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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

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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)