4. Cyclooxygenase protein receptor (COX-1 and COX-2)

3D model from PDB ID: 1PTH was obtained from SWISS-MODEL repository for cyclooxygenase-1 (COX-1) (http://www.rcsb.org/pdb/explore/explore.do?structure Id=1pth) and 3D model from PDB ID: 6COX for cyclooxygenase-2 (COX-2) [6, 8]. We used Ramachandran plot analysis for validation protein receptor [32].

In Figure 5 shows the Ramachandran plot analysis of COX-1 and COX-2 protein receptor before rigid docking. It showed that COX-1 protein receptor had 97.5% favored regions, 2.4% allowed regions, and, 0.2% outlier regions. Whereas, COX-2 protein receptor had 81.9% favored regions, 15.4% allowed regions and 2.7% outlier regions. Ramachandran plot displays the main chain torsion angles phi, psi (φ, Ψ) (Ramachandran angles) in a protein of known structure. The model was verified to guarantee the validity of programming and algorithms implemented. Results of the validity test showed that amino acid residues were distributed at the most favorable region in the Ramachandran plot. This is an indication of the stereochemical quality

Figure 5.

Ramachandran plot analysis of COX-1 and COX-2.

Virtual Screening of Sesquiterpenoid Pogostemon herba as Predicted Cyclooxygenase Inhibitor DOI: http://dx.doi.org/10.5772/intechopen.85319

of the model taken for the structural analysis and also validated the target-ligand binding efficacy of the structure. The Ramachandran plot presents the angle of phipsi torsion of all residues in the structure (except those at the chain termini) which were classified according to their regions in the quadrangle. The most favored regions are colored yellow, additional allowed/generously allowed region, and outlier regions are indicated as blue and pink fields, respectively [6, 8, 32].
