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. Author manuscript; available in PMC: 2015 Apr 1.
Published in final edited form as: Bioorg Med Chem. 2014 Mar 3;22(7):2149–2156. doi: 10.1016/j.bmc.2014.02.037

Figure 2.

Figure 2

(A) Tracked distances along the MD trajectory for the CYP2A6-Nic2b binding structure. Nam---Heme(Fe) represents the distance between the nitrogen atom on the amine group of Nic2b to the heme iron atom; Npy---N297(Nδ) represents the distance between the nitrogen atom on the pyridine group of Nic2b and the Nδ atom of the N297 side chain; Nam---G301(O) is the distance between the nitrogen atom on the amine group of Nic2b and the carbonyl oxygen atom on the backbone of residue G310; and Ofu---G301(N) represents the distance between the furan oxygen atom of Nic2b and the backbone nitrogen atom of residue G301. (B) QM/MM-optimized CYP2A6-Nic2b binding structure (optimized at B3LYP/6-31G*:Amber8 level). The binding structure is represented in the same color scheme as that in Figure 1B. The dashed line represents the averaged distance between the amine nitrogen atom of Nic2b and the heme iron atom based on the 10 QM/MM optimized structures. (C) Intermolecular interactions in the optimized CYP2A6-Nic2b binding structure. Residues from CYP2A6 within 5 Å of Nic2b are shown in stick style. The hydrogen-bond interaction between the nitrogen atom on the pyridine group of Nic2b and the Hδ atom of N297 side chain is represented as dashed line with labeled averaged distance based on the 10 QM/MM-optimized structures.