Sandbox Reserved 957: Difference between revisions
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Binding amino acid for the Sildenafil:<br \> | Binding amino acid for the Sildenafil:<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 [24]), <scene name='60/604476/R1-1/1'>Leu765</scene> and <scene name='60/604476/R1-1/1'>Ala767</scene> [21]. And there is hydrophobic interactions between the pyrazol ring and residues <scene name='60/604476/R1-2/1'>Val782, Leu785, Tyr612 and Phe820</scene> [24].<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 [24]), <scene name='60/604476/R1-1/1'>Leu765</scene> and <scene name='60/604476/R1-1/1'>Ala767</scene> [21]. And there is hydrophobic interactions between the pyrazol ring and residues <scene name='60/604476/R1-2/1'>Val782, Leu785, Tyr612 and Phe820</scene> [24].<br \> | ||
* R2 group is in the H pocket and has Van der Waals bounds with Val 782, Ala 783, Phe 786, Leu 804, Ile 813, Gln 817, Phe801. And interaction Pi-Pi between the phenyl ring and the Phe820.<br \> | * R2 group is in the H pocket and has Van der Waals bounds with <scene name='60/604476/R2/1'>Val 782, Ala 783, Phe 786, Leu 804, Ile 813, Gln 817, Phe801</scene>. And interaction Pi-Pi between the phenyl ring and the Phe820.<br \> | ||
* R3 group is in the L pocket and has contacts with Asn 662, Ser 663, Tyr 664, Ile 665 (in the H-loop), Leu 804, Phe 801 | * R3 group is in the L pocket and has contacts with Asn 662, Ser 663, Tyr 664, Ile 665 (in the H-loop), Leu 804, Phe 801 | ||
* Gly659 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. [21]<br \> | * Gly659 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. [21]<br \> | ||