PBD ID = 1R9O ^[2]

The steric energy values of flurbiprofen given in the preceding table were obtained via computational analysis, using CS Chem3D Pro v7.0. From the data obtained we can see that the relative change in total steric energy to be quite significant. The computational analysis displays nine different energy factors, which contributes to the total steric energy values of flurbiprofen complexed to P4502C9 and in the gas phase. However, it should be noted that the graphical representation of flurbiprofen in the dual energy states displayed, nearly shows no difference in the conformal structure at all. Below is a basic explanation of the steric energy components.

The Stretch component refers to when the bonds between the atoms are either elongated or compressed in a spring like fashion. As we can see right away, the stretch energy is the major contributing factor to the complexed flurbiprofen, while the minimized stretch energy is quite paltry in comparison. Thus, the protein flurbiprofen is complexed to causes quite a bit of stretching strain on the compound.

The Bend component is when the bond angles of the compound is strained away from its optimal / preferred angle. For both the complexed and the minimized steric energies, both do not play a significant role as a major contributing factor in the difference in steric energies.

The Stretch-Bend component is similar in idea of the previous two energy components, however the stretch-bend here refers to two or more bonds ‘hinged’ on an atom. Again these energies are quite insignificant compared with other energy components. As stated above, the bend component also displays minor steric contribution; this may be a clue as to the reason why the two graphical conformations are nearly identical.

The Torsion component is the rotational strain experienced by the compound’s dihedral angles. The energies of both the complexed and minimized flurbiprofen are major contributors to the overall steric energy of the compound. Granted, that before minimization the torsion energy is not as large as the stretch component, however the energy is large enough to warrant it as a major contributing factor. Likewise after minimization the torsion energy becomes the major component in flurbiprofen.

The Non-1,4 VDW is the energy experienced between two atoms that are at least three atoms apart. This energy is derived from the van der Waals’ attractive and repulsive forces. Although the contributions are not hugely significant, the energies are large enough to note their significance in the overall steric energy.

Like the Non-1,4 VDW, 1,4 VDW energies experience the same form of van der Waals’ forces, however the 1,4 VDW energy is experienced between two atoms that are exactly two atoms apart. This time however, 1,4 VDW forces do make an impact on the total steric energies. Leading to the reasoning that flurbiprofen experiences (relatively) large VDW forces with more close by atoms than those that are further away.

The Charge / Dipole component refers to the electrostatic energy which results from the interaction of a charged atom and a dipole. These energies relative to the total steric energies are also not significant (even more so before minimization), however it should be noted that both values are close together.

The Dipole / Dipole energy component are polar interactions between molecules can result from dipole-dipole interactions. These values are again not major contributors and like previously, are similar in both the pre-and post energy minimization energies. The individual charges can interact with the individual charges of opposite sign on another molecule, and the interaction can be extremely strong overall.

Above is the superimposed image of flurbiprofen before and after minimization and as you can see, there are very noticable changes in the attached flourine atom and the two oxygen atoms.


Part V: Protein-Ligand Interactions
Fom the wiring diagram, residues E and T at positions 300 and 301 are catalytic residues involved in the catalysis of reactions for the oxireductase protein. The red dotted amino acids are those that interact with the flurbiprofen ligand. The interesting thing is that the amino acids that interact in the secondary structure are also next to each other during the primary structure, such as in positions 292 to 305, where they all cluster around the catalytic active site.


From the Ligplot,obtained from the PDB site, it can be seen that two residues, Arginine and Asparagine at positions 108 and 204 respectively, have 3 hydrogen bonds directly interacting with the oxygens of flurbiprofen. The different hydrogen bonds are lengths of 2.96, 2.69, 3.22 Angstroms.


There are more pictures of the protein and heterocompound to display their interactions.

This is the protein in a solid grey ribbon.



These are images of the flurbiprofen compound interacting with the amino acids.



Part VI: Protein-Ligan Interaction Chart
This chart can be found here.

Part VII: Bibliography
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000). RCSB PDB site
J Biol Chem. 2004 Aug 20;279(34):35630-7. Epub 2004 Jun 4.Click here to read Links The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-A resolution. Wester MR, Yano JK, Schoch GA, Yang C, Griffin KJ, Stout CD, Johnson EF.
PDB Sum

Part VIII: Organization and Submission

This is what the final compound looks like:

^{[1] Hetro-compound located using:  
     Kleywegt, G.J. and Jones, T.A. (1998). Databases in protein crystallography. Acta Cryst D54, 1119-1131 (CCP4 Proceedings).  
     website: http://xray.bmc.uu.se/hicup/ (April 2007)
[2] PDB ID: 1R9O  
     Wester, M.R.,  Yano, J.K.,  Schoch, G.A.,  Yang, C.,  Griffin, K.J.,  Stout, C.D.,  Johnson, E.F.
     The Structure of Human Cytochrome P450 2C9 Complexed with Flurbiprofen at 2.0 A Resolution
     J.Biol.Chem. v279 pp.35630-35637 , 2004}