Nucleoside diphosphate kinase (NDK) protein of Porphyromonas gingivalis (P. gingivalis) plays an important role in immune evasion and apoptosis inhibition of host cells. It has the potential to cause cancer, however, its structure has not yet been determined. Here we established a 3D structure of P.gingivalis NDK protein using an in-silico approach and performed the structural analysis of the model protein. 3D structure of NDK was predicted through homology modelling using modeller. Structural domains predicted for the model belongs to the NDK family. Structural homology was further confirmed by functional annotation of the model which includes ATP binding and nucleotide diphosphate kinase function, indicating that it is an NDK protein. Structural alignment of the putative model shows the alpha-beta folds are structurally conserved among NDK from prokaryotes and eukaryotes. The structure-based phylogenetic analysis depicts a significant evolutionary relationship of the modeled protein with the NDK of prokaryotes. Furthermore, the MD simulation approach stabilized the model structure and provides a thermo-stable protein structure that can be used as a therapeutic target for further studies.