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darobactin A   Click here for help

GtoPdb Ligand ID: 14286

Compound class: Natural product
Comment: Darobactin A is an antibacterial compound isolated from Photorhabdus khanii, a species of bacteria that exists symbiotically in the gut of entomopathogenic nematodes [1]. Darobactin A has activity against a range of Gram-negative bacteria, including drug-resistant strains of Escherichia coli and Klebsiella pneumoniae [1]. It binds to BamA, the central component of the essential bacterial β-barrel assembly machinery (BAM) complex, which facilitates the folding and insertion of β-barrel proteins into the outer membrane of Gram-negative bacteria [1-2].
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 14
Rotatable bonds 16
Topological polar surface area 380.78
Molecular weight 966.01
XLogP -3.7
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 C1=CC=C(C=C1)C[C@@H](C(=O)O)NC(=O)[C@H](CO)NC(=O)[C@@H]2[C@@H](CCCN)C3=CC4=C(C=C3)C(=CN4)[C@@H]5[C@@H](C(=O)N[C@@H](CO)C(=O)N2)NC(=O)[C@H](CC(=O)N)NC(=O)[C@H](CC6=CNC7=C6C=CC=C7O5)N
Isomeric SMILES C1[C@@H](C(=O)N[C@H](C(=O)N[C@H]2[C@@H](C3=CNC4=C3C=CC(=C4)[C@@H]([C@H](NC(=O)[C@@H](NC2=O)CO)C(=O)N[C@@H](CO)C(=O)N[C@@H](CC5=CC=CC=C5)C(=O)O)CCCN)OC6=CC=CC7=C6NC=C71)CC(=O)N)N
InChI InChI=1S/C47H55N11O12/c48-13-5-9-25-23-11-12-27-28(19-51-30(27)16-23)40-39(58-42(63)31(17-36(50)61)53-41(62)29(49)15-24-18-52-37-26(24)8-4-10-35(37)70-40)46(67)56-34(21-60)44(65)57-38(25)45(66)55-33(20-59)43(64)54-32(47(68)69)14-22-6-2-1-3-7-22/h1-4,6-8,10-12,16,18-19,25,29,31-34,38-40,51-52,59-60H,5,9,13-15,17,20-21,48-49H2,(H2,50,61)(H,53,62)(H,54,64)(H,55,66)(H,56,67)(H,57,65)(H,58,63)(H,68,69)/t25-,29-,31-,32-,33-,34-,38-,39-,40+/m0/s1
InChI Key HRMCRRLPTVSYHJ-KUDSBEMESA-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/)
Bioactivity Comments
The MIC for antibacterial activity against clinical isolates of E. coli and K. pneumoniae, including drug-resistant strains, is in the range of 2-4 μg/ml in vitro [1]. Darobactin exhibits little activity against Gram-positive bacteria or against gut commensals, including Bacteroides spp. [1].
Darobactin binds to BamA with a Kd of 1.2 μM and inhibits BAM-dependent folding of the protease OmpT with an IC50 of 0.68-1 μM [1].