chemistry & the pdb msdchem
DESCRIPTION
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 - PowerPoint PPT PresentationTRANSCRIPT
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Chemistry & the PDB
MSDchem
Primary Developer: Dimitris Dimitropoulos
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The chemical database
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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 compoundAtoms and element typesBonds and bond ordersStereo configuration of atoms and bonds in cases
of stereo-isomers (R/S – E/Z) Atom names and coordinates are not fundamental
properties
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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.
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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
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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)
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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)
DCF
C4' R
C3' S
C1' R
DCM
C4' S
C3' R
C1' S
THIOALANINE (ALT)
CC(N)C(O)=S - C[C@H](N)C(O)=S
(2S)-2-aminopropanethioic O-acid
Smiles and detailed gifs Systematic IUPAC names
Click to see attributes
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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
Activate JME molecule editor
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Change atom type after drawing bonds
JME editor allows generation of SMILE string to enter search mode
Click when complete
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Search for ligand structures containing 3-chloro-phenol
Results
Click to get Details for EAA
Get PDB entries and bound molecule instances containing 3-chloro-phenol
EAA details
substructure of3-chloro-phenol
Get the PDB entries that include EAA
Get the bound molecule instances and site interaction details
Viewing & saving options
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<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>
PDB residue KWT
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Formula-fragment expression search
Formula expression Example: Search for ligands with more than 10 oxygens no nitrogens and sulphurs
Fragment expression Example: Search for ligands with furan rings but not any saturated carbon rings (cyclobutane,cyclopropane,cyclohexane)