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Record Information
Version2.0
Created at2022-09-11 14:42:51 UTC
Updated at2022-09-11 14:42:51 UTC
NP-MRD IDNP0315869
Secondary Accession NumbersNone
Natural Product Identification
Common Namemethymycin
DescriptionMethymycin belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars. Thus, methymycin is considered to be a macrolide lipid molecule. methymycin is found in Streptomyces venezuelae. methymycin was first documented in 1954 (PMID: 24542881). Methymycin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (PMID: 11720530) (PMID: 5439233) (PMID: 19830295) (PMID: 23866020) (PMID: 20695498) (PMID: 10421766).
Structure
Thumb
SynonymsNot Available
Chemical FormulaC25H43NO7
Average Mass469.6114 Da
Monoisotopic Mass469.30395 Da
IUPAC Name(3R,4S,5S,7R,9E,11S,12R)-4-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-1-oxacyclododec-9-ene-2,8-dione
Traditional Namemethymycin
CAS Registry NumberNot Available
SMILES
[H]\C1=C([H])/[C@](C)(O)[C@@]([H])(CC)OC(=O)[C@]([H])(C)[C@@]([H])(O[C@]2([H])O[C@]([H])(C)C[C@]([H])(N(C)C)[C@@]2([H])O)[C@@]([H])(C)C[C@@]([H])(C)C1=O
InChI Identifier
InChI=1S/C25H43NO7/c1-9-20-25(6,30)11-10-19(27)14(2)12-15(3)22(17(5)23(29)32-20)33-24-21(28)18(26(7)8)13-16(4)31-24/h10-11,14-18,20-22,24,28,30H,9,12-13H2,1-8H3/b11-10+/t14-,15+,16-,17-,18+,20-,21-,22+,24+,25+/m1/s1
InChI KeyHUKYPYXOBINMND-HYUJHOPRSA-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 venezuelaeLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentAminoglycosides
Alternative Parents
Substituents
  • Aminoglycoside core
  • Macrolide
  • Oxane
  • Tertiary alcohol
  • 1,2-aminoalcohol
  • Amino acid or derivatives
  • Carboxylic acid ester
  • Ketone
  • Lactone
  • Secondary alcohol
  • Tertiary amine
  • Tertiary aliphatic amine
  • Cyclic ketone
  • Monocarboxylic acid or derivatives
  • Acetal
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Oxacycle
  • Organopnictogen compound
  • Amine
  • Alcohol
  • Organonitrogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
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
logP2.05ALOGPS
logP3.28ChemAxon
logS-3ALOGPS
pKa (Strongest Acidic)12.77ChemAxon
pKa (Strongest Basic)8.38ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area105.53 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity125.67 m³·mol⁻¹ChemAxon
Polarizability51.04 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC11996
BioCyc IDCPD-13832
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5282034
PDB IDNot Available
ChEBI ID29630
Good Scents IDNot Available
References
General References
  1. Zhang Q, Sherman DH: Isolation and structure determination of novamethymycin, a new bioactive metabolite of the methymycin biosynthetic pathway in Streptomyces venezuelae. J Nat Prod. 2001 Nov;64(11):1447-50. doi: 10.1021/np010146r. [PubMed:11720530 ]
  2. Rickards RW, Smith RM: Macrolide antibiotic studies. 13. Partial absolute configurations of methymycin, neomethymycin, narbomycin and picromycin. Tetrahedron Lett. 1970 Mar;(13):1025-8. doi: 10.1016/s0040-4039(01)97897-9. [PubMed:5439233 ]
  3. Oh HS, Xuan R, Kang HY: Total synthesis of methymycin. Org Biomol Chem. 2009 Nov 7;7(21):4458-63. doi: 10.1039/b911200f. Epub 2009 Aug 18. [PubMed:19830295 ]
  4. Hansen DA, Rath CM, Eisman EB, Narayan AR, Kittendorf JD, Mortison JD, Yoon YJ, Sherman DH: Biocatalytic synthesis of pikromycin, methymycin, neomethymycin, novamethymycin, and ketomethymycin. J Am Chem Soc. 2013 Jul 31;135(30):11232-8. doi: 10.1021/ja404134f. Epub 2013 Jul 18. [PubMed:23866020 ]
  5. Borisova SA, Liu HW: Characterization of glycosyltransferase DesVII and its auxiliary partner protein DesVIII in the methymycin/picromycin biosynthetic pathway. Biochemistry. 2010 Sep 21;49(37):8071-84. doi: 10.1021/bi1007657. [PubMed:20695498 ]
  6. Tang L, Fu H, Betlach MC, McDaniel R: Elucidating the mechanism of chain termination switching in the picromycin/methymycin polyketide synthase. Chem Biol. 1999 Aug;6(8):553-8. doi: 10.1016/S1074-5521(99)80087-8. [PubMed:10421766 ]
  7. Xue Y, Wilson D, Sherman DH: Genetic architecture of the polyketide synthases for methymycin and pikromycin series macrolides. Gene. 2000 Mar 7;245(1):203-11. doi: 10.1016/s0378-1119(00)00003-2. [PubMed:10713461 ]
  8. Zhao L, Beyer NJ, Borisova SA, Liu HW: Beta-glucosylation as a part of self-resistance mechanism in methymycin/pikromycin producing strain Streptomyces venezuelae. Biochemistry. 2003 Dec 23;42(50):14794-804. doi: 10.1021/bi035501m. [PubMed:14674753 ]
  9. CHAVEZ MAX G, MENDEZ D: Preliminary report on the therapeutic action of methymycin in Brucella melitensis infection. Antibiot Chemother (Northfield). 1954 Jan;4(1):83-6. [PubMed:24542881 ]
  10. PERLMAN D: Chemical methods for determination of methymycin in fermentation samples. Antibiot Chemother (Northfield). 1954 Aug;4(8):859-63. [PubMed:24543211 ]
  11. PERLMAN D, O'BRIEN E: Microbiological production of methymycin and related antibiotics. Antibiot Chemother (Northfield). 1954 Aug;4(8):894-8. [PubMed:24543216 ]
  12. Manwaring DG, Rickards RW, Smith RM: Macrolide antibiotic studies. XIV. The total absolute configuration of methymycin. Tetrahedron Lett. 1970 Mar;(13):1029-32. doi: 10.1016/s0040-4039(01)97898-0. [PubMed:5439234 ]
  13. Xue Y, Wilson D, Zhao L, Liu Hw, Sherman DH: Hydroxylation of macrolactones YC-17 and narbomycin is mediated by the pikC-encoded cytochrome P450 in Streptomyces venezuelae. Chem Biol. 1998 Nov;5(11):661-7. doi: 10.1016/s1074-5521(98)90293-9. [PubMed:9831532 ]
  14. Graziani EI, Cane DE, Betlach MC, Kealey JT, McDaniel R: Macrolide biosynthesis: a single cytochrome P450, PicK, is responsible for the hydroxylations that generate methymycin, neomethymycin, and picromycin in Streptomyces venezuelae. Bioorg Med Chem Lett. 1998 Nov 17;8(22):3117-20. doi: 10.1016/s0960-894x(98)00553-8. [PubMed:9873687 ]
  15. LOTUS database [Link]