Chlorine in PDB 3vyf: Human Renin in Complex with Inhibitor 9

All present enzymatic activity of Human Renin in Complex with Inhibitor 9:
3.4.23.15;

The structure of Human Renin in Complex with Inhibitor 9, PDB code: 3vyf was solved by M.Takahashi, H.Hanzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 2.80
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	141.427, 141.427, 141.427, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 26.6

The binding sites of Chlorine atom in the Human Renin in Complex with Inhibitor 9 (pdb code 3vyf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human Renin in Complex with Inhibitor 9, PDB code: 3vyf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Human Renin in Complex with Inhibitor 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Renin in Complex with Inhibitor 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:28.5 occ:0.50 CL1 A:VYF402 0.0 28.5 0.5 CL1 A:VYF402 0.0 36.1 0.2 C17 A:VYF402 1.7 32.4 0.2 C17 A:VYF402 1.7 20.3 0.5 C18 A:VYF402 2.7 32.3 0.2 C18 A:VYF402 2.7 20.2 0.5 C16 A:VYF402 2.7 32.0 0.2 C16 A:VYF402 2.7 19.5 0.5 N10 A:VYF402 3.0 18.3 0.5 N10 A:VYF402 3.0 31.5 0.2 CE1 A:PHE119 3.5 30.2 1.0 C11 A:VYF402 3.6 30.6 0.2 C11 A:VYF402 3.6 15.6 0.5 C9 A:VYF402 3.6 17.7 0.5 C9 A:VYF402 3.6 31.2 0.2 CG A:PRO118 3.7 22.8 1.0 O13 A:VYF402 3.9 18.6 0.5 CD1 A:PHE119 3.9 29.3 1.0 CZ A:PHE119 3.9 31.1 1.0 O13 A:VYF402 3.9 31.6 0.2 C19 A:VYF402 4.0 32.2 0.2 C19 A:VYF402 4.0 20.3 0.5 C21 A:VYF402 4.0 31.8 0.2 C21 A:VYF402 4.0 19.2 0.5 CZ A:PHE124 4.0 24.7 1.0 CB A:PRO118 4.3 25.0 1.0 OG1 A:THR85 4.4 32.4 1.0 C20 A:VYF402 4.5 31.8 0.2 C20 A:VYF402 4.5 19.2 0.5 C8 A:VYF402 4.6 15.9 0.5 C14 A:VYF402 4.6 13.8 0.5 C8 A:VYF402 4.6 30.6 0.2 CG A:PHE119 4.7 29.6 1.0 CE2 A:PHE119 4.7 31.0 1.0 C14 A:VYF402 4.7 30.0 0.2 C12 A:VYF402 4.7 14.4 0.5 C12 A:VYF402 4.7 30.1 0.2 CE1 A:PHE124 4.8 27.2 1.0 CE2 A:PHE124 4.8 26.8 1.0 N A:PHE119 4.9 25.4 1.0 C A:PRO118 5.0 25.6 1.0 CD A:PRO118 5.0 23.5 1.0

Chlorine binding site 2 out of 4 in the Human Renin in Complex with Inhibitor 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Renin in Complex with Inhibitor 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:36.1 occ:0.25 CL1 A:VYF402 0.0 36.1 0.2 CL1 A:VYF402 0.0 28.5 0.5 C17 A:VYF402 1.7 32.4 0.2 C17 A:VYF402 1.7 20.3 0.5 C18 A:VYF402 2.7 32.3 0.2 C16 A:VYF402 2.7 32.0 0.2 C16 A:VYF402 2.7 19.5 0.5 C18 A:VYF402 2.7 20.2 0.5 N10 A:VYF402 3.0 18.3 0.5 N10 A:VYF402 3.0 31.5 0.2 CE1 A:PHE119 3.5 30.2 1.0 C9 A:VYF402 3.6 17.7 0.5 C11 A:VYF402 3.6 30.6 0.2 C11 A:VYF402 3.6 15.6 0.5 C9 A:VYF402 3.6 31.2 0.2 CG A:PRO118 3.6 22.8 1.0 O13 A:VYF402 3.9 18.6 0.5 O13 A:VYF402 3.9 31.6 0.2 CZ A:PHE119 3.9 31.1 1.0 CD1 A:PHE119 3.9 29.3 1.0 C19 A:VYF402 4.0 32.2 0.2 C21 A:VYF402 4.0 31.8 0.2 C21 A:VYF402 4.0 19.2 0.5 C19 A:VYF402 4.0 20.3 0.5 CZ A:PHE124 4.0 24.7 1.0 CB A:PRO118 4.3 25.0 1.0 OG1 A:THR85 4.4 32.4 1.0 C20 A:VYF402 4.5 31.8 0.2 C20 A:VYF402 4.5 19.2 0.5 C8 A:VYF402 4.6 15.9 0.5 C14 A:VYF402 4.6 13.8 0.5 C8 A:VYF402 4.6 30.6 0.2 C14 A:VYF402 4.7 30.0 0.2 CE2 A:PHE119 4.7 31.0 1.0 CG A:PHE119 4.7 29.6 1.0 C12 A:VYF402 4.7 14.4 0.5 C12 A:VYF402 4.7 30.1 0.2 CE1 A:PHE124 4.8 27.2 1.0 CE2 A:PHE124 4.9 26.8 1.0 N A:PHE119 4.9 25.4 1.0 C A:PRO118 5.0 25.6 1.0 CD A:PRO118 5.0 23.5 1.0

