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Zhu B, Strada S, Stevens T. Cyclic GMP-specific phosphodiesterase 5 regulates growth and apoptosis in pulmonary endothelial cells. Am J Physiol Lung Cell Mol Physiol 289: L196–L206, 2005.<br \></ref> and platelets and Corpus Cavernosum. In particular, it is implied in the NO pathway of penile erection and so in the Erectile Dysfunction (ED) <ref>[22]</ref>.<br \>

There are 11 families of PDE (from 1 to 9), there is 21 genes for PDE which code 60 different PDE. For the PDE5A, the only PDE5 subcategory, there are 4 isoforms but their catalytic domain is the same <ref>[24]</ref>.<br \>

We study here the PDE5A catalytic fragment formed of amino acid residues from the 535th to the 860th <ref>[23]</ref>. In the inhibition, we talk about the Sildenafil mostly, because it's the most known (active ingredient in the Viagra®).<br \>

The only catalytic fragment is effective, so the regulations sites and the dimerization to a trimeric enzyme are useless for the catalytic activity. Moreover, this catalytic moiety has the same activity that the wild-type enzyme, so maybe the enzyme is monomeric in the cell <ref>[24]</ref>.

Catalytic domain is conserved for the PDE family, between 20% and 40%, and the variant reactions of the PDE inhibitors on the different PDEs may be caused by the more variant regulatory sites <ref>[25]</ref>.<br \>

The catalytic domain has 3 helical subdomains <ref>[24]</ref>:<br \>

* A N-terminal cyclin-fold region with eight helixes <ref>[26]</ref>: 5 α-helixes (1, 3, 5, 6 and 8) and 3 3ind10-helixes (2,4, and 7),<scene name='60/604476/537_678/3'> from the 537th to the 678th residues</scene>.<br \>

* W2 binds <scene name='60/604476/Mg_zn/1'>Zn and Mg</scene> <ref>[24]</ref>,<br \>

* And there are 3 hydrogen bonds between 3 H2O and the conserved resides <scene name='60/604476/His657glu682his685/1'>His657, Asp682 and His685</scene> <ref>[24]</ref>.<br \>

* In particular the conserved residues <scene name='60/604476/Qsite1/1'>Gln817, Phe820, Val782 and Tyr612. <ref>[24]</ref></scene><br \>

* The hydrogen bonds, between <scene name='60/604476/Qsite2/1'>Gln817 and 775, Gln775 and Ala767, Gln775 and Trp853</scene>, imply an interaction between <scene name='60/604476/Gln817/1'>Gln817</scene> and the cGMP purine. Thus, it improves the specificity for the cGMP, against cAMP. <ref>[24]</ref><br \>

* And <scene name='60/604476/Qsite3/1'>Tyr612, Val782, Leu785 an Phe820</scene> bind the cGMP through this pyrazol ring and π-π interactions between Gln817 and the phenyl ring. <ref>[24]</ref><br \>

* In particular the residues <scene name='60/604476/Hsite1/1'>Phe786, Ala783, Leu804, Val782</scene>. <ref>[24]</ref><br \>

* In particular the hydrophobic residues <scene name='60/604476/Lsite1/1'>Tyr664, Met816, Ala823, Gly819</scene>. <ref>[24]</ref><br \>

Besides, the kcat of the catalytic fragment decreases 40-fold and 8-fold if the residues <scene name='60/604476/Lys603_leu644/1'>His603 and Asp644</scene> are mutated, and so there are important in the catalytic activity <ref>Liu S, Mansour MN, Dillman KS, Perez JR, Danley DE, Aeed PA, Simons SP, Lemotte PK, Menniti FS. Structural basis for the catalytic mechanism of human phosphodiesterase 9. Proc Natl Acad Sci USA 105: 13309–13314, 2008.Turko IV, Francis SH, Corbin JD. Potential roles of conserved amino acids in the catalytic domain of the cGMP-binding cGMPspecific phosphodiesterase. J Biol Chem 273: 6460–6466, 1998.</ref>. Two others residues are significant: <scene name='60/604476/Gln778/1'>the Gln778</scene> which is important for cGMP affinity but have no impact on cAMP affinity H-loop <ref>Zoraghi R, Corbin JD, Francis SH. Phosphodiesterase-5 Gln817 is critical for cGMP, vardenafil, or sildenafil affinity: its orientation impacts cGMP but not cAMP affinity. J Biol Chem 281: 5553–5558, 2006.</ref> and the conserved <scene name='60/604476/Gly659/1'>Gly659</scene> which is important for substrate affinity and catalytic activity because it determinates H-loop conformation <ref>[21]</ref> (see below).<br \>

