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Record Information
Version2.0
Created at2021-01-06 07:03:36 UTC
Updated at2021-07-15 17:37:18 UTC
NP-MRD IDNP0021795
Secondary Accession NumbersNone
Natural Product Identification
Common NamePholipomycin
Provided ByNPAtlasNPAtlas Logo
Description(2R)-3-{[hydroxy({[(2R,3S,4S,5S,6S)-5-hydroxy-3-{[(2S,3R,4R,5S,6R)-4-hydroxy-5-{[(2S,3R,4R,5S,6R)-4-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-5-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-[(2-hydroxy-5-oxocyclopent-1-en-1-yl)-C-hydroxycarbonimidoyl]oxan-2-yl]oxy}oxan-2-yl]oxy}-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-6-(C-hydroxycarbonimidoyl)-4-(C-hydroxycarbonimidoyloxy)-5-methyloxan-2-yl]oxy})phosphoryl]oxy}-2-{[(2Z,6E,13E)-3,8,8,14,18-pentamethyl-11-methylidenenonadeca-2,6,13,17-tetraen-1-yl]oxy}propanoic acid belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone. Pholipomycin is found in Streptomyces, Streptomyces lividoclavatus and Streptomyces lividoclavatus No.3176. Pholipomycin was first documented in 1977 (PMID: 599080). Based on a literature review very few articles have been published on (2R)-3-{[hydroxy({[(2R,3S,4S,5S,6S)-5-hydroxy-3-{[(2S,3R,4R,5S,6R)-4-hydroxy-5-{[(2S,3R,4R,5S,6R)-4-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-5-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-[(2-hydroxy-5-oxocyclopent-1-en-1-yl)-C-hydroxycarbonimidoyl]oxan-2-yl]oxy}oxan-2-yl]oxy}-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-6-(C-hydroxycarbonimidoyl)-4-(C-hydroxycarbonimidoyloxy)-5-methyloxan-2-yl]oxy})phosphoryl]oxy}-2-{[(2Z,6E,13E)-3,8,8,14,18-pentamethyl-11-methylidenenonadeca-2,6,13,17-tetraen-1-yl]oxy}propanoic acid.
Structure
Thumb
Synonyms
ValueSource
(2R)-3-{[hydroxy({[(2R,3S,4S,5S,6S)-5-hydroxy-3-{[(2S,3R,4R,5S,6R)-4-hydroxy-5-{[(2S,3R,4R,5S,6R)-4-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-5-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-[(2-hydroxy-5-oxocyclopent-1-en-1-yl)-C-hydroxycarbonimidoyl]oxan-2-yl]oxy}oxan-2-yl]oxy}-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-6-(C-hydroxycarbonimidoyl)-4-(C-hydroxycarbonimidoyloxy)-5-methyloxan-2-yl]oxy})phosphoryl]oxy}-2-{[(2Z,6E,13E)-3,8,8,14,18-pentamethyl-11-methylidenenonadeca-2,6,13,17-tetraen-1-yl]oxy}propanoateGenerator
Chemical FormulaC63H98N5O30P
Average Mass1436.4560 Da
Monoisotopic Mass1435.60342 Da
IUPAC Name(2R)-3-[({[(2R,3S,4S,5S,6S)-6-carbamoyl-4-(carbamoyloxy)-3-{[(2S,3R,4R,5S,6R)-3-acetamido-5-{[(2S,3R,4R,5S,6R)-3-acetamido-4-hydroxy-6-(hydroxymethyl)-5-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-[(2-hydroxy-5-oxocyclopent-1-en-1-yl)carbamoyl]oxan-2-yl]oxy}oxan-2-yl]oxy}-4-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-hydroxy-5-methyloxan-2-yl]oxy}(hydroxy)phosphoryl)oxy]-2-{[(2Z,6E,13E)-3,8,8,14,18-pentamethyl-11-methylidenenonadeca-2,6,13,17-tetraen-1-yl]oxy}propanoic acid
Traditional Name(2R)-3-({[(2R,3S,4S,5S,6S)-6-carbamoyl-4-(carbamoyloxy)-3-{[(2S,3R,4R,5S,6R)-3-acetamido-5-{[(2S,3R,4R,5S,6R)-3-acetamido-4-hydroxy-6-(hydroxymethyl)-5-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-[(2-hydroxy-5-oxocyclopent-1-en-1-yl)carbamoyl]oxan-2-yl]oxy}oxan-2-yl]oxy}-4-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-hydroxy-5-methyloxan-2-yl]oxy(hydroxy)phosphoryl}oxy)-2-{[(2Z,6E,13E)-3,8,8,14,18-pentamethyl-11-methylidenenonadeca-2,6,13,17-tetraen-1-yl]oxy}propanoic acid
