May be FATCAT can solve your question.

http://fatcat.burnham.org/fatcat-cgi/cgi/fatcat.pl?-func=search

It can search in SCOP, PDB, or JCSG databases.

you can use OpenEye ROCS (rapid overlay of chemical structures) & EONS  program, it can be available under academic license. Alternatively you can try 2D similarity search with openbabel MACCS or other fingerprint.. Also you can try the inbuilt similarity search of ligand database such as Zinc database.

As Pankaj says ROCS is designed specifically for this purpose; ligand alignment and similarity scoring. It is available for free for qualified academic users. See here

http://eyesopen.com/academic

for the details of the the academic license and a link for an application. We also provide pre-generated databases of compounds to search using ROCS.

BTW FATCAT searches for similar PROTEINS not similar ligands.

but i have a different question regarding this. i have to make the ligand database on discovery studio.. is this possible? if that possible then what will be the steps? 

For ligand superimposing, ROCS, FlexS, SuerflexSim, Phase, LigandMatch, FieldScreen, or other tools are available (or have been reported). There are similar functions in Discovery studio, or MOE.

Most of the tools support sdf and mol2 file formats, I think.

thanks mr. Kong..but how can i do it  in discovery studio. please give me the following steps

..thanks

Hi,Sourav, I currently don't have access to Discvoery studio. I checked the DS manuals (version 2.5) and found that there is no such function in DS (only manually RMSE alignment). Sorry for missleading. I said that there is similar function was based on my experince on the molecular alignment module in  Cerius 2 (2.10L). I found that they did not integrate this module into DS. I apologize for that.