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The effect of ubiquitous carcinogen pollutants in mammalian cells is the source of several problems. Carcinogenic compounds present in environment as persistent pollutants become the root of carcinoma, toxicity or cancer when they react with hereditary material. To study the cellular exposure of reaction and diffusion mechanism of these carcinogenic compounds in mammalian V79 cell earlier, mathematical modeling with the set of spatially distributed system (PDEs) was developed. In this paper, compartmental modeling approach have used with the inclusion of perinuclear space. The system reduced the spatially distributed (PDEs) system to the temporal (ODEs) system, thus reducing the complexity and computational cost. The compartmental system has been simulated computationally in Virtual Cell using homogenization technique. The quantitative consideration of the results of spatially distributed system and temporal system shows a nice agreement. We can extend the compartmental system adding more compartments, reaction and diffusion processes.