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Chlorine in PDB 8r16: Structure of Compound 12 Bound to Sars-Cov-2 Main Protease

Enzymatic activity of Structure of Compound 12 Bound to Sars-Cov-2 Main Protease

All present enzymatic activity of Structure of Compound 12 Bound to Sars-Cov-2 Main Protease:
3.4.22.69;

Protein crystallography data

The structure of Structure of Compound 12 Bound to Sars-Cov-2 Main Protease, PDB code: 8r16 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) 19.03 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.01, 101.83, 105.04, 90, 90, 90
R / Rfree (%) 18.1 / 20.7

Other elements in 8r16:

The structure of Structure of Compound 12 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 12 Bound to Sars-Cov-2 Main Protease (pdb code 8r16). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of Compound 12 Bound to Sars-Cov-2 Main Protease, PDB code: 8r16:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 8r16

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Chlorine binding site 1 out of 8 in the Structure of Compound 12 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 12 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:22.0
occ:0.70
 CL A:XJ9401 0.0 22.0 0.7
C13 A:XJ9401 1.7 21.0 1.0
C12 A:XJ9401 2.7 20.5 1.0
C14 A:XJ9401 2.7 21.6 1.0
O A:ARG188 3.1 18.0 1.0
CL1 A:XJ9401 3.1 25.4 0.7
C A:ARG188 3.2 17.6 1.0
N A:ARG188 3.4 16.1 1.0
N A:GLN189 3.5 18.8 1.0
CA A:ARG188 3.8 16.8 1.0
CA A:GLN189 3.8 19.8 1.0
SD A:MET165 3.9 30.7 1.0
C11 A:XJ9401 4.0 19.4 1.0
C9 A:XJ9401 4.0 20.5 1.0
C A:ASP187 4.0 15.4 1.0
OE1 A:GLN189 4.0 35.3 1.0
O A:VAL186 4.0 15.7 1.0
O A:HOH750 4.0 23.3 1.0
NE2 A:GLN192 4.2 18.1 1.0
CA A:ASP187 4.3 14.7 1.0
CB A:GLN189 4.5 22.5 1.0
C8 A:XJ9401 4.5 19.3 1.0
CD A:GLN189 4.8 30.4 1.0
O A:ASP187 4.8 16.6 1.0
C A:VAL186 5.0 15.6 1.0
CE A:MET165 5.0 27.6 1.0

Chlorine binding site 2 out of 8 in 8r16

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Chlorine binding site 2 out of 8 in the Structure of Compound 12 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 12 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:25.4
occ:0.70
 CL1 A:XJ9401 0.0 25.4 0.7
C14 A:XJ9401 1.7 21.6 1.0
C9 A:XJ9401 2.7 20.5 1.0
C13 A:XJ9401 2.7 21.0 1.0
CL A:XJ9401 3.1 22.0 0.7
C A:ASP187 3.3 15.4 1.0
O A:ASP187 3.3 16.6 1.0
SD A:MET49 3.5 35.0 0.5
CA A:ASP187 3.6 14.7 1.0
CB A:ASP187 3.7 15.1 1.0
CB A:HIS41 3.7 14.4 1.0
N A:ARG188 3.8 16.1 1.0
OH A:TYR54 3.8 16.9 1.0
CE A:MET49 4.0 31.8 0.5
C12 A:XJ9401 4.0 20.5 1.0
C8 A:XJ9401 4.0 19.3 1.0
CG A:HIS41 4.1 14.6 1.0
CD2 A:HIS41 4.1 15.4 1.0
SD A:MET49 4.3 28.2 0.5
CA A:ARG188 4.4 16.8 1.0
C11 A:XJ9401 4.5 19.4 1.0
CG A:MET49 4.6 25.8 0.5
C A:ARG188 4.8 17.6 1.0
CG A:ASP187 4.9 15.6 1.0
CG A:MET49 4.9 29.2 0.5
CB A:MET49 4.9 24.6 0.5

Chlorine binding site 3 out of 8 in 8r16

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Chlorine binding site 3 out of 8 in the Structure of Compound 12 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 12 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:13.3
occ:1.00
 O A:HOH555 3.6 29.4 1.0
O A:HOH580 3.7 18.8 1.0
NZ A:LYS102 3.9 22.9 1.0
CE A:LYS102 4.2 21.8 1.0
CD A:LYS102 4.2 20.9 1.0
O A:ASP153 4.4 17.6 0.5
CB A:ASP153 4.8 17.1 0.5
CB A:SER158 4.9 14.3 1.0
OG A:SER158 4.9 16.7 1.0
OD2 A:ASP153 5.0 16.8 0.5

Chlorine binding site 4 out of 8 in 8r16

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Chlorine binding site 4 out of 8 in the Structure of Compound 12 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 12 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:21.1
occ:1.00
 SG A:CYS145 3.0 23.3 1.0
OD1 A:ASN142 3.4 24.0 0.5
CB A:CYS145 3.6 15.9 1.0
N A:GLY143 3.6 17.7 1.0
CA A:GLY143 3.9 17.0 1.0
N A:CYS145 4.1 13.5 1.0
C4 A:XJ9401 4.1 16.9 1.0
C A:GLY143 4.3 15.4 1.0
C6 A:XJ9401 4.4 18.6 1.0
CA A:CYS145 4.5 13.8 1.0
C7 A:XJ9401 4.6 19.4 1.0
N A:SER144 4.6 14.2 1.0
CG A:ASN142 4.6 21.6 0.5
CB A:LEU27 4.7 15.8 1.0
CE1 A:HIS41 4.7 15.8 1.0
C A:ASN142 4.8 18.1 0.5
C A:ASN142 4.8 17.9 0.5
CD2 A:LEU27 4.8 16.8 1.0
C3 A:XJ9401 5.0 16.9 1.0
O A:GLY143 5.0 16.0 1.0
O A:THR26 5.0 21.1 1.0

