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Chemistry & the PDB MSDchem

Chemistry & the PDB MSDchem. Primary Developer: Dimitris Dimitropoulos. The chemical database. MSDchem ligand dictionary. Complete, clean, up to date collection of all the chemical species and small molecules in the PDB

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Chemistry & the PDB MSDchem

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  1. Chemistry & the PDB MSDchem Primary Developer: Dimitris Dimitropoulos

  2. The chemical database

  3. MSDchem ligand dictionary • Complete, clean, up to date collection of all the chemical species and small molecules in the PDB • A ligand in MSDchem is a complete, distinct stereo isomer of a chemical compound • Atoms and element types • Bonds and bond orders • Stereo configuration of atoms and bonds in cases of stereo-isomers (R/S – E/Z) • Atom names and coordinates are not fundamental properties

  4. Role in the MSD database • An integral component in the core of MSD database • Relational reference from entities where a molecule or atom name is used in the PDB (protein residues and atoms) • It is not possible for an ATOM line: HETATM 4342 C2 PLA 86 14.227 11.195 -8.256 1.00 67.95 C to be loaded if the “PLA” ligand is not defined or it does not include a “C2” atom.

  5. Chemistry and PDB • Eliminate chemical inconsistencies from new PDB entries • Structure and derived properties of a ligand apply automatically to residues and bound molecules that reference it • The basic structure is carefully determined during curation, and a rich set of derived attributes is calculated for each ligand • Graph isomorphism is being applied to check the consistency of the PDB, taking stereo-configuration into account • Old legacy PDB entries are chemically “corrected” when loaded in the MSD database • In thousands of cases errors are identified and corrected, involving most of them times inconsistent naming or different stereo-configuration • Exchanged in cooperation with RCSB and the wwPDB

  6. More than just the PDB codes All ligands are modelled as separate inter-related ligands and the appropriate one is referenced • No distinction is made in the PDB between ribo- and deoxyribonucleotides (all are identified with the same residue name i.e., A, C, G, T, U, I) • Modified nucleic acids are given as +A etc regardless of modification • No distinction between different topological variants (12 different variants can be found for HIS in PDB)

  7. Derived information • External scientific software (CACTVS, VEGA, CORINA, ACD-labs, CCP4, OELIB) together with in house development has been used to derive: • Stereochemistry (R/S – E/Z) DCM C4' S C3' R C1' S DCF C4' R C3' S C1' R • Smiles and detailed gifs • Systematic IUPAC names THIOALANINE (ALT) CC(N)C(O)=S - C[C@H](N)C(O)=S (2S)-2-aminopropanethioic O-acid

  8. Click to see attributes

  9. Search options • By ligand code • By ligand name or synonym • By formula or formula range • By non stereo substructure • By non stereo superstructure • By exact stereo or non stereo structure • By fingerprint similarity • By fragment expression

  10. Activate JME molecule editor

  11. Clear structure Delete atom Change atom type after drawing bonds JME editor allows generation of SMILE string to enter search mode Click when complete

  12. 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

  13. EAA details substructure of3-chloro-phenol

  14. Viewing & saving options Get the PDB entries that include EAA Get the bound molecule instances and site interaction details

  15. PDB residue KWT <chemComp> <code>KWT</code> <name>(1S,6BR,9AS,11R,11BR)-9A,11B-DIMETHYL-1-[(METHYLOXY)METHYL]-3,6,9-TRIOXO-1,6,6B,7,8,9,9A,10,11,11B-DECAHYDRO-3H-FURO[4,3,2-DE]INDENO[4,5-H][2]BENZOPYRAN-11-YL ACETATE</name> <nAtomsAll>55</nAtomsAll> <nAtomsNh>31</nAtomsNh> <overallCharge>0</overallCharge> <stereoSmiles>COC[C@H]1OC(=O)c2coc3C(=O)C4=C([C@@H](C[C@@]5(C)[C@H]4CCC5=O)OC(C)=O)[C@]1(C)c23</stereoSmiles> <systematicName>(1S,6bR,9aS,11R,11bR)-1-(methoxymethyl)-9a,11b-dimethyl-3,6,9-trioxo-1,6,6b,7,8,9,9a,10,11,11b-decahydro-3H-furo[4,3,2-de]indeno[4,5-h]isochromen-11-yl acetate</systematicName>

  16. Formula-fragment expression search Fragment expression Example: Search for ligands with furan rings but not any saturated carbon rings (cyclobutane,cyclopropane,cyclohexane) Formula expression Example: Search for ligands with more than 10 oxygens no nitrogens and sulphurs

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