Chlorine in PDB 8r11: Structure of Compound 7 Bound to Sars-Cov-2 Main Protease

Enzymatic activity of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease

All present enzymatic activity of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease:
3.4.22.69;

Protein crystallography data

The structure of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease, PDB code: 8r11 was solved by A.Mac Sweeney, J.Hazemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.02 / 1.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.088, 102.043, 104.658, 90, 90, 90
R / Rfree (%) 16.8 / 19.3

Other elements in 8r11:

The structure of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease also contains other interesting chemical elements:

Sodium (Na) 1 atom
Bromine (Br) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Compound 7 Bound to Sars-Cov-2 Main Protease (pdb code 8r11). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structure of Compound 7 Bound to Sars-Cov-2 Main Protease, PDB code: 8r11:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8r11

Go back to Chlorine Binding Sites List in 8r11
Chlorine binding site 1 out of 5 in the Structure of Compound 7 Bound to Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:22.3
occ:1.00
 CL A:XI0401 0.0 22.3 1.0
C14 A:XI0401 1.7 18.7 1.0
C13 A:XI0401 2.7 18.9 1.0
C15 A:XI0401 2.7 19.2 1.0
CA A:ASP187 3.5 14.4 1.0
CB A:ASP187 3.5 14.3 1.0
CD2 A:HIS41 3.5 16.1 1.0
O A:HIS164 3.7 14.9 1.0
CB A:MET165 3.7 17.9 1.0
CB A:HIS164 3.8 12.8 1.0
C12 A:XI0401 4.0 18.6 1.0
NE2 A:HIS41 4.0 17.6 1.0
C10 A:XI0401 4.0 18.2 1.0
C A:HIS164 4.1 13.3 1.0
CZ A:PHE181 4.3 14.7 1.0
C A:ASP187 4.3 15.1 1.0
O A:VAL186 4.3 14.7 1.0
CG A:MET165 4.4 19.7 1.0
CE A:MET49 4.4 20.8 1.0
SD A:MET165 4.5 26.1 1.0
CG A:HIS41 4.5 15.2 1.0
C11 A:XI0401 4.5 18.8 1.0
O A:HOH621 4.5 14.5 1.0
N A:ASP187 4.5 14.9 1.0
ND1 A:HIS164 4.5 13.0 1.0
CA A:HIS164 4.6 12.5 1.0
N A:MET165 4.7 13.7 1.0
CG A:HIS164 4.7 12.8 1.0
CA A:MET165 4.7 14.7 1.0
N A:ARG188 4.8 16.1 1.0
C A:VAL186 4.8 14.8 1.0
CG A:ASP187 5.0 14.6 1.0
O A:ASP187 5.0 16.4 1.0

Chlorine binding site 2 out of 5 in 8r11

Go back to Chlorine Binding Sites List in 8r11
Chlorine binding site 2 out of 5 in the Structure of Compound 7 Bound to Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:19.0
occ:1.00
 SG A:CYS145 3.0 24.9 1.0
O A:HOH586 3.0 39.0 1.0
N A:GLY143 3.3 18.9 1.0
CA A:GLY143 3.7 17.3 1.0
CB A:CYS145 3.7 15.8 1.0
ND2 A:ASN142 3.9 32.6 1.0
N A:CYS145 4.2 13.4 1.0
C A:GLY143 4.2 15.8 1.0
C4 A:XI0401 4.3 15.9 1.0
C6 A:XI0401 4.4 18.3 1.0
C A:ASN142 4.5 19.8 1.0
CE1 A:HIS41 4.5 16.4 1.0
CB A:LEU27 4.5 15.7 1.0
N A:SER144 4.5 14.5 1.0
CA A:CYS145 4.6 13.7 1.0
CD2 A:LEU27 4.7 16.7 1.0
O A:THR26 4.8 22.1 1.0
CA A:ASN142 4.8 20.9 1.0
O A:GLY143 4.9 16.3 1.0
CG A:ASN142 4.9 28.5 1.0
C3 A:XI0401 5.0 14.5 1.0

