EBI is an Outstation of the European Molecular Biology Laboratory. PDBeChem The Ligand Database

Why PDBeChem? Link between protein and chemistry Reference dictionary for the chemical definition of 3 letter coded single residues in the PDB (wwPDB CCD) Holds the single residue definitions for the PDB and represents it for all other databases at the EBI (PDBeChem database) How else will you find ligand structures !!!!! (PDBeChem search system)

What is a “Ligand” in PDB? Bound molecules (e.g. Sugars, lipids, inhibitors, biological coenzymes and cofactors), standard and modified amino acids and nucleic acids, atoms (metal, halogens, unknown atom) Identified by a unique 3 Letter code atoms, element type, connectivity, bond orders, stereochemical configuration

Source of Information -The wwPDB Ligand Dictionary Chemical Component Dictionary Reference dictionary, one record for each, different 3-letter code As mmCif file, available through ftp Exchanged and synchronised on a daily basis among the wwPDB partners Accommodates new entries and modifications from wwPDB partners Explicit connectivity and bond orders Representative co-ordinates (both model and ideal) data_ATP # _chem_comp.id ATP _chem_comp.name 'ADENOSINE-5'-TRIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.mon_nstd_flag n

Why have a “Dictionary” ? Eliminate chemical inconsistencies from new entries through better curation Legacy PDB entries are chemically “corrected” when loaded in PDBe Energy types used by refinement libraries improve new depositions Improvements are exchanged between wwPDB partners Curation PDBeChem PDBe DB Archive New entries refinement curation clean-up better depositions better curation better load

The PDBeChem database Collection of all chemical species and small molecules in the PDB Complete, up to date A ligand is a distinct stereo-isomer Atoms and element types Bonds and bond orders Stereo configuration of atoms and bonds in cases of stereo- isomers (R/S – E/Z) Names and co-ordinates not fundamental But there is a consistent set of identifiers Atoms, bond order, and stereochemistry Derived properties

For Stereochemistry (R/S – E/Z) Cheminformatics software used systematically in PDBeChem CACTVS, CORINA, VEGA, ACD-labs In-house development Smiles and detailed gifs Systematic IUPAC names THIOALANINE (ALT) CC(N)C(O)=S - (2S)-2-aminopropanethioic O-acid DCF C4' R C3' S C1' R DCM C4' S C3' R C1' S

Search options By ligand code By ligand name or synonym By formula or formula range By non-stereo smile By stereo smile By exact stereo or non- stereo structure By fingerprint similarity By fragment expression Some uses: Search for drug or ligands. Understand chemistry of ligand. Download ‘ideal’ coordinates for own analysis (docking etc) and study. PDBeChem

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Expression can be built with web form Example : O1-4 N3-100 F0 1 to 4 oxygens More than 3 nitrogens No Fluorine Anything else PDBeChem: Searching by Chemical Formula

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Web form Significant fragments Example : More than 2 benzimidazoles No piperazine Anything else PDBeChem: Search by Fragment

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PDBeChem: Search by sub-structure Click when complete Change atom type after drawing bonds JME editor allows generation of SMILE string to enter search mode Delete atom

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