52)28(48)14-6-13(59-4)7-19(46)22(14)27(16)47)29(49)36(17)62-41-35(55)37(26(42-3)12(2)60-41)63-40-34(54)33(53)30(50)20(10-45)61-40/h5-8,12,18,20,26,29-30,33-37,40-42,44-46,49-55H,9-10H2,1-4H3,(H,43,56)(H,57,58)/t12-,18+,20-,26+,29+,30+,33+,34-,35-,36+,37+,40+,41+/m1/s1
InChI KeyOCMFGTQYTXVJRJ-SUZGDMLVSA-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 verrucososporaLOTUS Database
Actinomadura verrucosospora subsp. neohibisca subsp. nov.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
logP0.11ALOGPS
logP-2.2ChemAxon
logS-2.6ALOGPS
pKa (Strongest Acidic)2.65ChemAxon
pKa (Strongest Basic)9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count21ChemAxon
Hydrogen Donor Count13ChemAxon
Polar Surface Area361.02 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity210.55 m³·mol⁻¹ChemAxon
Polarizability89.16 ųChemAxon
Number of Rings7ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA020614
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78442900
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound139588899
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Saitoh K, Sawada Y, Tomita K, Tsuno T, Hatori M, Oki T: Pradimicins L and FL: new pradimicin congeners from Actinomadura verrucosospora subsp. neohibisca. J Antibiot (Tokyo). 1993 Mar;46(3):387-97. doi: 10.7164/antibiotics.46.387. [PubMed:8478257 ]