virginiamycin S1   Click here for help

GtoPdb Ligand ID: 13755

Synonyms: staphylomycin S | virgimycin
Compound class: Natural product
Comment: Virginiamycin S1 is a streptogramin antibacterial produced by a Streptomyces sp. related to S. virginiae [5]. It is isolated as part of a virginiamycin complex containing M components (M1 and M2) and S components (S1-S4)(reviewed in [1]). Virginiamycin S1 and pristinamycin IIA (virginiamycin M1) are the major components of virginiamycin [2], an antibacterial used in veterinary medicine and also in animal husbandry as a growth promoter.
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 17
Hydrogen bond donors 4
Rotatable bonds 7
Topological polar surface area 224.19
Molecular weight 823.89
XLogP 1.42
No. Lipinski's rules broken 2

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES CC[C@@H]1C(=O)N2CCC[C@H]2C(=O)N(C)[C@@H](CC3=CC=CC=C3)C(=O)N4CCC(=O)C[C@H]4C(=O)N[C@@H](C5=CC=CC=C5)C(=O)O[C@H](C)[C@@H](C(=O)N1)NC(=O)C6=NC=CC=C6O
Isomeric SMILES CC[C@@H]1C(=O)N2CCC[C@H]2C(=O)N([C@H](C(=O)N3CCC(=O)C[C@H]3C(=O)N[C@H](C(=O)O[C@@H]([C@@H](C(=O)N1)NC(=O)C4=C(C=CC=N4)O)C)C5=CC=CC=C5)CC6=CC=CC=C6)C
InChI InChI=1S/C43H49N7O10/c1-4-29-40(56)49-21-12-17-30(49)41(57)48(3)32(23-26-13-7-5-8-14-26)42(58)50-22-19-28(51)24-31(50)37(53)47-35(27-15-9-6-10-16-27)43(59)60-25(2)34(38(54)45-29)46-39(55)36-33(52)18-11-20-44-36/h5-11,13-16,18,20,25,29-32,34-35,52H,4,12,17,19,21-24H2,1-3H3,(H,45,54)(H,46,55)(H,47,53)/t25-,29-,30+,31+,32+,34+,35+/m1/s1
InChI Key FEPMHVLSLDOMQC-IYPFLVAKSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
References
1. Cocito C. (1979)
Antibiotics of the virginiamycin family, inhibitors which contain synergistic components.
Microbiol Rev, 43 (2): 145-92. [PMID:117294]
2. Crooy P, De Neys R. (1972)
Virginiamycin: Nomenclature.
J Antibiot (Tokyo), 25 (6): 371-372. DOI: 10.7164/antibiotics.25.371
3. Di Giambattista M, Thielen AP, Maassen JA, Möller W, Cocito C. (1986)
Localization of virginiamycin S binding site on bacterial ribosome by fluorescence energy transfer.
Biochemistry, 25 (12): 3540-7. [PMID:3087416]
4. Hariharan H, Barnum DA. (1974)
Minimal inhibitory concentrations of twenty antimicrobial agents to animal pathogens.
Can J Comp Med, 38 (4): 437-42. [PMID:4373151]
5. Vanderhaeghe H, Parmentier G. (1960)
The Structure of Factor S of Staphylomycin.
J Am Chem Soc, 82 (16): 4414-4422. DOI: 10.1021/ja01501a070