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HOMCOS : Searching and Modeling of 3D Structures of Complexes

Searching Contact Proteins for Query Compound [Go to Japanese page]

Searching Contact Proteins for Query Compound Search contact proteins with similar compounds to a given query compounds

Overview of the search A user can specify a query 2D chemical structure (atoms and bonds, not 3D conformation)by various methods. The server performs a 2D similarity search with the given query chemical compound for the database of all of the chemical compound appearing in the PDB, using dkcombu program (Kawabata et al., 2013) in the KCOMBU program package. Each chemical structure in the PDB has its own unique 3-letter code(comp_id). Contacting proteins with these similar compounds are obtained by searching the contact table, and they are regarded as predicted contacting proteins with the query compound.
Input a query chemical structure
You can input a query compound structure by following various methods.
1. 3-letter compound code of PDB
  Each chemical structure stored in PDB has its own unique 3-letter compound code. For example, the code for "ADENOSINE-5'-TRIPHOSPHATE", "BETA-D-GALACTOSE" and "Gefitinib" is "ATP", "GAL" and "IRE", respectively. You can search the 3-letter code for the molecular name using several serveres, such as Ligand Expo and PDBj Chemie search.
2. SMILES string
  A string representation of SMILES is useful for copy and pasting chemical structures. Many chemical databases provides SMILES string representaions. The SMILES string of glycine and phenylalanine is "NCC(=O)O" and "OC(C(Cc1ccccc1)N)=O", respectively. Details of the SMILES string is described in wiki.
3. Uploading a chemical compound file
  Users can upload their own chemical structure file. Four formats, SDF, MOL, MOL2 and PDB are available.
Search results

We will show a result for the query Carazolol (3-letter PDB code:CAU). Carazolol is the partial inverse agonist for beta-2 adrenergic receptor. Following similar compounds to the query are shown after 1-2 minututes. Among these compounds, a user can choose compounds for further analysis for their interacting proteins, by clicking the radio buttons. The value "Tanimoto" shows the ratio of matched atoms, which ranges from 0 to 1. In this case, compounds with Tanimoto > 0.7 were checked.Finaly、the button is clicked.

Then, the list of proteins binding to one of the six chosen compounds is shown.　As we expected, the beta-1 and beta-2 adrenergic receptors were included in the list. Surprisingly, similar compounds to the carazolol can bind two enzymes, exoglucanse 1 (SNP, XX6, XX7) and lactotransferrin (RNP).　From this result, we can hypothesize that the carazolol may bind to exoglucanase 1 and lactotransferrin.

If one of the 3D icons is clicked, following 3D models are shown.

beta-2 adrenergic receptor and the molecule carazorol (CAU).

Exoglucanase 1 and the molecule SNP.

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