PDB files of "Characterization of ligand-induced thermal stability of the human organic cation transporter 2 (OCT2)"

The predicted alphafold structure of OCT2 (Uniprot O15244) was embedded in a DPPC model membrane, solvated with TIP3P water and subjected to 250 ns molecular dynamics simulation using the Desmond module of Schroedingers Drug Discovery Suite. The last 150 ns were used for clustering and the cluster with most of the members (cluster0) was selected as a model for OCT2. Based on that (still predicted, but optimised) model we performed docking with various substrates for which we also provide the obtained docking pose. See Publication in Frontiers in Pharmacology (DOI: 10.3389/fphar.2023.1154213) for details and results.将经AlphaFold预测的OCT2（UniProt编号O15244）结构嵌入DPPC（二棕榈酰磷脂酰胆碱）模型膜，采用TIP3P水分子模型进行溶剂化处理，并借助Schrödinger公司药物发现套件的Desmond模块完成了时长250 ns的分子动力学模拟。选取模拟轨迹的最后150 ns进行聚类分析，以成员占比最高的聚类（cluster0）作为OCT2的研究模型。基于该（仍为预测所得但已优化的）模型，我们针对多种底物开展了分子对接实验，并同步提供了所获得的对接构象。相关研究的详细内容与结果可参阅发表于《Frontiers in Pharmacology》（DOI: 10.3389/fphar.2023.1154213）的论文。