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Chlorine in PDB 8r14: Structure of Compound 11 Bound to Sars-Cov-2 Main Protease

Enzymatic activity of Structure of Compound 11 Bound to Sars-Cov-2 Main Protease

All present enzymatic activity of Structure of Compound 11 Bound to Sars-Cov-2 Main Protease:
3.4.22.69;

Protein crystallography data

The structure of Structure of Compound 11 Bound to Sars-Cov-2 Main Protease, PDB code: 8r14 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) 72.47 / 1.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.79, 101.23, 103.79, 90, 90, 90
R / Rfree (%) 19 / 23.8

Other elements in 8r14:

The structure of Structure of Compound 11 Bound to Sars-Cov-2 Main Protease also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Compound 11 Bound to Sars-Cov-2 Main Protease (pdb code 8r14). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of Compound 11 Bound to Sars-Cov-2 Main Protease, PDB code: 8r14:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8r14

Go back to Chlorine Binding Sites List in 8r14
Chlorine binding site 1 out of 6 in the Structure of Compound 11 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 11 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:16.9
occ:0.80
 CL1 A:XHW401 0.0 16.9 0.8
C5 A:XHW401 1.7 14.2 0.8
C6 A:XHW401 2.7 14.1 0.8
C4 A:XHW401 2.7 13.6 0.8
O B:HOH954 3.4 24.3 1.0
OE2 A:GLU166 3.5 15.5 1.0
O A:HOH735 3.7 23.8 1.0
N B:SER1 3.7 17.0 1.0
O A:HOH779 3.7 47.8 1.0
O A:PHE140 3.8 15.2 1.0
CD A:GLU166 3.8 16.4 1.0
O A:HOH855 3.9 36.1 1.0
N1 A:XHW401 3.9 13.4 0.8
C2 A:XHW401 4.0 14.3 0.8
N A:ASN142 4.0 16.7 0.5
N A:ASN142 4.1 16.3 0.5
OE1 A:GLU166 4.1 19.6 1.0
CA A:LEU141 4.1 15.9 1.0
C A:LEU141 4.1 16.0 1.0
OD1 A:ASN142 4.3 23.6 0.5
CB A:GLU166 4.3 15.5 1.0
C3 A:XHW401 4.4 14.6 0.8
C A:PHE140 4.6 13.9 1.0
CG A:GLU166 4.7 15.8 1.0
OG B:SER1 4.8 25.3 1.0
CG A:ASN142 4.8 20.6 0.5
O A:LEU141 4.8 15.8 1.0
N A:LEU141 4.8 14.8 1.0
CA A:ASN142 4.8 16.9 0.5
CA A:ASN142 4.8 16.4 0.5

Chlorine binding site 2 out of 6 in 8r14

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Chlorine binding site 2 out of 6 in the Structure of Compound 11 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 11 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:24.2
occ:0.80
 CL2 A:XHW401 0.0 24.2 0.8
C15 A:XHW401 1.7 20.2 0.8
C14 A:XHW401 2.7 20.0 0.8
C10 A:XHW401 2.7 20.2 0.8
C9 A:XHW401 3.0 19.3 0.8
CD2 A:HIS41 3.2 15.7 1.0
CB A:ASP187 3.5 14.3 1.0
CA A:ASP187 3.5 14.4 1.0
CE A:MET49 3.8 26.8 1.0
NE2 A:HIS41 3.9 15.7 1.0
SD A:MET165 3.9 20.1 0.6
C13 A:XHW401 3.9 19.9 0.8
C11 A:XHW401 4.0 20.3 0.8
O A:HIS164 4.0 14.1 1.0
C A:ASP187 4.0 14.9 1.0
CG A:HIS41 4.0 14.2 1.0
CB A:MET165 4.1 16.4 0.6
CB A:MET165 4.1 16.6 0.4
CG A:MET165 4.3 18.0 0.4
CG A:MET165 4.4 17.2 0.6
N A:ARG188 4.4 15.7 1.0
CB A:HIS41 4.4 14.5 1.0
C12 A:XHW401 4.4 20.9 0.8
O A:ASP187 4.5 16.3 1.0
N3 A:XHW401 4.5 17.9 0.8
CB A:HIS164 4.5 13.1 1.0
C A:HIS164 4.6 13.1 1.0
O A:VAL186 4.7 15.8 1.0
O A:HOH618 4.7 14.3 1.0
N A:ASP187 4.7 14.2 1.0
CE1 A:HIS41 4.8 15.8 1.0
CE A:MET165 4.9 19.5 0.6
ND1 A:HIS41 4.9 15.2 1.0
CG A:ASP187 4.9 14.1 1.0