CAS Registry NumberNot Available
SMILES
CC(C)=CCC\C(C)=C\CC(=C)CCC(C)(C)\C=C\CC\C(C)=C/CO[C@H](COP(O)(=O)O[C@H]1O[C@H](C(N)=O)[C@@](C)(O)[C@@H](OC(N)=O)[C@@H]1O[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O[C@@H]3O[C@H]([C@H](O)[C@H](O)[C@H]3O)C(=O)NC3=C(O)CCC3=O)[C@H](O)[C@H]2NC(C)=O)[C@H](O)[C@H]1NC(C)=O)C(O)=O
InChI Identifier
InChI=1S/C63H98N5O30P/c1-29(2)14-13-16-30(3)17-18-32(5)21-24-62(8,9)23-12-11-15-31(4)22-25-88-39(56(82)83)28-89-99(86,87)98-60-51(52(97-61(65)84)63(10,85)53(96-60)54(64)80)95-58-42(67-34(7)72)43(75)48(37(26-69)91-58)92-57-41(66-33(6)71)44(76)49(38(27-70)90-57)93-59-47(79)45(77)46(78)50(94-59)55(81)68-40-35(73)19-20-36(40)74/h12,14,17,22-23,37-39,41-53,57-60,69-70,73,75-79,85H,5,11,13,15-16,18-21,24-28H2,1-4,6-10H3,(H2,64,80)(H2,65,84)(H,66,71)(H,67,72)(H,68,81)(H,82,83)(H,86,87)/b23-12+,30-17+,31-22-/t37-,38-,39-,41-,42-,43-,44-,45+,46-,47-,48-,49-,50-,51+,52+,53-,57+,58+,59-,60-,63+/m1/s1
InChI KeyXYJIXNBDVDMTFA-QGROGYFUSA-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
StreptomycesNPAtlas
Streptomyces lividoclavatusLOTUS Database
Streptomyces lividoclavatus No.3176Bacteria
Chemical Taxonomy
Description Belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTerpene glycosides
Direct ParentTerpene glycosides
Alternative Parents
Substituents
  • Oligosaccharide phosphate
  • Oligosaccharide
  • Terpene glycoside
  • N-acyl-alpha-hexosamine
  • O-glycosyl compound
  • Glycosyl compound
  • Monoterpenoid
  • Monocyclic monoterpenoid
  • Dialkyl phosphate
  • Glyceric_acid
  • Alkyl phosphate
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Vinylogous acid
  • Tertiary alcohol
  • Cyclic ketone
  • Secondary alcohol
  • Ketone
  • Oxacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Polyol
  • Monocarboxylic acid or derivatives
  • Ether
  • Dialkyl ether
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Acetal
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Imine
  • Carbonyl group
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
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
logP1.6ALOGPS
logP-1.6ChemAxon
logS-4.5ALOGPS
pKa (Strongest Acidic)1.58ChemAxon
pKa (Strongest Basic)-3.8ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count27ChemAxon
Hydrogen Donor Count16ChemAxon
Polar Surface Area548.75 ŲChemAxon
Rotatable Bond Count36ChemAxon
Refractivity342.23 m³·mol⁻¹ChemAxon
Polarizability143.41 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA021110
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78443621
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound139589144
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Arai M, Nakayama R, Yoshida K, Takeuchi M, Teramoto S, Torikata A: Pholipomycin, a new member of phosphoglycolipid antibiotics. II. Physico-chemical properties and comparison with other members of this family of antibiotics. J Antibiot (Tokyo). 1977 Dec;30(12):1055-9. doi: 10.7164/antibiotics.30.1055. [PubMed:599080 ]