mureidomycin C   Click here for help

GtoPdb Ligand ID: 13517

Compound class: Natural product
Comment: Mureidomycins are ureidyl peptide nucleoside antibacterial compounds, originally isolated from the culture broth of Streptomyces flavidoviridens as a mixture of four components (mureidomycin A-D) [3]. We show the structure for mureidomycin C which is reported to have the most potent antibacterial activity [5]. Functionally, mureidomycin C inhibits phospho-N-acetylmuramoyl-pentapeptide-transferase (MraY, translocase I) [4], an essential enzyme in bacterial peptidoglycan biosynthesis.
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 22
Hydrogen bond donors 11
Rotatable bonds 26
Topological polar surface area 356.69
Molecular weight 897.95
XLogP -4.77
No. Lipinski's rules broken 4

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](C(=O)NC=C1CC(C(N2C=CC(=O)NC2=O)O1)O)NC(=O)[C@H](CCSC)NC(=O)NC(CC3=CC=CC(=C3)O)C(=O)O)N(C)C(=O)[C@H](CC4=CC=CC(=C4)O)NC(=O)CN
Isomeric SMILES CC([C@H](C(=O)NC=C1CC(C(O1)N2C=CC(=O)NC2=O)O)NC(=O)[C@H](CCSC)NC(=O)NC(CC3=CC(=CC=C3)O)C(=O)O)N(C)C(=O)[C@H](CC4=CC(=CC=C4)O)NC(=O)CN
InChI InChI=1S/C40H51N9O13S/c1-21(48(2)36(57)28(43-32(54)19-41)16-22-6-4-8-24(50)14-22)33(35(56)42-20-26-18-30(52)37(62-26)49-12-10-31(53)46-40(49)61)47-34(55)27(11-13-63-3)44-39(60)45-29(38(58)59)17-23-7-5-9-25(51)15-23/h4-10,12,14-15,20-21,27-30,33,37,50-52H,11,13,16-19,41H2,1-3H3,(H,42,56)(H,43,54)(H,47,55)(H,58,59)(H2,44,45,60)(H,46,53,61)/t21?,27-,28-,29?,30?,33+,37?/m0/s1
InChI Key DODUWDVIPJZWOY-JHYHWTEUSA-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. ANDERSON JS, MATSUHASHI M, HASKIN MA, STROMINGER JL. (1965)
LIPID-PHOSPHOACETYLMURAMYL-PENTAPEPTIDE AND LIPID-PHOSPHODISACCHARIDE-PENTAPEPTIDE: PRESUMED MEMBRANE TRANSPORT INTERMEDIATES IN CELL WALL SYNTHESIS.
Proc Natl Acad Sci U S A, 53 (4): 881-9. [PMID:14324547]
2. Heydanek Jr MG, Neuhaus FC. (1969)
The initial stage in peptidoglycan synthesis. IV. Solubilization of phospho-N-acetylmuramyl-pentapeptide translocase.
Biochemistry, 8 (4): 1474-81. [PMID:5805290]
3. Inukai M, Isono F, Takahashi S, Enokita R, Sakaida Y, Haneishi T. (1989)
Mureidomycins A-D, novel peptidylnucleoside antibiotics with spheroplast forming activity. I. Taxonomy, fermentation, isolation and physico-chemical properties.
J Antibiot (Tokyo), 42 (5): 662-6. [PMID:2498273]
4. Inukai M, Isono F, Takatsuki A. (1993)
Selective inhibition of the bacterial translocase reaction in peptidoglycan synthesis by mureidomycins.
Antimicrob Agents Chemother, 37 (5): 980-3. [PMID:8517724]
5. Isono F, Katayama T, Inukai M, Haneishi T. (1989)
Mureidomycins A-D, novel peptidylnucleoside antibiotics with spheroplast forming activity. III. Biological properties.
J Antibiot (Tokyo), 42 (5): 674-9. [PMID:2498275]
6. STRUVE WG, NEUHAUS FC. (1965)
EVIDENCE FOR AN INITIAL ACCEPTOR OF UDP-NAC-MURAMYL-PENTAPEPTIDE IN THE SYNTHESIS OF BACTERIAL MUCOPEPTIDE.
Biochem Biophys Res Commun, 18: 6-12. [PMID:14265759]