Chlorine in PDB 8cyu: Crystal Structure of Sars-Cov-2 Mpro with Compound C5

Enzymatic activity of Crystal Structure of Sars-Cov-2 Mpro with Compound C5

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Mpro with Compound C5:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Mpro with Compound C5, PDB code: 8cyu was solved by L.J.Worrall, J.Lee, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.75 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.29, 102.64, 102.2, 90, 100.25, 90
R / Rfree (%) 21.2 / 24.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5 (pdb code 8cyu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5, PDB code: 8cyu:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8cyu

Go back to Chlorine Binding Sites List in 8cyu
Chlorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Sars-Cov-2 Mpro with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:35.4
occ:1.00
 CL01 A:P5X401 0.0 35.4 1.0
C18 A:P5X401 1.8 31.8 1.0
C09 A:P5X401 2.8 32.1 1.0
C12 A:P5X401 2.8 32.5 1.0
CE A:MET165 3.2 36.8 1.0
CA A:ASP187 3.4 27.5 1.0
CB A:ASP187 3.4 26.5 1.0
O A:HIS164 3.7 23.9 1.0
ND1 A:HIS41 3.7 24.2 1.0
CB A:MET165 3.7 30.1 1.0
CB A:HIS164 3.7 22.4 1.0
CZ A:PHE181 4.0 25.9 1.0
C19 A:P5X401 4.0 31.1 1.0
CE1 A:HIS41 4.1 23.7 1.0
C A:HIS164 4.1 23.5 1.0
S01 A:P5X401 4.2 37.2 1.0
C A:ASP187 4.3 29.3 1.0
O A:VAL186 4.4 27.9 1.0
N A:ASP187 4.4 27.7 1.0
ND1 A:HIS164 4.5 22.6 1.0
CA A:HIS164 4.5 22.2 1.0
CA A:MET165 4.6 27.0 1.0
CE A:MET49 4.6 43.1 1.0
CG A:HIS164 4.6 22.2 1.0
N A:MET165 4.6 24.3 1.0
SD A:MET165 4.6 40.4 1.0
CG A:MET165 4.7 32.5 1.0
O A:HOH601 4.7 22.3 1.0
N A:ARG188 4.7 30.9 1.0
C A:VAL186 4.8 28.1 1.0
CE1 A:PHE181 4.8 26.0 1.0
CE2 A:PHE181 4.9 25.1 1.0
CG A:HIS41 4.9 23.9 1.0
O A:ASP187 4.9 29.2 1.0
CG A:ASP187 4.9 26.6 1.0

Chlorine binding site 2 out of 4 in 8cyu

Go back to Chlorine Binding Sites List in 8cyu
Chlorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Sars-Cov-2 Mpro with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:24.9
occ:1.00
 CL01 B:P5X401 0.0 24.9 1.0
C18 B:P5X401 1.8 26.3 1.0
C09 B:P5X401 2.7 25.9 1.0
C12 B:P5X401 2.8 27.0 1.0
CB B:ASP187 3.4 25.1 1.0
CA B:ASP187 3.4 25.3 1.0
CB B:MET165 3.6 22.9 1.0
ND1 B:HIS41 3.7 27.6 1.0
O B:HIS164 3.7 19.6 1.0
CB B:HIS164 3.7 17.4 1.0
CE B:MET165 3.8 29.3 1.0
C19 B:P5X401 4.0 27.2 1.0
CZ B:PHE181 4.0 19.9 1.0
CE1 B:HIS41 4.1 28.1 1.0
C B:HIS164 4.2 18.5 1.0
S01 B:P5X401 4.3 28.3 1.0
O B:VAL186 4.3 23.1 1.0
C B:ASP187 4.3 26.9 1.0
N B:ASP187 4.4 24.0 1.0
ND1 B:HIS164 4.5 17.2 1.0
CA B:HIS164 4.5 17.4 1.0
CA B:MET165 4.6 21.2 1.0
CE B:MET49 4.6 33.5 1.0
CG B:HIS164 4.6 16.7 1.0
N B:MET165 4.6 18.8 1.0
CG B:MET165 4.7 26.6 1.0
C B:VAL186 4.7 23.3 1.0
SD B:MET165 4.7 30.0 1.0
O B:HOH603 4.7 16.4 1.0
CE2 B:PHE181 4.7 19.2 1.0
CE1 B:PHE181 4.8 20.4 1.0
N B:ARG188 4.9 28.8 1.0
CG B:ASP187 4.9 25.6 1.0
CG B:HIS41 5.0 26.9 1.0
O B:ASP187 5.0 27.0 1.0

