Penta-coordinated phosphorus structure analysis on kinases

摘要

In this paper, based on the known crystal structures of Square Pyramid (SP) and Trigonal Bipyramid (TBP) penta-coordinated phosphorus compounds containing amino acid side chains, such as amino, carboxyl, hydroxyl or thiol, a software designed to survey the P(5)-Structure of phosphorylated proteins. By this software, it was found that 382 of 398 phos- phorus-related kinases (96%) from current PDB could go through the penta-coordinated phos- phorus transition state or intermediate. For example, in protein 1HE8, amino group in Lysine16 was within 3.58 ?from the phosphorus atom, and a potential TBP structure consisting GNP2 and NZ could be overlapped with an authentic TBP with an RMSD value of 0.71 ?.