Major facilitator superfamily domain containing 2A (MFSD2A) gene encodes for a sodium-dependent lysophosphatidylcholine transporter, NLS1. It is essential for importing of fatty acids, like docosahexaenoic acid (DHA), into human brain [1]. Importing of DHA, is essential for normal human brain growth and cognitive function. Also, NLS1 is involved in microcephaly, a condition characterized by a smaller cerebral cortex, where brain weight is reduced. Because exact structure of NLS1 is still unknown, our research could help to get the insight into the molecular mechanism of NLS1. In this research we constructed a tridimensional model for hNLS1 using sequences of two proteins, melibiose and NLS1. Using computational biology tools, we were able to build and analyze protein, especially at the sodium binding site level. The apo NLS1 (without sodium in the binding site) allowed the binding of three different sodium ions during a 300 ns all atom molecular dynamics (MD) simulation. The sodium-bound MD simulation with a sodium placed between Asp 93 and Asp 97 (named Asp67 and Asp71 in this work) remained stable throughout the 300 ns simulation. Root Mean Square Deviation values of equilibration and production show that molecule has stabilized with time. Using Visual Molecular Dynamics (VMD) and the Bendix algorithm we were able to represent helical torsions and bending of specific helices derived from the MD simulation. To speed up the analysis of results we used the R-based Bio3D suite, which allowed us to get RMSD, PCA, DCCM and RMSF plots. Using computational biology tools, we have been able to validate the sodium binding site in NLS1. This study yields a robust three-dimensional model, which satisfies, so far, the experimental data available on NLS1. In structural biology, this model is a very useful tool to design mutants for NLS1 in order to obtain a three-dimensional structure of a functional protein.