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PDBeChem
The Ligand Database
EBI is an Outstation of the European Molecular Biology Laboratory.
Why PDBeChem?
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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?
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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
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atoms, element type, connectivity, bond orders, stereochemical configuration
Source of Information -The wwPDB Ligand
Dictionary
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Chemical Component Dictionary
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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)
http://www.wwpdb.org/ccd.html
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” ?
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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
PDBeChem
refinement
New entries
better
depositions
clean-up
Archive
curation
Curation
better
curation
better load
PDBe DB
The PDBeChem database
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Collection of all chemical species and small molecules in
the PDB
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A ligand is a distinct stereo-isomer
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Complete, up to date
Atoms and element types
Bonds and bond orders
Stereo configuration of atoms and bonds in cases of stereoisomers (R/S – E/Z)
Names and co-ordinates not fundamental
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But there is a consistent set of identifiers
• Atoms, bond order, and stereochemistry
• Derived properties
Derived properties
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For Stereochemistry (R/S – E/Z)
Cheminformatics software used systematically in
PDBeChem
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CACTVS, CORINA, VEGA, ACD-labs
In-house development
DCF
DCM
C4' R
C4' S
C3' S
C3' R
C1' R
C1' S
THIOALANINE (ALT)
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Smiles and detailed gifs
Systematic IUPAC names
CC(N)C(O)=S - C[[email protected]](N)C(O)=S
(2S)-2-aminopropanethioic O-acid
Search options
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By ligand code
By ligand name or synonym
By formula or formula range
By non-stereo smile
By stereo smile
By exact stereo or nonstereo structure
PDBeChem
By fingerprint similarity
Some uses:
By fragment expression
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Search for drug or ligands.
Understand chemistry of ligand.
Download ‘ideal’ coordinates for
own analysis (docking etc) and
study.
PDBeChem: Search by Formula
Activate the editor
PDBeChem: Searching by Chemical 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
PDBeChem: Search by Fragment
Activate the Editor
PDBeChem: Search by Fragment
• Web form
• Significant
fragments
• Example :
• More than 2
benzimidazoles
• No piperazine
• Anything else
PDBeChem: Search by sub-structure
Activate the JME Editor
PDBeChem: Search by sub-structure
Delete atom
Change atom type
after drawing bonds
JME editor allows
generation of SMILE
string to enter search
mode
Click when
complete
Results from using search by substructure
Search criteria
PDBeChem: Search by sub-structure
Substructure of 3-chlorophenol
Atoms and Bond Description for DCN
PDBeChem: Output formats for you!
Additional information about the ligand
Chemsearch
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