There are several antibacterial targets are available. if your compounds were not designed and synthesized against any particular target, then you can check the chemical scaffold or basic nucleus (chemistry) and select your probable target.

For example Quinolone derivatives then your probable target may be bacterial DNA gyrase enzyme.

selection of targets depends on  chemical nature molecules (chemical class)

There are several antibacterial targets are available. if your compounds were not designed and synthesized against any particular target, then you can check the chemical scaffold or basic nucleus (chemistry) and select your probable target.

For example Quinolone derivatives then your probable target may be bacterial DNA gyrase enzyme.

selection of targets depends on  chemical nature molecules (chemical class)

PLOS ONE, vol. 8, no. 3, e-58346-e-58357, 2013.

Curr. Med. Chem., vol. 19, no. 24, pp. 4184 – 4193, 2012.

see these papers..........and contact to

Franco Sir.

Dr. Manivannan, I had Sulfamethoxazole, Sulfadiazine, Sulfamethazine derivatives.

The PDB ID is 4CKL and 1AB4.. the name of the protein is DNA gyrase. But this protein only responsible for fluoroquinlone derivative compounds...the most of the research persons using this type of protein for several antibacterial compounds. 

Thanks Manivannan Elangovan, Gourisankar Roymahapatra, Bala Subramaniyan

It depends. If you know the target take a look at protein databank for its 3d strucuture. If not, try looking at the literatura about similar compounds and their mechanism of action. Or you could try to predict their target by your experimental activity.

Why do you think by apriori that this target is known? Why do you think that (bio)informatic should be able to answer your question? The first idea is to collaborate with biochimists who are able to characterize this target: (randomly) DNA, RNA, protein, lipid, sugar, macro-molecular complexes, membrane, wall, etc. Make science is also make experiment(s)… The good analysis of tests you did to determine the activity of your molecule can help you to define its target(s)… Sincerely, CC

Thanks Christian cibert. I will work on it.

I would suggest you carry out a similarity search of your compounds on DrugBank, then dock towards the binding pockets of the targets of the most similar compounds, e.g. those with Tanimoto coefficients > 0.7