title: Classification of binding site conformations of protein tyrosine phosphatase 1B.
abstract: Hundred and two binding sites from 91 Protein Data Bank files for protein tyrosine phosphatase 1B with different ligands have been compared. It was found that they can be divided into five clusters. Additional clusters were formed by the unliganded and oxidized enzyme. The centroids of the clusters can be used as starting points for further studies of enzyme-inhibitor interaction by computer simulations. A special software tool has been created for the investigation of protein tyrosine phosphatase 1B and other enzymes. It performs multiple comparisons of selected parts of Protein Data Bank files, as well as further clustering, and determines mobility of separate residues.
authors.affiliation: Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, Murmanska 1, 02660 Kyiv-94, Ukraine. v_tanchuk@yahoo.com
authors.forename: Vsevolod Yu
authors.initials: VY
authors.lastname: Tanchuk
authors.forename: Volodymyr O
authors.initials: VO
authors.lastname: Tanin
authors.forename: Andriy I
authors.initials: AI
authors.lastname: Vovk
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D003198:Computer Simulation; D030562:Databases, Protein; D054562:Protein Tyrosine Phosphatase, Non-Receptor Type 1 / Q000737:chemistry* / Q000378:metabolism
chemical_list: D054562:Protein Tyrosine Phosphatase, Non-Receptor Type 1