H-loop is important in the substrate recognition and the interactions with, it is <scene name='60/604476/H_loop/1'>from 660th to 693th residues</scene>. H-loop has the same interactions with cGMP and Sildenafil (cf. Inhibitor) because it's related to its role of substrate binding<ref>[21]</ref>. But The H-loop is not well understood, because when it's modified, the enzyme's function is practically not modified.<ref>Wang H, Liu Y, Huai Q, Cai J, Zoraghi R, Francis SH, Corbin JD, Robinson H, Xin Z, Lin G, Ke H. Multiple conformations of phosphodiesterase-5: implications for enzyme function and drug development. J Biol Chem 281: 21469–21479, 2006.</ref> But it also may have a role for inhibitor fixation.<br \>

* R1 group have contacts with <scene name='60/604476/R1-1/1'>Gln817</scene> (2 hydrogen bounds, so it increases Sildenafil affinity), <scene name='60/604476/R1-1/1'>Phe820</scene> (Sildenafil stacks against it), <scene name='60/604476/R1-1/1'>Try612</scene> (hydrogen bound so it increases Sildenafil affinity <ref>[24]</ref>), <scene name='60/604476/R1-1/1'>Leu765</scene> and <scene name='60/604476/R1-1/1'>Ala767</scene> <ref>[21]</ref>. And there is hydrophobic interactions between the pyrazol ring and residues <scene name='60/604476/R1-2/1'>Val782, Leu785, Tyr612 and Phe820</scene> <ref>[24]</ref>.<br \>

* <scene name='60/604476/Gly659/2'>Gly659</scene> is modified by Sildenafil presence in PDE5, ϕ and φ angles are increased (from 76-105° to 104-109° for ϕ and from 3-22° to 139-141° for φ) and ω angle is not changed. <ref>[21]</ref><br \>

* For an unliganded PDE5, <scene name='60/604476/H_loop/1'>H-loop</scene>  take a coil conformation. <ref>[21]</ref><br \>

* In case of Sildenafil binding, a turn and an 3ind10<scene name='60/604476/3-10helix/1'> helix (from 672 to 675)</scene> appear, and  <scene name='60/604476/668_676/1'>from 668 to 676</scene> The all loop cover the active site (by migrate of 24 Å from unliganded PDE5 loop structure, so the active site become a closed pocket). <ref>[21]</ref><br \>

As it is written over, there are 2 regulatory domains (GAF A and GAF B). In cGMP pathway, PDE5 allows a negative feedback of the molecule: first, in presence of cGMP, it binds GAF A which stimulates the catalysis in the active site, and vice versa. Moreover, cGMP actives PKG which phophorylates PDE5, that is stimulated by the presence of cGMP on the GAF A or/and the active site. If the protein is not binding with cGMP but it is phophorylated, that stimulates the binding of cGMP on GAF A and the catalytic site. So cGMP presence overstimulates the catalysis <ref>[19]</ref>. And it also increase inhibitor's affinity<ref>[20]</ref> and without cGMP, inhibitor don’t bind the PDE5 <ref>[22]</ref>.<br \>

In the penile erection example, the nervous cell and/or epithelial cells are produced Nitrogen Oxide (NO) by the NOS (NO synthetase) from L-arginine and O2. They release NO in the extracellular environment going into vascular smooth cells and binding the Guanylyl Cyclase. This enzyme synthesizes cGMP from GMP, which stimulates the PKG. Finally, the calcium level is lower and the muscle cell relaxes and the Corpus Cavernosum rigidity increases. The PDE5 regulates the cGMP level making a negative feedback and can stop the rigidity. <ref>[22]</ref><br \>