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Record Information
Version2.0
Created at2022-09-06 10:56:57 UTC
Updated at2022-09-06 10:56:57 UTC
NP-MRD IDNP0230488
Secondary Accession NumbersNone
Natural Product Identification
Common Name(10r,11r,12e,17e,19e,21s)-14,21-dihydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triazatricyclo[23.2.1.0³,⁷]octacosa-1(27),6,12,14,17,19,25(28)-heptaene-2,8,23-trione
DescriptionVirginiamycin M1, also known as mikamycin a or streptogramin a, belongs to the class of organic compounds known as macrolide lactams. These are cyclic polyketides containing both a cyclic amide and a cyclic ester group. Virginiamycin M1 is a drug which is used for the treatment of bacterial infections. Virginiamycin M1 is a moderately basic compound (based on its pKa). (10r,11r,12e,17e,19e,21s)-14,21-dihydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triazatricyclo[23.2.1.0³,⁷]octacosa-1(27),6,12,14,17,19,25(28)-heptaene-2,8,23-trione is found in Apis cerana. (10r,11r,12e,17e,19e,21s)-14,21-dihydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triazatricyclo[23.2.1.0³,⁷]octacosa-1(27),6,12,14,17,19,25(28)-heptaene-2,8,23-trione was first documented in 1986 (PMID: 3096930). A macrolide that is (together with pristinamycin IA) a component of pristinamycin, an oral streptogramin antibiotic produced by Streptomyces pristinaespiralis (PMID: 25223995) (PMID: 15480455) (PMID: 24324222) (PMID: 24687494).
Structure
Thumb
Synonyms
ValueSource
Mikamycin aChEBI
Ostreogrycin aChEBI
Streptogramin aChEBI
Virginiamycin factor m1ChEBI
Pristinamycin iiaKegg
Ostreogrycin gMeSH
Pristinamycin iibMeSH
Staphylomycin mMeSH
Staphylomycin M1MeSH
Virginiamycin iibMeSH
Virginiamycin M1ChEBI
PIIAPhytoBank
VM1PhytoBank
Vernamycin APhytoBank
Chemical FormulaC28H35N3O7
Average Mass525.5934 Da
Monoisotopic Mass525.24750 Da
IUPAC Name(10R,11R,12E,17E,19E,21S)-21-hydroxy-11,19-dimethyl-10-(propan-2-yl)-9,26-dioxa-3,15,28-triazatricyclo[23.2.1.0^{3,7}]octacosa-1(27),6,12,17,19,25(28)-hexaene-2,8,14,23-tetrone
Traditional Name(10R,11R,12E,17E,19E,21S)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triazatricyclo[23.2.1.0^{3,7}]octacosa-1(27),6,12,17,19,25(28)-hexaene-2,8,14,23-tetrone
CAS Registry NumberNot Available
SMILES
CC(C)[C@H]1OC(=O)C2=CCCN2C(=O)C2=COC(CC(=O)C[C@H](O)\C=C(/C)\C=C\CNC(=O)\C=C\[C@H]1C)=N2
InChI Identifier
InChI=1S/C28H35N3O7/c1-17(2)26-19(4)9-10-24(34)29-11-5-7-18(3)13-20(32)14-21(33)15-25-30-22(16-37-25)27(35)31-12-6-8-23(31)28(36)38-26/h5,7-10,13,16-17,19-20,26,32H,6,11-12,14-15H2,1-4H3,(H,29,34)/b7-5+,10-9+,18-13+/t19-,20-,26-/m1/s1
InChI KeyDAIKHDNSXMZDCU-FQTGFAPKSA-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
Apis ceranaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as macrolide lactams. These are cyclic polyketides containing both a cyclic amide and a cyclic ester group.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassMacrolide lactams
Sub ClassNot Available
Direct ParentMacrolide lactams
Alternative Parents
Substituents
  • Macrolide lactam
  • Macrolactam
  • Alpha-amino acid or derivatives
  • 2-heteroaryl carboxamide
  • Azole
  • Oxazole
  • Heteroaromatic compound
  • Pyrroline
  • Tertiary carboxylic acid amide
  • Enoate ester
  • Alpha,beta-unsaturated carboxylic ester
  • Carboxamide group
  • Carboxylic acid ester
  • Ketone
  • Lactam
  • Lactone
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Cyclic ketone
  • Monocarboxylic acid or derivatives
  • Oxacycle
  • Carboxylic acid derivative
  • Azacycle
  • Organoheterocyclic compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Alcohol
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic 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
logP2.6ALOGPS
logP2.38ChemAxon
logS-3.9ALOGPS
pKa (Strongest Acidic)11.38ChemAxon
pKa (Strongest Basic)-0.16ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area139.04 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity144.17 m³·mol⁻¹ChemAxon
Polarizability55.73 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDDB01669
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC11299
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPristinamycin_IIA
METLIN IDNot Available
PubChem Compound5459319
PDB IDNot Available
ChEBI ID9997
Good Scents IDNot Available
References
General References
  1. Stogios PJ, Kuhn ML, Evdokimova E, Courvalin P, Anderson WF, Savchenko A: Potential for reduction of streptogramin A resistance revealed by structural analysis of acetyltransferase VatA. Antimicrob Agents Chemother. 2014 Dec;58(12):7083-92. doi: 10.1128/AAC.03743-14. Epub 2014 Sep 15. [PubMed:25223995 ]
  2. Dang J, Bergdahl M, Separovic F, Brownlee RT, Metzger RP: Solvent affects the conformation of virginiamycin M1 (pristinamycin IIA, streptogramin A). Org Biomol Chem. 2004 Oct 21;2(20):2919-24. doi: 10.1039/B407724E. Epub 2004 Sep 16. [PubMed:15480455 ]
  3. Li J, Li B, Wendlandt S, Schwarz S, Wang Y, Wu C, Ma Z, Shen J: Identification of a novel vga(E) gene variant that confers resistance to pleuromutilins, lincosamides and streptogramin A antibiotics in staphylococci of porcine origin. J Antimicrob Chemother. 2014 Apr;69(4):919-23. doi: 10.1093/jac/dkt482. Epub 2013 Dec 8. [PubMed:24324222 ]
  4. Hot C, Berthet N, Chesneau O: Characterization of sal(A), a novel gene responsible for lincosamide and streptogramin A resistance in Staphylococcus sciuri. Antimicrob Agents Chemother. 2014 Jun;58(6):3335-41. doi: 10.1128/AAC.02797-13. Epub 2014 Mar 31. [PubMed:24687494 ]
  5. Aumercier M, Bouhallab S, Capmau ML, Le Goffic F: Irreversible binding of pristinamycin IIA (streptogramin A) to ribosomes explains its "lasting damage" effect. J Antibiot (Tokyo). 1986 Sep;39(9):1322-8. doi: 10.7164/antibiotics.39.1322. [PubMed:3096930 ]
  6. LOTUS database [Link]