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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

The Ligand Database


Why pdbechem
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
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
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

http://www.wwpdb.org/ccd.html


Why have a dictionary

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


The pdbechem database
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


Derived properties

DCF

C4' R

C3' S

C1' R

DCM

C4' S

C3' R

C1' S

THIOALANINE (ALT)

CC(N)C(O)=S - C[[email protected]](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


Search options

PDBeChem

  • 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


Pdbechem search by formula
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
PDBeChem: Search by sub-structure

Activate the JME Editor


Pdbechem search by sub structure1
PDBeChem: Search by sub-structure

Change atom type after drawing bonds

Delete atom

JME editor allows generation of SMILE string to enter search mode

Click when complete



Pdbechem search by sub structure2
PDBeChem: Search by sub-structure

Substructure of 3-chlorophenol







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