Chlorine binding site 3 out of 5 in 8r11

Go back to Chlorine Binding Sites List in 8r11
Chlorine binding site 3 out of 5 in the Structure of Compound 7 Bound to Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:24.5
occ:1.00
 CL B:XI0701 0.0 24.5 1.0
C14 B:XI0701 1.7 20.7 1.0
C13 B:XI0701 2.7 21.0 1.0
C15 B:XI0701 2.7 21.6 1.0
CE B:MET165 3.5 25.5 1.0
CD2 B:HIS41 3.5 19.0 1.0
CB B:ASP187 3.5 15.5 1.0
CA B:ASP187 3.6 16.0 1.0
O B:HIS164 3.7 16.0 1.0
CB B:MET165 3.7 17.3 1.0
CB B:HIS164 3.8 13.8 1.0
NE2 B:HIS41 4.0 20.2 1.0
C12 B:XI0701 4.0 21.0 1.0
C10 B:XI0701 4.0 20.6 1.0
C B:HIS164 4.1 14.1 1.0
CG B:HIS41 4.4 17.9 1.0
C B:ASP187 4.4 17.7 1.0
O B:VAL186 4.4 14.8 1.0
CG B:MET165 4.5 19.1 1.0
C11 B:XI0701 4.5 21.3 1.0
SD B:MET165 4.5 23.9 1.0
CZ B:PHE181 4.5 14.4 1.0
CE B:MET49 4.5 28.1 1.0
ND1 B:HIS164 4.5 14.1 1.0
CA B:HIS164 4.6 13.6 1.0
O B:HOH877 4.6 16.1 1.0
N B:ASP187 4.6 15.6 1.0
N B:MET165 4.6 15.4 1.0
CG B:HIS164 4.7 13.3 1.0
CA B:MET165 4.7 15.1 1.0
N B:ARG188 4.9 19.6 1.0
C B:VAL186 4.9 14.8 1.0
CB B:HIS41 4.9 17.0 1.0
CE1 B:HIS41 5.0 19.0 1.0
CG B:ASP187 5.0 15.5 1.0

Chlorine binding site 4 out of 5 in 8r11

Go back to Chlorine Binding Sites List in 8r11
Chlorine binding site 4 out of 5 in the Structure of Compound 7 Bound to Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl704

b:25.7
occ:1.00
 SG B:CYS145 3.1 26.8 1.0
N B:GLY143 3.5 19.3 1.0
CB B:CYS145 3.7 18.0 1.0
CA B:GLY143 3.9 18.7 1.0
N B:CYS145 4.2 15.8 1.0
C4 B:XI0701 4.3 18.8 1.0
C6 B:XI0701 4.3 20.9 1.0
C B:GLY143 4.4 17.1 1.0
CB B:LEU27 4.6 17.7 1.0
CE1 B:HIS41 4.6 19.0 1.0
N B:SER144 4.6 16.5 1.0
CA B:CYS145 4.6 16.2 1.0
C B:ASN142 4.7 21.3 1.0
CD2 B:LEU27 4.7 18.5 1.0
O B:THR26 4.8 25.1 1.0
CA B:ASN142 5.0 22.1 1.0

Chlorine binding site 5 out of 5 in 8r11

Go back to Chlorine Binding Sites List in 8r11
Chlorine binding site 5 out of 5 in the Structure of Compound 7 Bound to Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Compound 7 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl705

b:20.4
occ:1.00
 O B:HOH976 3.8 22.5 1.0
CE2 B:PHE223 4.0 16.6 1.0
O B:HOH953 4.2 32.1 1.0
O B:HOH980 4.5 36.4 1.0
CB B:ASN221 4.7 17.2 1.0
CD2 B:PHE223 4.8 16.1 1.0
CZ B:PHE223 4.9 16.8 1.0

Reference:

A.Mac Sweeney, J.Hazemann. Identification of Sars-Cov-2 Mpro Inhibitors Through Deep Reinforcement Learning For De Novo Drug Design and Computational Chemistry Approaches To Be Published.
Page generated: Tue Jul 30 12:06:42 2024

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