Chlorine binding site 5 out of 8 in 8r16

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Chlorine binding site 5 out of 8 in the Structure of Compound 12 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 12 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:26.1
occ:1.00
 N A:LYS5 3.5 15.2 1.0
NH1 A:ARG4 3.7 19.9 1.0
CD A:ARG4 3.7 20.0 1.0
CB A:LYS5 4.0 17.5 1.0
CG B:LYS5 4.1 25.2 1.0
CA A:ARG4 4.3 15.2 1.0
CB A:ARG4 4.3 16.6 1.0
CA A:LYS5 4.4 15.5 1.0
CB B:LYS5 4.4 22.4 1.0
C A:ARG4 4.4 14.6 1.0
CG A:LYS5 4.4 19.9 1.0
O A:LYS5 4.5 17.8 1.0
NZ B:LYS5 4.5 28.1 1.0
CZ A:ARG4 4.6 18.9 1.0
NE A:ARG4 4.7 18.8 1.0
CG A:ARG4 4.7 17.6 1.0
O A:HOH788 4.8 36.2 1.0
O B:GLN127 4.9 18.8 1.0
C A:LYS5 5.0 15.5 1.0

Chlorine binding site 6 out of 8 in 8r16

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Chlorine binding site 6 out of 8 in the Structure of Compound 12 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 6 of Structure of Compound 12 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:22.0
occ:0.70
 CL B:XJ9401 0.0 22.0 0.7
C13 B:XJ9401 1.7 21.3 1.0
C12 B:XJ9401 2.7 19.4 1.0
C14 B:XJ9401 2.7 20.8 1.0
O B:ARG188 3.0 20.7 1.0
CL1 B:XJ9401 3.2 22.5 0.7
C B:ARG188 3.3 20.4 1.0
N B:ARG188 3.5 18.1 1.0
O B:HOH620 3.6 25.6 1.0
N B:GLN189 3.7 22.1 1.0
CA B:ARG188 3.9 20.0 1.0
O B:VAL186 3.9 14.7 1.0
CA B:GLN189 3.9 22.8 1.0
C B:ASP187 4.0 17.0 1.0
C11 B:XJ9401 4.0 19.0 1.0
C9 B:XJ9401 4.0 19.8 1.0
NE2 B:GLN192 4.0 15.1 1.0
CE B:MET165 4.1 26.2 1.0
SD B:MET165 4.2 26.2 1.0
CA B:ASP187 4.3 15.4 1.0
C8 B:XJ9401 4.5 19.1 1.0
CG B:MET49 4.6 28.8 0.5
CB B:GLN189 4.7 26.2 1.0
O B:ASP187 4.7 18.7 1.0
C B:VAL186 4.9 14.0 1.0

Chlorine binding site 7 out of 8 in 8r16

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Chlorine binding site 7 out of 8 in the Structure of Compound 12 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 7 of Structure of Compound 12 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:22.5
occ:0.70
 CL1 B:XJ9401 0.0 22.5 0.7
C14 B:XJ9401 1.7 20.8 1.0
C9 B:XJ9401 2.7 19.8 1.0
C13 B:XJ9401 2.7 21.3 1.0
SD B:MET49 3.1 30.9 0.5
CL B:XJ9401 3.2 22.0 0.7
C B:ASP187 3.2 17.0 1.0
O B:ASP187 3.2 18.7 1.0
CG B:MET49 3.6 28.8 0.5
CA B:ASP187 3.6 15.4 1.0
CB B:HIS41 3.7 14.7 1.0
CB B:ASP187 3.8 15.5 1.0
N B:ARG188 3.8 18.1 1.0
CE B:MET49 3.8 29.5 0.5
OH B:TYR54 3.9 17.7 1.0
C12 B:XJ9401 4.0 19.4 1.0
C8 B:XJ9401 4.0 19.1 1.0
CG B:HIS41 4.1 14.9 1.0
CD2 B:HIS41 4.1 15.7 1.0
SD B:MET49 4.2 25.6 0.5
CA B:ARG188 4.3 20.0 1.0
C11 B:XJ9401 4.5 19.0 1.0
CG B:MET49 4.5 24.7 0.5
CE B:MET49 4.6 25.8 0.5
C B:ARG188 4.7 20.4 1.0
CB B:MET49 4.8 26.0 0.5
CG B:ASP187 4.9 14.8 1.0
ND1 B:HIS41 5.0 15.8 1.0

Chlorine binding site 8 out of 8 in 8r16

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Chlorine binding site 8 out of 8 in the Structure of Compound 12 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 8 of Structure of Compound 12 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:29.6
occ:1.00
 O B:HOH535 2.7 35.5 1.0
O B:HOH507 2.8 37.5 1.0
SG B:CYS145 3.0 20.5 1.0
CB B:CYS145 3.6 15.3 1.0
N B:GLY143 3.7 14.9 1.0
CA B:GLY143 4.0 15.3 1.0
N B:CYS145 4.0 13.6 1.0
C4 B:XJ9401 4.2 17.6 1.0
C B:GLY143 4.3 13.8 1.0
CA B:CYS145 4.5 13.8 1.0
N B:SER144 4.5 13.8 1.0
C6 B:XJ9401 4.6 19.0 1.0
CB B:LEU27 4.6 15.0 1.0
C7 B:XJ9401 4.8 19.5 1.0
CD2 B:LEU27 4.8 16.1 1.0
C B:ASN142 4.8 16.1 1.0
CE1 B:HIS41 4.9 16.1 1.0
C3 B:XJ9401 5.0 16.2 1.0
O B:THR26 5.0 18.9 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: Sun Jul 13 13:43:51 2025

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