Nucleotide sequence alignment and predicted protein structure depicting the functional relevance of non-synonymous SNP in abiotic stress-responsive protein kinase gene. Non-synonymous SNP validated in calcium dependent protein kinase gene (LOC_Os01g09580) showing differentiation between 22 drought tolerant upland indica/aus and 30 drought sensitive lowland rice genotype groups. Missense transversional substitution of the second nucleotide in the triplet codon of upland indica/aus genotypes coding for amino acid in the glycine-rich ATP conserved catalytic binding domain of protein kinase by another nucleotide resulted in the formation of new triplet codon for novel amino acid in lowland indica group. The substitution mutation predicted to alter three dimensional secondary structures of protein including peptide-substrate and Ca2+ ligand-binding site of catalytic domain in protein kinase which may produce functionally different proteins between upland and lowland genotypes. Missense non-synonymous SNP site, different protein structure and DNA binding domain are highlighted.