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Protein Data Bank in Europe www.pdbe.org
Bringing Structure to Biology: Small Molecules and the PDBe
Protein Data Bank in Europe www.pdbe.org
PDBe overview
• PDB is a core molecular database at EMBL-EBI• PDBe is a founding partner of Worldwide Protein Data
Bank (wwPDB)• Founder of Electron Microscopy Data Bank (EMDB)• Mission: Bringing Structure to Biology• Major activities:
• Deposition and annotation site for structural data on biomacromolecules (X-ray, NMR, EM)
• Integrated resource of high-quality macromolecular structural data and related information
• Provide tools and services for accessing, exploiting and disseminating structural data to the wider biomedical community
Protein Data Bank in Europe www.pdbe.org
PDB Depositions
10,000th PDBe annotated structure - April 2011 (2yf6)www.pdbe.org/2yf6
Protein Data Bank in Europe www.pdbe.org
Chemical Component Dictionary
• Compounds in the PDB• Small molecules bound to macromolecules• Individual components of macromolecules
• wwPDB maintains dictionary descriptions for all unique chemical components• Name, synonyms, formula, SMILES, …
• Atoms and bonds
• Ideal and representative coordinates
• Each new component assigned a unique 3-letter identifier• Release coincides with the release of the
parent PDB entry
Protein Data Bank in Europe www.pdbe.org
Molecule search options
• Compound name• Ligand 3-letter code• SMILES• Formula (exact or range)
e.g. C6-10 N4 O2 S0• Chemical substructure
www.pdbe.org/chem
Protein Data Bank in Europe www.pdbe.org
PDBe Home Page http://www.ebi.ac.uk/pdbe
Protein Data Bank in Europe www.pdbe.org
Ligands and the PDBe
Open chemistry sketchpad
Protein Data Bank in Europe www.pdbe.org
Ligands and the PDBe
Protein Data Bank in Europe www.pdbe.org
Ligands and the PDBe
Protein Data Bank in Europe www.pdbe.org
2D Ligand Interaction Diagrams
• Interaction diagrams for any given PDB entry
• Interactive control of distance criteria
• Diagram customisation
• Image exportpng, jpg, eps…
www.pdbe.org/leview
S-benzyl-glutathione (GSB) Human Glyoxalase inhibitor (1guh)
Protein Data Bank in Europe www.pdbe.org
PDBeXpress: rapid access to protein-ligand interaction statistics
• Understand and assess binding site interactions • Provide chemists with quick answers to common questions
without the need to construct complex search queries• What residues interact?• Which enzymes interact?• What binds here?
• www.pdbe.org/express
Protein Data Bank in Europe www.pdbe.org
What residues interact?
RTL - Retinol• PDB three-letter ligand code• Ligand name
Protein Data Bank in Europe www.pdbe.org
What residues interact?
RTL - Retinol
Protein Data Bank in Europe www.pdbe.org
MAN – Mannose
Which enzymes interact?
• PDB three-letter ligand code• Ligand name
Protein Data Bank in Europe www.pdbe.org
MAN – Mannose
Which enzymes interact?
• PDB three-letter ligand code• Ligand name
Protein Data Bank in Europe www.pdbe.org
What binds here?
• Search for ligands that interact with a given set of residues• Can specify a partial or exact binding environment
Protein Data Bank in Europe www.pdbe.org
What binds here?
Protein Data Bank in Europe www.pdbe.org
• PDBeXpress modules driven by PDBeMotif
• PDBeMotif allows to combine protein sequence, chemical structure and 3D data in a single search
PDBeMotif: powerful and flexible searching
Protein Data Bank in Europe www.pdbe.org
• construct queries based on -
• ligands and their 3D environment
• secondary structure elements and small 3D motifs
• protein φ/ψ angle sequences - sequential representation of the protein geometry
• results can be analysed against UniProt, CATH, PFAM or EC
PDBeMotif: powerful and flexible searching
Protein Data Bank in Europe www.pdbe.org
Ligands need careful validation
• CCDC analysis of ligand geometries (using Relibase+/Mogul/EDS)• Around 20% of recently determined structures have geometric errors
that could potentially cause a misleading interpretation of the binding interactions
Wrong
Unusual/Strained
Correct
Liebeschuetz, J.W., Hennemann, J. The good, the bad and the twisted: A survey of ligand geometry in protein crystal structuresJ. Comput. Aid. Mol. Des., 26, 169-183 (2012)
Protein Data Bank in Europe www.pdbe.org
The solution…
• Mogul – a Knowledge-based library of molecular geometry derived from the Cambridge Structural Database (CSD)
• Enables rapidly validation of the complete geometry of a given query structure and identification of unusual features
Protein Data Bank in Europe www.pdbe.org
Protein Data Bank in Europe www.pdbe.org
MoU with CCDC
• wwPDB/CCDC Memorandum of Understanding• wwPDB gets to use Mogul for validation of all current and future
compounds in the PDB• wwPDB gets to incorporate and redistribute CSD coordinates for
all current and future ligand compounds in the PDB• wwPDB gets to use Mogul and CSD coordinates to derive
dictionaries for all current and future compounds in the PDB
Protein Data Bank in Europe www.pdbe.org
Prevention is the best cure
• Thanks to collaboration with CCDC• We can add CSD coordinates for all existing small molecules in
the PDB (and variants, e.g. D-amino acids) that also occur in the CSD
• We can use these coordinates and Mogul to derive refinement dictionaries• Grade (Global Phasing; uses Mogul and RM1)
• Will improve quality and consistency of the archive• We can provide reasonable starting coordinates and refinement
dictionaries for all existing compounds in the PDB
Protein Data Bank in Europe www.pdbe.org
Future of the PDB?
• At present PDB is a historic archive• We have to accept and distribute everything• “Archive” – i.e., what was described in the literature
• Essentially provider-centric• We capture X-ray detector type but not ligand function…• Organised by entry rather than molecule/complex/…
• Shifting user communities/demands• We must serve the consumers of structural data (non-experts)• Don’t think in terms of PDB entry codes• Can’t tell a good from a bad model
Protein Data Bank in Europe www.pdbe.org
PDBe Team February 2012
Protein Data Bank in Europe www.pdbe.org
Funding
Protein Data Bank in Europe www.pdbe.org
• Tutorials…
http://www.ebi.ac.uk/pdbe/resources/educationTabContent/tutorials/PDBeChem.pdf http://www.ebi.ac.uk/pdbe-apps/quips?story=XmasFactor&auxpage=XmasChemTut http://www.ebi.ac.uk/pdbe/docs/Tutorials/PDBeChem.html
• Contact us…www.pdbe.org
pdbehelp@ebi.ac.uk
• Follow us…
Thank you!
http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope
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