Three-Dimensional Chemical Structure Search Using the Conformational Code for Organic Molecules (CCOM) Program.

Abstract:

: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 fragment mb_3a6c4c of mevastatin () 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.

journal_name

Chirality

journal_title

Chirality

authors

Izumi H,Nafie LA,Dukor RK

doi

10.1002/chir.22596

subject

Has Abstract

pub_date

2016-05-01 00:00:00

pages

370-5

issue

5

eissn

0899-0042

issn

1520-636X

journal_volume

28

pub_type

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