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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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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


Why have a dictionary






better load


New entries


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


C4' R

C3' S

C1' R


C4' S

C3' R

C1' S


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


    • In-house development

  • Smiles and detailed gifs

  • Systematic IUPAC names

Search options


  • 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

Results from using search by substructure

Results from using search by substructure

Search criteria

Pdbechem search by sub structure2

PDBeChem: Search by sub-structure

Substructure of 3-chlorophenol

Atoms and bond description for dcn

Atoms and Bond Description for DCN

Pdbechem output formats for you

PDBeChem: Output formats for you!

Additional information about the ligand

Additional information about the ligand





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