Chlorine binding site 3 out of 4 in the Human Renin in Complex with Inhibitor 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Renin in Complex with Inhibitor 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:46.4 occ:0.50 CL1 B:VYF402 0.0 46.4 0.5 CL1 B:VYF402 0.1 51.3 0.2 C17 B:VYF402 1.7 49.1 0.2 C17 B:VYF402 1.7 42.0 0.5 C18 B:VYF402 2.6 49.4 0.2 C18 B:VYF402 2.7 42.8 0.5 C16 B:VYF402 2.7 48.1 0.2 C16 B:VYF402 2.7 39.9 0.5 N10 B:VYF402 3.0 36.9 0.5 N10 B:VYF402 3.0 46.8 0.2 C11 B:VYF402 3.5 33.9 0.5 C11 B:VYF402 3.5 45.5 0.2 CG B:PRO118 3.6 49.2 1.0 CE1 B:PHE119 3.6 50.5 1.0 C9 B:VYF402 3.7 35.9 0.5 C9 B:VYF402 3.8 46.3 0.2 CD1 B:PHE119 3.8 49.5 1.0 C19 B:VYF402 3.9 49.2 0.2 C19 B:VYF402 4.0 42.8 0.5 C21 B:VYF402 4.0 48.4 0.2 C21 B:VYF402 4.0 41.0 0.5 CZ B:PHE124 4.0 39.1 1.0 O13 B:VYF402 4.1 35.3 0.5 CB B:PRO118 4.1 48.9 1.0 O13 B:VYF402 4.1 46.2 0.2 CZ B:PHE119 4.2 48.8 1.0 N B:PHE119 4.4 49.6 1.0 C20 B:VYF402 4.5 49.3 0.2 C B:PRO118 4.5 50.0 1.0 CG B:PHE119 4.5 49.2 1.0 C20 B:VYF402 4.5 43.0 0.5 CE2 B:PHE124 4.5 38.8 1.0 CB B:ALA122 4.6 44.2 1.0 CA B:PHE119 4.6 49.1 1.0 C12 B:VYF402 4.7 32.0 0.5 C8 B:VYF402 4.7 33.4 0.5 C14 B:VYF402 4.7 31.7 0.5 OG1 B:THR85 4.7 50.3 1.0 C12 B:VYF402 4.7 44.7 0.2 O B:PRO118 4.7 50.6 1.0 C8 B:VYF402 4.7 45.2 0.2 C14 B:VYF402 4.8 44.6 0.2 CE2 B:PHE119 4.8 49.0 1.0 CD B:PRO118 4.8 49.5 1.0 CA B:PRO118 4.9 49.4 1.0 CD2 B:PHE119 4.9 49.3 1.0

Chlorine binding site 4 out of 4 in the Human Renin in Complex with Inhibitor 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human Renin in Complex with Inhibitor 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:51.3 occ:0.25 CL1 B:VYF402 0.0 51.3 0.2 CL1 B:VYF402 0.1 46.4 0.5 C17 B:VYF402 1.7 49.1 0.2 C17 B:VYF402 1.8 42.0 0.5 C18 B:VYF402 2.7 49.4 0.2 C16 B:VYF402 2.7 48.1 0.2 C16 B:VYF402 2.7 39.9 0.5 C18 B:VYF402 2.7 42.8 0.5 N10 B:VYF402 3.0 36.9 0.5 N10 B:VYF402 3.0 46.8 0.2 C11 B:VYF402 3.5 33.9 0.5 C11 B:VYF402 3.5 45.5 0.2 CG B:PRO118 3.6 49.2 1.0 CE1 B:PHE119 3.6 50.5 1.0 C9 B:VYF402 3.7 35.9 0.5 C9 B:VYF402 3.7 46.3 0.2 CD1 B:PHE119 3.8 49.5 1.0 C19 B:VYF402 4.0 49.2 0.2 C21 B:VYF402 4.0 48.4 0.2 C21 B:VYF402 4.0 41.0 0.5 C19 B:VYF402 4.0 42.8 0.5 CZ B:PHE124 4.0 39.1 1.0 O13 B:VYF402 4.1 35.3 0.5 O13 B:VYF402 4.1 46.2 0.2 CB B:PRO118 4.1 48.9 1.0 CZ B:PHE119 4.1 48.8 1.0 N B:PHE119 4.4 49.6 1.0 CG B:PHE119 4.5 49.2 1.0 C20 B:VYF402 4.5 49.3 0.2 CE2 B:PHE124 4.5 38.8 1.0 C B:PRO118 4.5 50.0 1.0 C20 B:VYF402 4.5 43.0 0.5 CB B:ALA122 4.6 44.2 1.0 C14 B:VYF402 4.6 31.7 0.5 C12 B:VYF402 4.7 32.0 0.5 C8 B:VYF402 4.7 33.4 0.5 CA B:PHE119 4.7 49.1 1.0 C12 B:VYF402 4.7 44.7 0.2 OG1 B:THR85 4.7 50.3 1.0 C8 B:VYF402 4.7 45.2 0.2 C14 B:VYF402 4.7 44.6 0.2 CE2 B:PHE119 4.8 49.0 1.0 O B:PRO118 4.8 50.6 1.0 CD B:PRO118 4.8 49.5 1.0 CD2 B:PHE119 4.9 49.3 1.0 CA B:PRO118 4.9 49.4 1.0

Y.Mori, Y.Ogawa, A.Mochizuki, Y.Nakamura, C.Sugita, S.Miyazaki, K.Tamaki, Y.Matsui, M.Takahashi, T.Nagayama, Y.Nagai, S.Inoue, T.Nishi. Design and Discovery of New (3S,5R)-5-[4-(2-Chlorophenyl)-2,2-Dimethyl-5-Oxopiperazin-1- Yl]Piperidine-3-Carboxamides As Potent Renin Inhibitors Bioorg.Med.Chem.Lett. V. 22 7677 2012.
ISSN: ISSN 0960-894X
PubMed: 23122821
DOI: 10.1016/J.BMCL.2012.09.103