Chlorine in PDB 5yjk: Human Kallikrein 7 in Complex with 1,4-Diazepane-7-One 1-Acetamide Derivative

All present enzymatic activity of Human Kallikrein 7 in Complex with 1,4-Diazepane-7-One 1-Acetamide Derivative:
3.4.21.117;

The structure of Human Kallikrein 7 in Complex with 1,4-Diazepane-7-One 1-Acetamide Derivative, PDB code: 5yjk was solved by H.Sugawara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.93 / 2.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	59.286, 86.576, 89.059, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.2

The binding sites of Chlorine atom in the Human Kallikrein 7 in Complex with 1,4-Diazepane-7-One 1-Acetamide Derivative (pdb code 5yjk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Human Kallikrein 7 in Complex with 1,4-Diazepane-7-One 1-Acetamide Derivative, PDB code: 5yjk:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Human Kallikrein 7 in Complex with 1,4-Diazepane-7-One 1-Acetamide Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Kallikrein 7 in Complex with 1,4-Diazepane-7-One 1-Acetamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:35.0 occ:1.00 CL2 A:8VX301 0.0 35.0 1.0 C9 A:8VX301 1.7 34.7 1.0 C8 A:8VX301 2.7 35.2 1.0 C10 A:8VX301 2.7 34.0 1.0 O A:TRP215 3.4 17.9 1.0 CA A:GLY226 3.5 14.2 1.0 OD1 A:ASN189 3.8 22.4 1.0 C A:TRP215 3.9 17.1 1.0 O A:ALA190 3.9 16.2 1.0 CB A:ALA190 4.0 18.0 1.0 C7 A:8VX301 4.0 34.8 1.0 C5 A:8VX301 4.0 33.6 1.0 N A:VAL227 4.0 13.3 1.0 C A:GLY226 4.3 13.8 1.0 C A:ALA190 4.4 18.0 1.0 N A:GLY216 4.4 18.3 1.0 CA A:GLY216 4.4 19.6 1.0 N A:ALA190 4.5 19.5 1.0 CG1 A:VAL213 4.5 14.9 1.0 CA A:ALA190 4.5 18.4 1.0 C6 A:8VX301 4.5 33.2 1.0 CG A:ASN189 4.7 22.4 1.0 CA A:TRP215 4.7 16.2 1.0 N A:TRP215 4.7 16.3 1.0 N A:GLY226 4.8 14.8 1.0 O A:VAL227 4.8 11.5 1.0

Chlorine binding site 2 out of 3 in the Human Kallikrein 7 in Complex with 1,4-Diazepane-7-One 1-Acetamide Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Kallikrein 7 in Complex with 1,4-Diazepane-7-One 1-Acetamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:29.7 occ:1.00 NH1 A:ARG50 3.7 40.2 1.0 N A:GLN111 3.9 22.6 1.0 CB A:SER110 4.1 19.0 1.0 CA A:SER110 4.2 18.1 1.0 CZ A:ARG50 4.4 37.4 1.0 NH2 A:ARG50 4.4 38.0 1.0 CB A:GLN111 4.5 24.9 1.0 C A:SER110 4.6 20.0 1.0 CG A:GLN111 4.7 26.1 1.0 CA A:GLN111 4.8 23.7 1.0

Chlorine binding site 3 out of 3 in the Human Kallikrein 7 in Complex with 1,4-Diazepane-7-One 1-Acetamide Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Kallikrein 7 in Complex with 1,4-Diazepane-7-One 1-Acetamide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:30.9 occ:1.00 NZ A:LYS59 3.7 25.6 1.0 NE A:ARG90 3.8 27.1 1.0 N A:ARG90 3.9 22.4 1.0 NH1 A:ARG90 4.0 30.1 1.0 O A:SER88 4.2 23.2 1.0 CA A:PHE89 4.3 22.1 1.0 CZ A:ARG90 4.4 28.9 1.0 CB A:ARG90 4.5 22.6 1.0 C A:PHE89 4.6 21.9 1.0 CG A:ARG90 4.7 24.3 1.0 CA A:ARG90 4.7 22.0 1.0 CE A:LYS59 4.8 25.8 1.0 O A:ARG90 4.8 21.6 1.0 CD A:ARG90 4.9 25.6 1.0

H.Murafuji, H.Sakai, M.Goto, S.Imajo, H.Sugawara, T.Muto. Discovery and Structure-Activity Relationship Study of 1,3,6-Trisubstituted 1,4-Diazepane-7-Ones As Novel Human Kallikrein 7 Inhibitors Bioorg. Med. Chem. Lett. V. 27 5272 2017.
ISSN: ESSN 1464-3405
PubMed: 29102227
DOI: 10.1016/J.BMCL.2017.10.030