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myxopyronin B   Click here for help

GtoPdb Ligand ID: 14300

PDB Ligand
Compound class: Natural product
Comment: Myxopyronin is a natural product with antibacterial activity, originally isolated from cultures of the soil-dwelling myxobacterium Myxococcus fulvus as a mixture of two components (myxopyronin A and myxopyronin B) [5]. Total synthesis has been reported [4]. We show the structure for myxopyronin B which is reported to be the component with the greater activity [5]. Functionally, it inhibits bacterial RNA polymerase [5].
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 7
Hydrogen bond donors 2
Rotatable bonds 13
Topological polar surface area 101.93
Molecular weight 431.52
XLogP 4.86
No. Lipinski's rules broken 1

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 CCCC/C(=C/C=C(\C)/C(=O)C1=C(C=C([C@H](C)CC/C=C/NC(=O)OC)OC1=O)O)/C
Isomeric SMILES CCCC/C(=C/C=C(\C)/C(=O)C1=C(C=C(OC1=O)[C@H](C)CC/C=C/NC(=O)OC)O)/C
InChI InChI=1S/C24H33NO6/c1-6-7-10-16(2)12-13-18(4)22(27)21-19(26)15-20(31-23(21)28)17(3)11-8-9-14-25-24(29)30-5/h9,12-15,17,26H,6-8,10-11H2,1-5H3,(H,25,29)/b14-9+,16-12+,18-13+/t17-/m1/s1
InChI Key SPQDIDVJAZFBRL-WXFBSNOUSA-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. Belogurov GA, Vassylyeva MN, Sevostyanova A, Appleman JR, Xiang AX, Lira R, Webber SE, Klyuyev S, Nudler E, Artsimovitch I et al.. (2009)
Transcription inactivation through local refolding of the RNA polymerase structure.
Nature, 457 (7227): 332-5. [PMID:18946472]
2. Brauer M, Herrmann J, Zühlke D, Müller R, Riedel K, Sievers S. (2022)
Myxopyronin B inhibits growth of a Fidaxomicin-resistant Clostridioides difficile isolate and interferes with toxin synthesis.
Gut Pathog, 14 (1): 4. [PMID:34991700]
3. Doundoulakis T, Xiang AX, Lira R, Agrios KA, Webber SE, Sisson W, Aust RM, Shah AM, Showalter RE, Appleman JR et al.. (2004)
Myxopyronin B analogs as inhibitors of RNA polymerase, synthesis and biological evaluation.
Bioorg Med Chem Lett, 14 (22): 5667-72. [PMID:15482944]
4. Hu T, Schaus JV, Lam K, Palfreyman MG, Wuonola M, Gustafson G, Panek JS. (1998)
Total Synthesis and Preliminary Antibacterial Evaluation of the RNA Polymerase Inhibitors ±-Myxopyronin A and B.
J. Org. Chem., 63 (7): 2401-2406. DOI: 10.1021/jo9721610
5. Irschik H, Gerth K, Höfle G, Kohl W, Reichenbach H. (1983)
The myxopyronins, new inhibitors of bacterial RNA synthesis from Myxococcus fulvus (Myxobacterales).
J Antibiot (Tokyo), 36 (12): 1651-8. [PMID:6420386]
6. Moy TI, Daniel A, Hardy C, Jackson A, Rehrauer O, Hwang YS, Zou D, Nguyen K, Silverman JA, Li Q et al.. (2011)
Evaluating the activity of the RNA polymerase inhibitor myxopyronin B against Staphylococcus aureus.
FEMS Microbiol Lett, 319 (2): 176-9. [PMID:21477256]
7. Mukhopadhyay J, Das K, Ismail S, Koppstein D, Jang M, Hudson B, Sarafianos S, Tuske S, Patel J, Jansen R et al.. (2008)
The RNA polymerase "switch region" is a target for inhibitors.
Cell, 135 (2): 295-307. [PMID:18957204]