Chlorine in PDB 8gtv: Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07

All present enzymatic activity of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07:
3.4.22.69;

The structure of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07, PDB code: 8gtv was solved by H.X.Su, T.Q.Nie, H.Xie, M.J.Li, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.50 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.647, 82.133, 89.123, 90, 96.76, 90
R / Rfree (%)	22.4 / 24.7

The binding sites of Chlorine atom in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07 (pdb code 8gtv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07, PDB code: 8gtv:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:52.7 occ:1.00 CL1 A:KAE401 0.0 52.7 1.0 C18 A:KAE401 1.7 52.3 1.0 C17 A:KAE401 2.7 48.4 1.0 C19 A:KAE401 2.7 55.1 1.0 O A:ASP187 3.2 55.9 1.0 CL2 A:KAE401 3.2 64.3 1.0 OH A:TYR54 3.3 46.8 1.0 C A:ASP187 3.4 53.4 1.0 CB A:HIS41 3.6 41.2 1.0 N A:ARG188 3.7 53.0 1.0 CA A:ARG188 3.9 58.5 1.0 C16 A:KAE401 4.0 47.5 1.0 C20 A:KAE401 4.0 49.2 1.0 CA A:ASP187 4.1 50.4 1.0 CG A:HIS41 4.2 40.6 1.0 CB A:ASP187 4.2 51.9 1.0 SG A:CYS44 4.4 65.5 1.0 CD2 A:HIS41 4.5 39.8 1.0 C15 A:KAE401 4.5 46.2 1.0 C A:ARG188 4.7 62.0 1.0 CZ A:TYR54 4.7 45.7 1.0 CA A:HIS41 4.9 41.4 1.0

Chlorine binding site 2 out of 4 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:64.3 occ:1.00 CL2 A:KAE401 0.0 64.3 1.0 C19 A:KAE401 1.7 55.1 1.0 C20 A:KAE401 2.7 49.2 1.0 C18 A:KAE401 2.7 52.3 1.0 CL1 A:KAE401 3.2 52.7 1.0 CA A:ASP187 3.5 50.4 1.0 C A:ASP187 3.8 53.4 1.0 CB A:ASP187 3.9 51.9 1.0 N A:ARG188 3.9 53.0 1.0 CB A:MET165 3.9 40.5 1.0 C15 A:KAE401 4.0 46.2 1.0 C17 A:KAE401 4.0 48.4 1.0 CD2 A:HIS41 4.0 39.8 1.0 O A:VAL186 4.3 44.7 1.0 CE A:MET165 4.3 51.1 1.0 SD A:MET165 4.4 50.0 1.0 O A:HIS164 4.4 38.4 1.0 C16 A:KAE401 4.5 47.5 1.0 O A:ASP187 4.5 55.9 1.0 NE2 A:HIS41 4.6 39.7 1.0 CG A:MET165 4.7 43.4 1.0 CG A:HIS41 4.7 40.6 1.0 N A:ASP187 4.7 46.8 1.0 CA A:ARG188 4.8 58.5 1.0 O A:ARG188 4.9 58.9 1.0 C A:VAL186 4.9 46.3 1.0

Chlorine binding site 3 out of 4 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:48.8 occ:1.00 CL1 B:KAE401 0.0 48.8 1.0 C18 B:KAE401 1.7 46.5 1.0 C17 B:KAE401 2.7 41.1 1.0 C19 B:KAE401 2.7 49.3 1.0 CL2 B:KAE401 3.1 59.1 1.0 O B:ASP187 3.2 42.7 1.0 OH B:TYR54 3.5 40.4 1.0 C B:ASP187 3.5 41.6 1.0 CB B:HIS41 3.6 34.0 1.0 N B:ARG188 3.9 40.3 1.0 SD B:MET49 4.0 77.1 1.0 C16 B:KAE401 4.0 39.8 1.0 C20 B:KAE401 4.0 43.0 1.0 CA B:ARG188 4.0 45.2 1.0 CG B:HIS41 4.1 36.7 1.0 CA B:ASP187 4.3 38.2 1.0 CB B:ASP187 4.4 37.2 1.0 SG B:CYS44 4.5 63.5 1.0 CD2 B:HIS41 4.5 36.0 1.0 C15 B:KAE401 4.5 38.1 1.0 CE B:MET49 4.6 78.9 1.0 C B:ARG188 4.8 51.5 1.0 CZ B:TYR54 4.8 40.9 1.0 CA B:HIS41 4.9 35.2 1.0 ND1 B:HIS41 5.0 38.3 1.0

Chlorine binding site 4 out of 4 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-07 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:59.1 occ:1.00 CL2 B:KAE401 0.0 59.1 1.0 C19 B:KAE401 1.7 49.3 1.0 C20 B:KAE401 2.7 43.0 1.0 C18 B:KAE401 2.7 46.5 1.0 CL1 B:KAE401 3.1 48.8 1.0 CA B:ASP187 3.6 38.2 1.0 C B:ASP187 3.8 41.6 1.0 CB B:ASP187 3.9 37.2 1.0 CD2 B:HIS41 4.0 36.0 1.0 N B:ARG188 4.0 40.3 1.0 C15 B:KAE401 4.0 38.1 1.0 C17 B:KAE401 4.0 41.1 1.0 CB B:MET165 4.0 40.1 1.0 SD B:MET165 4.1 53.5 1.0 O B:VAL186 4.4 35.0 1.0 O B:HIS164 4.5 33.1 1.0 O B:ASP187 4.5 42.7 1.0 C16 B:KAE401 4.5 39.8 1.0 CG B:MET165 4.6 49.0 1.0 NE2 B:HIS41 4.6 35.4 1.0 CG B:HIS41 4.6 36.7 1.0 N B:ASP187 4.8 36.2 1.0 CA B:ARG188 4.8 45.2 1.0 O B:ARG188 4.9 52.5 1.0 CB B:HIS41 4.9 34.0 1.0

Y.C.Xu, Y.Zang, Y.Zhou. Development of Novel Inhibitors Against Sars-Cov-2 3CLPRO To Be Published.