A new version of the CREDO database has been released today comprising 41,691 protein-ligand complexes from the PDB.
New features include:
Variationstables has been added containing mutation information from dbSNP, EnsEMBL, OMIM and COSMIC
Ligandstable now contains an
ismfield to store isomeric SMILES (very useful for heteropeptides)
ResidueRingtables now contain an
FragmentPropertiesnow contains all descriptors from OEMolProp
For instructions on how to download and install the CREDO database, please go to the CREDO website.
This PyMOL screenshot shows the alignment of two PDB structures, the first, a caspase-3 complexed with a nonpeptidic inhibitor (molecule shown as sticks) and the second, caspase-3 in complex with XIAP-BIR2 (shown as cartoon).
In : from credopymol import * In : s = StructureAdaptor().fetchByPDB('1YWN') In : s.load() # modified residues are automatically highlighted in green In : s.Ligands Out: [Ligand(301, LIF, A)] In : s.Ligands.showContacts() In : s.showMutations() In : s.getAbstract ()
In : from credopymol import * In : s = StructureAdaptor().fetchByPDB('3BU5') In : s Out: <Structure('3BU5')> In : s.title Out: 'CRYSTAL STRUCTURE OF THE INSULIN RECEPTOR KINASE IN COMPLEX WITH IRS2 KRLB PEPTIDE AND ATP' In : s.load() In : s.getMutations() Out: [<XRef(Residue,OMIM,610549)>, <XRef(Residue,OMIM,125853)>, <XRef(Residue,OMIM,125853)>] In : mutations = s.getMutations() In : mutations.description Out: 'G/V Insulin-resistant diabetes mellitus with acanthosis nigricans type A (IRAN type A)'
In : from credopymol import * In : s = StructureAdaptor().fetchByPDB('2Z5X') In : s.load() In : xref = s.getMutations() In : xref Out: <XRef(Residue,dbSNP,rs1803986)> In : xref.description Out: 'M/I NON_SYNONYMOUS_CODING' In : mut_res = xref.getObject() In : mut_res Out: <Residue(445, MET, )> In : mut_res.show() In : s.Ligands Out: Ligand(600, FAD, A) In : s.Ligands.showContacts()
The image shows the structural interactions of the bound inhibitors in the aligned chains 'A' of 2C4G and 2P33. Both ligands were found to be leaves of the same node in a SCOP-based SIFt clustering.
The image shows two crystal structures of human CDK2 in complex with inhibitors (1Y8Y, 2C6L). Structural interaction fingerprints (SIFts) were clustered (based on UniProt accession of the protein) and these two ligands were found to be neighbouring leaves on the same node. The structures can be loaded into PyMOL, aligned and the interactions visualised with command below. The resulting PyMOL scene can be downloaded from the bottom of this page.
In : from credopymol import * In : s = StructureAdaptor().fetchByPDB('2P33') In : s.load() In : s.Ligands.showContacts() In : s.Ligands.showFragmentContactDensity()