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PDBeChem

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)

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PDBeChem

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  1. PDBeChem The Ligand Database

  2. 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)

  3. C9H14N3O7P DCM C4' S C3' R C1' S DFC C4' R C3' S C1' R 2'-DEOXY-L-RIBO-FURANOSYL CYTOSINE-5'-MONOPHOSPHATE 2'- DEOXYCYTIDINE- 5'- MONOPHOSPHATE What is a “Ligand” in PDB? • Bound molecules, standard and modified amino acids and nucleic acids, atoms • Absolute stereochemistry, atoms, bonds, bond orders • Unique 3-letter code

  4. 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 every day between wwPDB partners • Accommodates new entries and modifications from wwPDB partners • Explicit connectivity and bond orders • Representative co-ordinates 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 http://www.wwpdb.org/ccd.html

  5. PDBeChem Archive clean-up refinement curation better load PDBe DB New entries Curation better depositions better curation 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

  6. 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

  7. DCF C4' R C3' S C1' R DCM C4' S C3' R C1' S THIOALANINE (ALT) CC(N)C(O)=S - C[C@H](N)C(O)=S (2S)-2-aminopropanethioic O-acid 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

  8. Some uses: • Search for drug or ligands. • Understand chemistry of ligand. • Download ‘ideal’ coordinates for own analysis (docking etc) and study. 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

  9. PDBeChem: Search by Formula Activate Formula editor

  10. PDBeChem: Search by Formula • 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

  11. PDBeChem: Search by Fragment Fragment search

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

  13. Activate JME molecule editor PDBeChem: Search by sub-structure

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

  15. Search for ligand structures containing 3-chloro-phenol Results Get PDB entries and bound molecule instances containing 3-chloro-phenol Click to get Details for EAA PDBeChem: Search by sub-structure

  16. EAA details substructure of3-chloro-phenol PDBeChem: Search by sub-structure

  17. PDBeChem: Output formats for you! Viewing & saving options Get the PDB entries that include EAA

  18. Summary • The wwPDB ligand dictionary provides the chemistry of the PDB • The original PDBeChem database has been merged in the remediation project • The state of the dictionary has improved • The PDBeChem web application provides searching of the dictionary • Name • Formula • Substructure • Fragments - similarity

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