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Katanosin B   Click here for help

GtoPdb Ligand ID: 10970

Synonyms: Lysobactin
Compound class: Natural product
Comment: Katanosins (lysobactins) are antibacterial compounds [2]. They have been isolated from Cytophaga [4] or the Gram-negative bacterium Lysobacter sp [5]. Katanosin B is also known as lysobactin. This can now be chemically synthesised [1,6]. Katanosins target bacterial cell wall biosynthesis [3] and they are potent against problematic Gram-positive hospital pathogens such as staphylococci and enterococci.
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 32
Hydrogen bond donors 18
Rotatable bonds 25
Topological polar surface area 531.73
Molecular weight 1275.72
XLogP 5.16
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 OCC1NC(=O)C(NC(=O)CNC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(C(OC1=O)c1ccccc1)NC(=O)C(NC(=O)C(CC(C)C)N)CC(C)C)C(C(C)C)O)CC(C)C)CCCN=C(N)N)C(CC)C)C(O)C)C(C(=O)N)O
Isomeric SMILES OCC1NC(=O)C(NC(=O)CNC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(C(OC1=O)c1ccccc1)NC(=O)C(NC(=O)C(CC(C)C)N)CC(C)C)C(C(C)C)O)CC(C)C)CCCN=C(N)N)C(CC)C)C(O)C)C(C(=O)N)O
InChI InChI=1S/C58H97N15O17/c1-12-30(10)39-53(85)71-40(31(11)75)52(84)64-24-38(76)69-42(45(78)47(60)79)55(87)68-37(25-74)57(89)90-46(32-17-14-13-15-18-32)43(73-51(83)36(23-28(6)7)66-48(80)33(59)21-26(2)3)56(88)72-41(44(77)29(8)9)54(86)67-35(22-27(4)5)50(82)65-34(49(81)70-39)19-16-20-63-58(61)62/h13-15,17-18,26-31,33-37,39-46,74-75,77-78H,12,16,19-25,59H2,1-11H3,(H2,60,79)(H,64,84)(H,65,82)(H,66,80)(H,67,86)(H,68,87)(H,69,76)(H,70,81)(H,71,85)(H,72,88)(H,73,83)(H4,61,62,63)
InChI Key KQMKBWMQSNKASI-UHFFFAOYSA-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. Guzman-Martinez A, Lamer R, VanNieuwenhze MS. (2007)
Total synthesis of lysobactin.
J Am Chem Soc, 129 (18): 6017-21. [PMID:17432854]
2. Kato T, Hinoo H, Terui Y, Kikuchi J, Shoji J. (1988)
The structures of katanosins A and B.
J Antibiot, 41 (6): 719-25. [PMID:3403365]
3. Lee W, Schaefer K, Qiao Y, Srisuknimit V, Steinmetz H, Müller R, Kahne D, Walker S. (2016)
The Mechanism of Action of Lysobactin.
J Am Chem Soc, 138 (1): 100-3. [PMID:26683668]
4. O'Sullivan J, McCullough JE, Tymiak AA, Kirsch DR, Trejo WH, Principe PA. (1988)
Lysobactin, a novel antibacterial agent produced by Lysobacter sp. I. Taxonomy, isolation and partial characterization.
J Antibiot, 41 (12): 1740-4. [PMID:3209465]
5. Shoji J, Hinoo H, Matsumoto K, Hattori T, Yoshida T, Matsuura S, Kondo E. (1988)
Isolation and characterization of katanosins A and B.
J Antibiot, 41 (6): 713-8. [PMID:3403364]
6. von Nussbaum F, Anlauf S, Benet-Buchholz J, Häbich D, Köbberling J, Musza L, Telser J, Rübsamen-Waigmann H, Brunner NA. (2007)
Structure and total synthesis of lysobactin (katanosin B).
Angew Chem Int Ed Engl, 46 (12): 2039-42. [PMID:17211904]