Chlorine binding site 3 out of 6 in 8r14

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Chlorine binding site 3 out of 6 in the Structure of Compound 11 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 11 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:21.7
occ:1.00
 O B:HOH909 2.9 42.2 1.0
O A:HOH674 3.3 30.1 1.0
N A:LYS5 3.4 14.2 1.0
NH1 A:ARG4 3.5 18.0 1.0
CD A:ARG4 3.6 17.2 1.0
CB A:LYS5 3.9 18.5 1.0
CG A:LYS5 4.1 22.1 1.0
CA A:ARG4 4.1 13.3 1.0
CA A:LYS5 4.2 15.4 1.0
C A:ARG4 4.2 13.1 1.0
CG B:LYS5 4.3 24.5 1.0
CB A:ARG4 4.3 13.9 1.0
CZ A:ARG4 4.5 16.9 1.0
NE A:ARG4 4.5 16.9 1.0
O A:LYS5 4.5 19.2 1.0
O A:HOH698 4.6 35.2 1.0
CB B:LYS5 4.6 21.7 1.0
NZ B:LYS5 4.6 28.2 1.0
CG A:ARG4 4.6 14.9 1.0
CD A:LYS5 4.8 25.8 1.0
C A:LYS5 4.9 15.6 1.0
O B:GLN127 5.0 18.8 1.0

Chlorine binding site 4 out of 6 in 8r14

Go back to Chlorine Binding Sites List in 8r14
Chlorine binding site 4 out of 6 in the Structure of Compound 11 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 11 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:15.0
occ:1.00
 O A:HOH591 3.6 29.0 1.0
NZ A:LYS102 4.0 24.2 1.0
CE A:LYS102 4.2 22.2 1.0
CD A:LYS102 4.3 21.0 1.0
O A:ASP153 4.5 27.2 1.0
CB A:ASP153 4.9 19.8 1.0
CB A:SER158 4.9 14.7 1.0

Chlorine binding site 5 out of 6 in 8r14

Go back to Chlorine Binding Sites List in 8r14
Chlorine binding site 5 out of 6 in the Structure of Compound 11 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 11 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:16.8
occ:0.80
 CL1 B:XHW701 0.0 16.8 0.8
C5 B:XHW701 1.7 13.8 0.8
C4 B:XHW701 2.7 13.3 0.8
C6 B:XHW701 2.7 14.5 0.8
C3 A:PGE402 2.9 32.8 1.0
O3 A:PGE402 3.2 30.0 1.0
C4 A:PGE402 3.4 30.4 1.0
OE2 B:GLU166 3.5 14.9 1.0
O A:HOH514 3.5 24.4 1.0
CD B:GLU166 3.8 14.9 1.0
O B:PHE140 3.8 13.7 1.0
OE1 B:GLU166 3.9 17.7 1.0
N1 B:XHW701 3.9 13.1 0.8
C2 B:XHW701 4.0 14.3 0.8
N B:ASN142 4.0 14.7 1.0
O B:HOH1067 4.0 36.4 1.0
N A:SER1 4.0 13.8 1.0
CA B:LEU141 4.0 13.6 1.0
C B:LEU141 4.0 13.9 1.0
OD1 B:ASN142 4.1 18.3 0.4
O2 A:PGE402 4.1 31.0 1.0
C5 A:PGE402 4.3 31.9 1.0
C3 B:XHW701 4.4 14.4 0.8
CB B:GLU166 4.5 13.8 1.0
C B:PHE140 4.5 12.9 1.0
O B:LEU141 4.7 13.2 1.0
N B:LEU141 4.7 13.7 1.0
CA B:ASN142 4.8 15.3 0.6
CG B:GLU166 4.8 14.5 1.0
CA B:ASN142 4.8 15.1 0.4
CG B:ASN142 4.9 16.8 0.4

Chlorine binding site 6 out of 6 in 8r14

Go back to Chlorine Binding Sites List in 8r14
Chlorine binding site 6 out of 6 in the Structure of Compound 11 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 11 Bound to Sars-Cov-2 Main Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:22.9
occ:0.80
 CL2 B:XHW701 0.0 22.9 0.8
C15 B:XHW701 1.7 20.2 0.8
C14 B:XHW701 2.6 20.3 0.8
C10 B:XHW701 2.6 21.3 0.8
C9 B:XHW701 3.0 20.6 0.8
CD2 B:HIS41 3.3 16.6 1.0
CA B:ASP187 3.6 14.5 1.0
CB B:ASP187 3.6 14.4 1.0
O B:HIS164 3.9 14.6 1.0
CE B:MET49 3.9 30.1 1.0
NE2 B:HIS41 3.9 17.8 1.0
C13 B:XHW701 3.9 21.8 0.8
C11 B:XHW701 3.9 22.1 0.8
CB B:MET165 4.1 18.0 1.0
CG B:HIS41 4.1 16.0 1.0
C B:ASP187 4.1 16.1 1.0
C12 B:XHW701 4.4 22.3 0.8
CE B:MET165 4.4 27.9 1.0
N B:ARG188 4.4 17.8 1.0
N3 B:XHW701 4.4 19.2 0.8
C B:HIS164 4.5 13.4 1.0
CB B:HIS41 4.5 15.3 1.0
CB B:HIS164 4.5 12.2 1.0
O B:ASP187 4.6 16.4 1.0
O B:VAL186 4.7 13.7 1.0
CG B:MET165 4.8 21.2 1.0
O B:HOH882 4.8 15.1 1.0
CE1 B:HIS41 4.8 17.6 1.0
N B:ASP187 4.8 13.5 1.0
C8 B:XHW701 4.8 18.9 0.8
SD B:MET165 4.9 28.2 1.0
ND1 B:HIS41 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: Sun Jul 13 13:43:04 2025

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