Chlorine in PDB 8gtw: Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26

All present enzymatic activity of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26:
3.4.22.69;

The structure of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26, PDB code: 8gtw 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)	31.56 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.616, 81.708, 89.079, 90, 97.19, 90
R / Rfree (%)	19.8 / 22.7

The structure of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Chlorine atom in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26 (pdb code 8gtw). 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-26, PDB code: 8gtw:
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-26


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-26 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:48.2 occ:1.00 CL1 A:K9U401 0.0 48.2 1.0 C4 A:K9U401 1.7 47.4 1.0 C3 A:K9U401 2.7 44.4 1.0 C5 A:K9U401 2.7 50.0 1.0 CL2 A:K9U401 3.2 57.0 1.0 O A:ASP187 3.3 37.5 1.0 OH A:TYR54 3.5 38.6 1.0 C A:ASP187 3.7 35.7 1.0 CB A:HIS41 3.7 35.3 1.0 CG A:MET49 3.8 77.3 1.0 CA A:ARG188 3.8 45.6 1.0 N A:ARG188 3.9 38.7 1.0 C2 A:K9U401 4.0 42.9 1.0 C6 A:K9U401 4.0 44.6 1.0 SG A:CYS44 4.2 59.5 1.0 CG A:HIS41 4.4 34.9 1.0 C1 A:K9U401 4.5 42.0 1.0 C A:ARG188 4.5 49.2 1.0 CA A:ASP187 4.6 31.8 1.0 O A:MET49 4.6 71.3 1.0 CB A:ASP187 4.7 31.4 1.0 CB A:CYS44 4.8 54.8 1.0 CD2 A:HIS41 4.8 34.8 1.0 CG A:PRO52 4.8 56.9 1.0 CZ A:TYR54 4.9 38.4 1.0 CB A:MET49 4.9 76.2 1.0 CB A:ARG188 4.9 49.7 1.0 SD A:MET49 4.9 82.6 1.0 CA A:HIS41 4.9 35.2 1.0 CA A:MET49 5.0 72.8 1.0 N A:GLN189 5.0 51.8 1.0

Chlorine binding site 2 out of 4 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26


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-26 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:57.0 occ:1.00 CL2 A:K9U401 0.0 57.0 1.0 C5 A:K9U401 1.7 50.0 1.0 C6 A:K9U401 2.7 44.6 1.0 C4 A:K9U401 2.7 47.4 1.0 CL1 A:K9U401 3.2 48.2 1.0 N A:ARG188 3.5 38.7 1.0 C A:ASP187 3.5 35.7 1.0 CA A:ASP187 3.5 31.8 1.0 SD A:MET165 3.8 48.7 1.0 C1 A:K9U401 4.0 42.0 1.0 C3 A:K9U401 4.0 44.4 1.0 O A:ARG188 4.0 46.4 1.0 CB A:ASP187 4.0 31.4 1.0 O A:ASP187 4.1 37.5 1.0 CA A:ARG188 4.2 45.6 1.0 CD2 A:HIS41 4.3 34.8 1.0 C A:ARG188 4.3 49.2 1.0 O A:VAL186 4.3 32.0 1.0 CB A:MET165 4.4 37.5 1.0 C2 A:K9U401 4.5 42.9 1.0 N A:ASP187 4.7 30.6 1.0 CG A:MET165 4.8 40.6 1.0 CG A:HIS41 4.8 34.9 1.0 O A:HIS164 5.0 34.6 1.0

Chlorine binding site 3 out of 4 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26


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-26 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:48.6 occ:1.00 CL1 B:K9U401 0.0 48.6 1.0 C4 B:K9U401 1.7 48.1 1.0 C3 B:K9U401 2.7 44.6 1.0 C5 B:K9U401 2.7 50.9 1.0 CL2 B:K9U401 3.2 60.1 1.0 O B:ASP187 3.3 44.5 1.0 OH B:TYR54 3.5 42.5 1.0 C B:ASP187 3.7 44.4 1.0 CB B:HIS41 3.8 37.5 1.0 CA B:ARG188 3.9 51.9 1.0 C2 B:K9U401 4.0 43.7 1.0 C6 B:K9U401 4.0 45.3 1.0 N B:ARG188 4.0 46.8 1.0 SG B:CYS44 4.2 63.3 1.0 CG B:HIS41 4.4 39.2 1.0 CG B:MET49 4.5 78.3 1.0 C1 B:K9U401 4.5 42.3 1.0 CA B:ASP187 4.5 40.2 1.0 C B:ARG188 4.6 53.1 1.0 CB B:ASP187 4.7 37.3 1.0 CB B:CYS44 4.8 58.7 1.0 CD2 B:HIS41 4.8 39.2 1.0 CZ B:TYR54 4.8 39.6 1.0 SD B:MET49 4.8 82.1 1.0 CB B:MET49 4.9 75.5 1.0 N B:GLN189 5.0 53.1 1.0 CA B:HIS41 5.0 37.3 1.0

Chlorine binding site 4 out of 4 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26


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-26 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:60.1 occ:1.00 CL2 B:K9U401 0.0 60.1 1.0 C5 B:K9U401 1.7 50.9 1.0 C6 B:K9U401 2.7 45.3 1.0 C4 B:K9U401 2.7 48.1 1.0 CL1 B:K9U401 3.2 48.6 1.0 N B:ARG188 3.6 46.8 1.0 CA B:ASP187 3.6 40.2 1.0 C B:ASP187 3.7 44.4 1.0 C1 B:K9U401 4.0 42.3 1.0 C3 B:K9U401 4.0 44.6 1.0 SD B:MET165 4.0 50.8 1.0 O B:ARG188 4.1 51.0 1.0 CA B:ARG188 4.2 51.9 1.0 CB B:ASP187 4.2 37.3 1.0 O B:VAL186 4.2 35.9 1.0 C B:ARG188 4.3 53.1 1.0 O B:ASP187 4.3 44.5 1.0 CB B:MET165 4.4 38.6 1.0 C2 B:K9U401 4.5 43.7 1.0 CD2 B:HIS41 4.5 39.2 1.0 N B:ASP187 4.8 37.5 1.0 CG B:MET165 5.0 44.3 1.0 C B:VAL186 5.0 37.4 1.0

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