Three dimensional X-ray crystallographic investigations for a novel pyrimidine derivative namely 6-(2-Hydroxy-4,6-dimethyl-phenyl)-4-(2-methoxyphenyl)-5-nitro-3,4-dihydro-1H-pyrimidin-2-one, Methanol have been worked out using single crystal X-ray diffraction technique. Hirshfeld surface analysis carried out to visualize the inter molecular interaction and the effect of the solvent molecule in interaction. To correlate the structure-function relationship of a particular molecule, the compounds have been tested for its biological response, molecular docking studies carried out using Hex and Schrodinger softwares.