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Record Information
Version2.0
Created at2022-09-06 09:35:07 UTC
Updated at2022-09-06 09:35:07 UTC
NP-MRD IDNP0229500
Secondary Accession NumbersNone
Natural Product Identification
Common Namemethyl (1r,3s,4r,5r,7r,9r,11s,12s,13s)-5-(6-aminopurin-9-yl)-1,12-dihydroxy-4-methoxy-13-{[(2e)-2-methylbut-2-enoyl]oxy}-2,6,10-trioxatricyclo[7.4.0.0³,⁷]tridecane-11-carboxylate
DescriptionHerbicidin F belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether). methyl (1r,3s,4r,5r,7r,9r,11s,12s,13s)-5-(6-aminopurin-9-yl)-1,12-dihydroxy-4-methoxy-13-{[(2e)-2-methylbut-2-enoyl]oxy}-2,6,10-trioxatricyclo[7.4.0.0³,⁷]tridecane-11-carboxylate was first documented in 2017 (PMID: 27876750). Based on a literature review very few articles have been published on Herbicidin F (PMID: 31615513).
Structure
Thumb
SynonymsNot Available
Chemical FormulaC23H29N5O10
Average Mass535.5100 Da
Monoisotopic Mass535.19144 Da
IUPAC Namemethyl (1R,3S,4R,5R,7R,9R,11S,12S,13S)-5-(6-amino-9H-purin-9-yl)-1,12-dihydroxy-4-methoxy-13-{[(2E)-2-methylbut-2-enoyl]oxy}-2,6,10-trioxatricyclo[7.4.0.0^{3,7}]tridecane-11-carboxylate
Traditional Namemethyl (1R,3S,4R,5R,7R,9R,11S,12S,13S)-5-(6-aminopurin-9-yl)-1,12-dihydroxy-4-methoxy-13-{[(2E)-2-methylbut-2-enoyl]oxy}-2,6,10-trioxatricyclo[7.4.0.0^{3,7}]tridecane-11-carboxylate
CAS Registry NumberNot Available
SMILES
CO[C@@H]1[C@H]2O[C@]3(O)[C@@H](C[C@H]2O[C@H]1N1C=NC2=C(N)N=CN=C12)O[C@@H]([C@@H](O)[C@@H]3OC(=O)C(\C)=C\C)C(=O)OC
InChI Identifier
InChI=1S/C23H29N5O10/c1-5-9(2)21(30)37-17-13(29)15(22(31)34-4)36-11-6-10-14(38-23(11,17)32)16(33-3)20(35-10)28-8-27-12-18(24)25-7-26-19(12)28/h5,7-8,10-11,13-17,20,29,32H,6H2,1-4H3,(H2,24,25,26)/b9-5+/t10-,11-,13-,14+,15+,16-,17+,20-,23-/m1/s1
InChI KeyPXURTMJWRXVZEJ-SYDSVXEMSA-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 OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentGlycosylamines
Alternative Parents
Substituents
  • C-glycosyl compound
  • Disaccharide
  • N-glycosyl compound
  • 6-aminopurine
  • Purine
  • Imidazopyrimidine
  • Furopyran
  • Aminopyrimidine
  • Beta-hydroxy acid
  • Fatty acid ester
  • Imidolactam
  • Hydroxy acid
  • Fatty acyl
  • N-substituted imidazole
  • Pyrimidine
  • Pyran
  • Dicarboxylic acid or derivatives
  • Primary aromatic amine
  • Oxane
  • Azole
  • Heteroaromatic compound
  • Furan
  • Alpha,beta-unsaturated carboxylic ester
  • Enoate ester
  • Imidazole
  • Methyl ester
  • Oxolane
  • Amino acid or derivatives
  • Secondary alcohol
  • Hemiacetal
  • Carboxylic acid ester
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Azacycle
  • Dialkyl ether
  • Oxacycle
  • Ether
  • Carbonyl group
  • Hydrocarbon derivative
  • Amine
  • Organopnictogen compound
  • Primary amine
  • Organonitrogen compound
  • Organic oxide
  • Alcohol
  • Organic nitrogen compound
  • 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
logP0.27ChemAxon
pKa (Strongest Acidic)10.09ChemAxon
pKa (Strongest Basic)3.92ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area199.6 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity125.54 m³·mol⁻¹ChemAxon
Polarizability51.08 ųChemAxon
Number of Rings5ChemAxon
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 IDC00018238
Chemspider ID4944753
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6440493
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Zhang JC, Yang YB, Chen GY, Li XZ, Hu M, Wang BY, Ruan BH, Zhou H, Zhao LX, Ding ZT: 8'-epimer of herbicidin F and its congeners from Streptomyces sp. YIM 66142. J Antibiot (Tokyo). 2017 Mar;70(3):313-316. doi: 10.1038/ja.2016.133. Epub 2016 Nov 16. [PubMed:27876750 ]
  2. Shi Y, Gu R, Li Y, Wang X, Ren W, Li X, Wang L, Xie Y, Hong B: Exploring novel herbicidin analogues by transcriptional regulator overexpression and MS/MS molecular networking. Microb Cell Fact. 2019 Oct 15;18(1):175. doi: 10.1186/s12934-019-1225-7. [PubMed:31615513 ]
  3. LOTUS database [Link]