Three-Dimensional Chemical Structure Search Using the Conformational Code for Organic Molecules (CCOM) Program
Three-Dimensional Chemical Structure Search Using the Conformational Code for Organic Molecules (CCOM) Program
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使用有机分子构象代码 (CCOM) 程序进行三维化学结构搜索
DOI：
10.1002/chir.22596
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发表时间：
2016
期刊：
影响因子：
2
通讯作者：
Rina K. Dukor
中科院分区：
文献类型：
--
作者：
Hiroshi Izumi;Laurence A. Nafie;Rina K. Dukor
由于X射线和理论计算的几何形状之间的结构差异以及取代基的构象灵活性，搜索有机分子的三维结构片段具有挑战性。称为有机分子构象代码（CCOM）的编码程序可用于将各种分子的三维构象数据明确地转换为一维数据。从国际纯粹与应用化学联合会（IUPAC）有机化学命名规则E‐5.6的两个偏差被引入到CCOM程序中进行3D片段搜索。首先，为了确定二面角，对优先级最高的原子的搜索被限制在距离中心键两个键的距离内。其次，对于实验观察到的溶液结构中难以区分的原子，选择分子模型中原子指数数最小的原子作为确定二面角的优先原子。对美伐他汀三维构象片段mb_3a6c4c的搜索(1)结合SMiles任意靶蛋白规范（SMARTS）描述表明，该片段构象的改变可能是美伐他汀与靶蛋白分离的驱动力。手性，2016。©2016 Wiley期刊公司
Searching the 3D structural fragments of organic molecules is challenging because of structural differences between X‐ray and theoretically calculated geometries and the conformational flexibility of substituents. The codification program called Conformational Code for Organic Molecules (CCOM) can be used to unambiguously convert 3D conformational data for various molecules to 1D data. Two deviations from Rule E‐5.6 of the International Union of Pure and Applied Chemistry (IUPAC) Rules for Nomenclature of Organic Chemistry were introduced to the CCOM program for 3D fragment searching. First, the search for the highest priority atom was limited to a distance of two bonds from the center bond for dihedral angle determination. Second, for indistinguishable atoms in experimentally observed solution structures, the smallest number of atom index in the molecular model was chosen as the priority atom for dihedral angle determination. A search of the 3D conformational fragmentmb_3a6c4cof mevastatin (1) in combination with the SMiles ARbitrary Target Specification (SMARTS) description suggested that a change in the conformation of this fragment may be the driving force for dissociation of mevastatin from its target protein.Chirality 28:370–375, 2016. © 2016 Wiley Periodicals, Inc.