viomycin   Click here for help

GtoPdb Ligand ID: 13252

Synonyms: celiomycin | florimycin | tuberactinomycin B
Approved drug
viomycin is an approved drug (FDA (1953))
Compound class: Natural product
Comment: Viomycin was the first member of the tuberactinomycin class of antimycobacterial compounds to be identified and was originally isolated from cultures of the actinomycete Streptomyces puniceus [1,3].
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 23
Hydrogen bond donors 15
Rotatable bonds 12
Topological polar surface area 392.86
Molecular weight 685.69
XLogP -4.06
No. Lipinski's rules broken 3

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 C(C[C@@H](CC(=O)N[C@H]1CNC(=O)[C@H]([C@H]2C[C@@H](N=C(N)N2)O)NC(=O)/C(=C/NC(=O)N)/NC(=O)[C@H](CO)NC(=O)[C@H](CO)NC1=O)N)CN
Isomeric SMILES C1[C@@H](NC(=N[C@H]1O)N)[C@H]2C(=O)NC[C@@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N/C(=C\NC(=O)N)/C(=O)N2)CO)CO)NC(=O)C[C@H](CCCN)N
InChI InChI=1S/C25H43N13O10/c26-3-1-2-10(27)4-16(41)32-12-6-30-23(47)18(11-5-17(42)37-24(28)36-11)38-20(44)13(7-31-25(29)48)33-21(45)14(8-39)35-22(46)15(9-40)34-19(12)43/h7,10-12,14-15,17-18,39-40,42H,1-6,8-9,26-27H2,(H,30,47)(H,32,41)(H,33,45)(H,34,43)(H,35,46)(H,38,44)(H3,28,36,37)(H3,29,31,48)/b13-7-/t10-,11+,12-,14-,15-,17-,18-/m0/s1
InChI Key GXFAIFRPOKBQRV-GHXCTMGLSA-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. Bartz QR, Ehrlich J, Mold JD, Penner MA, Smith RM. (1951)
Viomycin, a new tuberculostatic antibiotic.
Am Rev Tuberc, 63 (1): 4-6. [PMID:14799784]
2. Holm M, Borg A, Ehrenberg M, Sanyal S. (2016)
Molecular mechanism of viomycin inhibition of peptide elongation in bacteria.
Proc Natl Acad Sci U S A, 113 (4): 978-83. [PMID:26755601]
3. Steenken Jr W, Wolinsky E. (1950)
Effects of antimicrobial agents on the tubercle bacillus and on experimental tuberculosis.
Am J Med, 9 (5): 633-53. [PMID:14783133]
4. Zhang L, Wang YH, Zhang X, Lancaster L, Zhou J, Noller HF. (2020)
The structural basis for inhibition of ribosomal translocation by viomycin.
Proc Natl Acad Sci U S A, 117 (19): 10271-10277. [PMID:32341159]