Chlorine binding site 3 out of 4 in 8cyu

Go back to Chlorine Binding Sites List in 8cyu
Chlorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Sars-Cov-2 Mpro with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:29.1
occ:1.00
 CL01 C:P5X401 0.0 29.1 1.0
C18 C:P5X401 1.8 28.5 1.0
C09 C:P5X401 2.7 26.7 1.0
C12 C:P5X401 2.8 26.9 1.0
CB C:ASP187 3.4 25.9 1.0
CA C:ASP187 3.4 25.6 1.0
CB C:HIS164 3.7 20.1 1.0
ND1 C:HIS41 3.7 28.6 1.0
CB C:MET165 3.8 27.8 1.0
O C:HIS164 3.9 22.3 1.0
CZ C:PHE181 3.9 22.6 1.0
C19 C:P5X401 4.0 26.9 1.0
C C:HIS164 4.2 21.6 1.0
CE1 C:HIS41 4.2 29.3 1.0
S01 C:P5X401 4.2 31.5 1.0
O C:VAL186 4.2 24.1 1.0
C C:ASP187 4.3 27.7 1.0
CG C:MET165 4.3 29.2 1.0
N C:ASP187 4.4 24.9 1.0
ND1 C:HIS164 4.4 20.3 1.0
CE C:MET49 4.5 31.4 1.0
CG C:HIS164 4.5 19.6 1.0
CA C:HIS164 4.6 20.1 1.0
O C:HOH593 4.6 20.9 1.0
CE C:MET165 4.6 37.0 1.0
C C:VAL186 4.7 24.4 1.0
N C:MET165 4.7 22.4 1.0
CA C:MET165 4.7 24.3 1.0
CE2 C:PHE181 4.7 21.2 1.0
CE1 C:PHE181 4.8 22.7 1.0
SD C:MET165 4.8 34.9 1.0
N C:ARG188 4.8 28.9 1.0
CG C:ASP187 4.8 26.7 1.0
O C:ASP187 4.9 27.5 1.0
CG C:HIS41 5.0 28.1 1.0

Chlorine binding site 4 out of 4 in 8cyu

Go back to Chlorine Binding Sites List in 8cyu
Chlorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Sars-Cov-2 Mpro with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:38.3
occ:1.00
 CL01 D:P5X401 0.0 38.3 1.0
C18 D:P5X401 1.8 31.3 1.0
C12 D:P5X401 2.8 34.3 1.0
C09 D:P5X401 2.8 33.2 1.0
CB D:ASP187 3.3 24.6 1.0
CA D:ASP187 3.3 25.7 1.0
CE D:MET165 3.5 40.3 1.0
CB D:MET165 3.7 29.1 1.0
CB D:HIS164 3.7 22.0 1.0
O D:HIS164 3.7 22.9 1.0
ND1 D:HIS41 3.7 25.2 1.0
CZ D:PHE181 3.9 24.3 1.0
C19 D:P5X401 4.0 31.4 1.0
C D:HIS164 4.1 23.1 1.0
CE1 D:HIS41 4.1 25.2 1.0
S01 D:P5X401 4.2 39.0 1.0
C D:ASP187 4.2 27.4 1.0
N D:ASP187 4.3 26.0 1.0
O D:VAL186 4.3 27.2 1.0
CA D:HIS164 4.5 21.7 1.0
ND1 D:HIS164 4.5 22.8 1.0
CA D:MET165 4.5 25.9 1.0
O D:HOH620 4.6 19.0 1.0
CG D:HIS164 4.6 22.2 1.0
N D:MET165 4.6 23.3 1.0
CE D:MET49 4.6 37.4 1.0
CG D:MET165 4.7 32.4 1.0
CE1 D:PHE181 4.7 24.3 1.0
C D:VAL186 4.7 26.8 1.0
N D:ARG188 4.7 29.0 1.0
CE2 D:PHE181 4.8 23.7 1.0
CG D:ASP187 4.8 24.7 1.0
O D:ASP187 4.9 27.2 1.0
SD D:MET165 4.9 44.4 1.0
CG D:HIS41 4.9 24.7 1.0

Reference:

J.Perez-Vargas, L.J.Worrall, A.D.Olmstead, A.T.Ton, J.Lee, I.Villanueva, C.A.H.Thompson, S.Dudek, S.Ennis, J.R.Smith, T.Shapira, J.De Guzman, S.Gang, F.Ban, M.Vuckovic, M.Bielecki, S.Kovacic, C.Kenward, C.Y.Hong, D.G.Gordon, P.N.Levett, M.Krajden, R.Leduc, P.L.Boudreault, M.Niikura, M.Paetzel, R.N.Young, A.Cherkasov, N.C.J.Strynadka, F.Jean. A Novel Class of Broad-Spectrum Active-Site-Directed 3C-Like Protease Inhibitors with Nanomolar Antiviral Activity Against Highly Immune-Evasive Sars-Cov-2 Omicron Subvariants. Emerg Microbes Infect V. 12 46594 2023.
ISSN: ESSN 2222-1751
PubMed: 37555275
DOI: 10.1080/22221751.2023.2246594
Page generated: Tue Jul 30 08:18:24 2024

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