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evybactin   Click here for help

GtoPdb Ligand ID: 12922

Synonyms: GLXC-26146
Compound class: Natural product
Comment: Evybactin is a novel cyclic depsipeptide DNA gyrase inhibitor produced by Photorhabdus noenieputensis, with potent antibacterial activity that is selective for Mycobacterium tuberculosis [1].
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 42
Hydrogen bond donors 24
Rotatable bonds 32
Topological polar surface area 662.22
Molecular weight 1488.52
XLogP -4.92
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 C[C@H]([C@@H](C(=O)N[C@H](CCCNC(=N)N)C(=O)N[C@H]1[C@@H](C)OC(=O)C[C@@H](C(=O)O)NC(=O)[C@H](CO)NC(=O)[C@@H](CCCNC(=N)N)NC(=O)CNC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@@H](CO)NC(=O)C[C@@H](C(=O)O)NC(=O)[C@H](CC3=CN=CN3C)NC1=O)NC(=O)[C@H](CC4=CNC5=C4C=CC=C5)NC=O)O
Isomeric SMILES C[C@@H]1[C@@H](C(=O)N[C@H](C(=O)N[C@@H](CC(=O)N[C@@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@@H](C(=O)N[C@H](C(=O)N[C@@H](CC(=O)O1)C(=O)O)CO)CCCNC(=N)N)CC2=CC=CC=C2)CO)C(=O)O)CC3=CN=CN3C)NC(=O)[C@@H](CCCNC(=N)N)NC(=O)[C@H]([C@@H](C)O)NC(=O)[C@H](CC4=CNC5=CC=CC=C54)NC=O
InChI InChI=1S/C64H89N21O21/c1-31(89)50(83-55(96)40(74-30-88)20-34-24-72-37-14-8-7-13-36(34)37)59(100)77-39(16-10-18-71-64(67)68)54(95)84-51-32(2)106-49(92)23-44(62(104)105)81-58(99)46(28-87)82-53(94)38(15-9-17-70-63(65)66)75-48(91)26-73-52(93)41(19-33-11-5-4-6-12-33)78-57(98)45(27-86)76-47(90)22-43(61(102)103)80-56(97)42(79-60(51)101)21-35-25-69-29-85(35)3/h4-8,11-14,24-25,29-32,38-46,50-51,72,86-87,89H,9-10,15-23,26-28H2,1-3H3,(H,73,93)(H,74,88)(H,75,91)(H,76,90)(H,77,100)(H,78,98)(H,79,101)(H,80,97)(H,81,99)(H,82,94)(H,83,96)(H,84,95)(H,102,103)(H,104,105)(H4,65,66,70)(H4,67,68,71)/t31-,32-,38-,39-,40+,41+,42+,43+,44+,45-,46+,50+,51+/m1/s1
InChI Key WUDFNHIMHPHZCA-RMKJKUPCSA-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/)
No information available.
Mechanism Of Action and Pharmacodynamic Effects Click here for help
Evybactin is a DNA gyrase inhibitor, with selective activity against M. tuberculosis, binding to an allosteric site of the enzyme which overlaps with synthetic thiophene poisons [1]. The mechanism of selectivity may be due to the uptake of this hydrophilic compound into the cell by BacA, a multi-solute membrane transporter [1].