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Ligand binding sites. Roman Laskowski. Representations of protein ligand-binding sites. Surface coloured by residue conservation. Clefts. Clefts in surface. Visualization of binding-site properties. Visualization of binding-site properties. Depictions of pharmacophores. H-bond acceptors.
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Ligand binding sites Roman Laskowski
Depictions of pharmacophores H-bond acceptors Hydrophobic Aromatic H-bond donors
3tmn – thermolysin + Val-Trp LIGPLOT protein-ligand schematic diagrams
Protein-ligand interaction diagrams PoseView LIGPLOT MOE AstexViewer
Comparing binding of different ligands to same protein 1err 1qku (raloxifene) (estradiol ) Human estrogen receptor
Allosteric site Somewhere else Catalytic site Ligand clusters What ligands bind to a given protein?
Ligand clusters Link
Protein-ligand matrix PHA-739358 PD173955 PD180970 Imatinib Molecular similarity Abl-1 100% 90% 80% 70% 60% 50% 40% C-kit 30% aurora-2 Abl-1 Sequence identity
Dynamic graphs of related Pfam domain architectures
2jz3: NMR structure of fragment SH2 domain and SOCS box domain Other structures in PDB: Dynamic graphs of related Pfam domain architectures Suppressor of cytokine signaling 3 (mouse)
ArchSchema graphs Each node shows the Pfam domain architecture: Can add UniProt seqs as satellite nodes:
ArchSchema graphs
Indicate 3D coverage: Can add PDB structures: Addition of 3D structural info