Np mrd loader

Record Information
Version2.0
Created at2022-09-05 22:21:54 UTC
Updated at2022-09-05 22:21:54 UTC
NP-MRD IDNP0220920
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2e)-n-[(3ar,4s,5s,6r,7s,7as)-4,6,7-trihydroxy-hexahydro-2h-1,3-benzodioxol-5-yl]-3-(4-{[(2s,3s,4s,5s)-5-acetyl-3,4-dihydroxyoxolan-2-yl]oxy}-3-hydroxyphenyl)-2-methylprop-2-enimidic acid
DescriptionHygromycin A belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. (2e)-n-[(3ar,4s,5s,6r,7s,7as)-4,6,7-trihydroxy-hexahydro-2h-1,3-benzodioxol-5-yl]-3-(4-{[(2s,3s,4s,5s)-5-acetyl-3,4-dihydroxyoxolan-2-yl]oxy}-3-hydroxyphenyl)-2-methylprop-2-enimidic acid is found in Streptomyces hygroscopicus. (2e)-n-[(3ar,4s,5s,6r,7s,7as)-4,6,7-trihydroxy-hexahydro-2h-1,3-benzodioxol-5-yl]-3-(4-{[(2s,3s,4s,5s)-5-acetyl-3,4-dihydroxyoxolan-2-yl]oxy}-3-hydroxyphenyl)-2-methylprop-2-enimidic acid was first documented in 2020 (PMID: 32430474). Based on a literature review a small amount of articles have been published on Hygromycin A (PMID: 35064242) (PMID: 34762823) (PMID: 34716444) (PMID: 34619078).
Structure
Thumb
Synonyms
ValueSource
HygromycinMeSH
Chemical FormulaC23H29NO12
Average Mass511.4800 Da
Monoisotopic Mass511.16898 Da
IUPAC Name(2E)-N-[(3aR,4S,5S,6R,7S,7aS)-4,6,7-trihydroxy-hexahydro-2H-1,3-benzodioxol-5-yl]-3-(4-{[(2S,3S,4S,5S)-5-acetyl-3,4-dihydroxyoxolan-2-yl]oxy}-3-hydroxyphenyl)-2-methylprop-2-enimidic acid
Traditional Name(2E)-N-[(3aR,4S,5S,6R,7S,7aS)-4,6,7-trihydroxy-hexahydro-2H-1,3-benzodioxol-5-yl]-3-(4-{[(2S,3S,4S,5S)-5-acetyl-3,4-dihydroxyoxolan-2-yl]oxy}-3-hydroxyphenyl)-2-methylprop-2-enimidic acid
CAS Registry NumberNot Available
SMILES
CC(=O)[C@H]1O[C@@H](OC2=CC=C(\C=C(/C)C(O)=N[C@@H]3[C@H](O)[C@H]4OCO[C@H]4[C@@H](O)[C@@H]3O)C=C2O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C23H29NO12/c1-8(22(32)24-13-14(27)16(29)21-20(15(13)28)33-7-34-21)5-10-3-4-12(11(26)6-10)35-23-18(31)17(30)19(36-23)9(2)25/h3-6,13-21,23,26-31H,7H2,1-2H3,(H,24,32)/b8-5+/t13-,14+,15-,16-,17-,18-,19+,20+,21-,23+/m0/s1
InChI KeyYQYJSBFKSSDGFO-KEHBMHOOSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces hygroscopicusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPhenolic glycosides
Alternative Parents
Substituents
  • Phenolic glycoside
  • Hydroxycinnamic acid or derivatives
  • Cinnamic acid or derivatives
  • Cinnamic acid amide
  • O-glycosyl compound
  • Pentose monosaccharide
  • Phenoxy compound
  • Phenol ether
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Benzenoid
  • Monosaccharide
  • Monocyclic benzene moiety
  • Cyclitol or derivatives
  • Tetrahydrofuran
  • Cyclic alcohol
  • Meta-dioxolane
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Ketone
  • Carboxamide group
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Carboxylic acid derivative
  • Acetal
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic 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
logP-0.87ChemAxon
pKa (Strongest Acidic)5.48ChemAxon
pKa (Strongest Basic)2.13ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area207.96 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity118.08 m³·mol⁻¹ChemAxon
Polarizability50.57 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00018293
Chemspider ID16735855
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkTotomycin
METLIN IDNot Available
PubChem Compound20054941
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Ding X, Yuan T, Chen W, Wang X, Chu Y, Liu X, Hu Y, Hu L: Hygromycin A derivatives isolated from Streptomyces sp. PC-22 in the rhizosphere soil of Pulsatilla chinensis. J Antibiot (Tokyo). 2022 Mar;75(3):176-180. doi: 10.1038/s41429-022-00506-w. Epub 2022 Jan 21. [PubMed:35064242 ]
  2. Arnaboldi PM, Narasimhan S: Hygromycin A in the Lymelight. Cell Host Microbe. 2021 Nov 10;29(11):1599-1601. doi: 10.1016/j.chom.2021.10.007. [PubMed:34762823 ]
  3. Villanueva MT: Rediscovering hygromycin A for Lyme disease treatment. Nat Rev Drug Discov. 2021 Dec;20(12):896. doi: 10.1038/d41573-021-00180-x. [PubMed:34716444 ]
  4. Leimer N, Wu X, Imai Y, Morrissette M, Pitt N, Favre-Godal Q, Iinishi A, Jain S, Caboni M, Leus IV, Bonifay V, Niles S, Bargabos R, Ghiglieri M, Corsetti R, Krumpoch M, Fox G, Son S, Klepacki D, Polikanov YS, Freliech CA, McCarthy JE, Edmondson DG, Norris SJ, D'Onofrio A, Hu LT, Zgurskaya HI, Lewis K: A selective antibiotic for Lyme disease. Cell. 2021 Oct 14;184(21):5405-5418.e16. doi: 10.1016/j.cell.2021.09.011. Epub 2021 Oct 6. [PubMed:34619078 ]
  5. Lozano GL, Guan C, Cao Y, Borlee BR, Broderick NA, Stabb EV, Handelsman J: A Chemical Counterpunch: Chromobacterium violaceum ATCC 31532 Produces Violacein in Response to Translation-Inhibiting Antibiotics. mBio. 2020 May 19;11(3):e00948-20. doi: 10.1128/mBio.00948-20. [PubMed:32430474 ]
  6. LOTUS database [Link]