Linking into BindingDB

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The following generic search URLs allow you to link into BindingDB by protein, small molecule, PDB ID, and/or PubMed ID. Please feel free to suggest other search methods.

1. Protein ("target") Links
   • Link/query by BindingDB Target Name
     The following URL retrieves all enzyme inhibition data for a given target protein, based upon its BindingDB Target Name.
     http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_ki.jsp?tag=tg&kiunit=nM&icunit=nM&column=ki&submit=Search&energyterm=kJ%2Fmole&target=target
     The following URL retrieves all ITC data for a given target protein, based upon its BindingDB Target Name.
     http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_itc.jsp?tag=tg&column=delta_G0&energyterm=kJ%2Fmole&startPg=0&Increment=50&submit=Search&target=target

     The list of BindingDB Target Names is here http://www.bindingdb.org/bind/BindingDB_targets.txt and here http://www.bindingdb.org/bind/ByTargetNames.jsp

     Example: http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_ki.jsp?tag=tg&kiunit=nM&icunit=nM&column=ki&submit=Search&energyterm=kJ%2Fmole&target=ABL

     Other options: Units of Ki and IC50 can be changed from nanomolar to micromolar by specifying kiunit=uM, icunit=uM instead of kiunit=nM, icunit=nM. Energy units can be changed from kJ/mol to kcal/mol by specifying kcal instead of kJ. Number of data per page can be changed from 50 to, for example, 100, by changing Increment=50 to Increment=100.

   • Link/query by BLAST search
     The following URL searches BindingDB for proteins with sequences similar to the query sequence:
     http://www.bindingdb.org/bind/blastResult.jsp?DATASOURCE=protein&Search=B2&blastSeq=Protein Sequence

     The list of all BindingDB protein sequences is available here http://www.bindingdb.org/bind/BindingDB_sequences.txt and see also http://www.bindingdb.org/bind/BySequence.jsp

     Example: http://www.bindingdb.org/bind/blastResult.jsp?DATASOURCE=protein&Search=B2&blastSeq=VKCGSRRERCGYRLVRRQRSADEQLHCAGKAKRSGGHAPRVRELLLD

2. Small molecule ("compound") Links
   • Link by BindingDB Monomer ID
     If you know the Monomer ID of a compund in BindingDB, you can directly link to it in BindingDB with the following URL:
     http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=BindingDB Monomer ID

     The list of all BindingDB Monomer IDs, with their associated SMILES strings, is available here: http://www.bindingdb.org/bind/BindingDB_SMILES.txt

     Example: http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=100

   • Link by SMILES strings
     Exact compound match
     http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=4&submit=Search&smilesStr=SMILES string

     Example: http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=4&submit=Search&smilesStr=CC%28C%29C1%28C%29SC%28Nc2ccccc2C%28F%29%28F%29F%29%3DNC1%3DO+%7Cc%3A18%7C

     Similar compounds, based upon Jmol bitstrings and Tanimoto similarity
     http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=3&similarity=similarity&submit=Search&smilesStr=SMILES string

     Example: http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=3&Similarity=0.9&submit=Search&smilesStr=CC(C)C1(C)SC(Nc2ccccc2C(F)(F)F)=NC1=O

     Substructure search
     http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=2&submit=Search&smilesStr=SMILES string

     Example: http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=2&submit=Search&smilesStr=CC(C)C1(C)SC(Nc2ccccc2C(F)(F)F)=NC1=O

     The list of all SMILES strings in BindingDB is available here: http://www.bindingdb.org/bind/BindingDB_SMILES.txt

3. Protein Data Bank ID (PDB ID)
   BindingDB provides hard links to binding data corresponding to a specific PDB entry if the BindingDB Target is >85% identical to the protein in the PDB entry, according to BLAST, and if the ligand in the PDB entry is identical to the ligand in BindingDB.
   http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pdbids.jsp?pdbids_submit=Search&pdbids=PDB ID

   Example: http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pdbids.jsp?pdbids_submit=Search&pdbids=1OKZ

   The list of all PDB IDs represented in BindingDB is available here: http://www.bindingdb.org/bind/BindingDB_PDB.txt

4. PubMedID
   The following generic URL returns all BindingDB data obtained from the article with the selected PubMed ID.
   http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pubmed.jsp?pubmed_submit=Search&pubmed=PubMed ID

   Example: http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pubmed.jsp?pubmed_submit=Search&pubmed=17408953

   The list of all PubMed IDs in BindingDB is available here:  http://www.bindingdb.org/bind/BindingDB_PubMed.txt and see also http://www.bindingdb.org/bind/ByPubMed.jsp.