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Chlorine in PDB 7gnd: Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601)

Enzymatic activity of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601)

All present enzymatic activity of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601):
3.4.22.69;

Protein crystallography data

The structure of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601), PDB code: 7gnd was solved by D.Fearon, A.Aimon, J.C.Aschenbrenner, B.H.Balcomb, F.K.R.Bertram, J.Brandao-Neto, A.Dias, A.Douangamath, L.Dunnett, A.S.Godoy, T.J.Gorrie-Stone, L.Koekemoer, T.Krojer, R.M.Lithgo, P.Lukacik, P.G.Marples, H.Mikolajek, E.Nelson, C.D.Owen, A.J.Powell, V.L.Rangel, R.Skyner, C.M.Strain-Damerell, W.Thompson, C.W.E.Tomlinson, C.Wild, M.A.Walsh, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.09 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.886, 100.387, 104.118, 90, 90, 90
R / Rfree (%) 21.4 / 23.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601) (pdb code 7gnd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601), PDB code: 7gnd:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7gnd

Go back to Chlorine Binding Sites List in 7gnd
Chlorine binding site 1 out of 3 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:18.2
occ:1.00
 NE2 A:GLN110 3.2 20.9 1.0
N A:GLN107 3.3 17.3 1.0
CA A:ILE106 3.7 17.0 1.0
CB A:GLN110 3.8 14.7 1.0
CG A:GLN110 3.9 16.0 1.0
CB A:ILE106 3.9 16.6 1.0
C A:ILE106 4.0 17.4 1.0
CD A:GLN110 4.0 20.3 1.0
CB A:GLN107 4.0 19.8 1.0
CG A:GLN107 4.1 23.6 1.0
CA A:GLN107 4.2 18.0 1.0
CG2 A:ILE106 4.2 16.6 1.0
O A:GLN107 4.5 18.4 1.0
O A:ARG105 4.8 19.4 1.0
O A:HOH720 4.8 23.5 1.0
C A:GLN107 4.9 18.7 1.0

Chlorine binding site 2 out of 3 in 7gnd

Go back to Chlorine Binding Sites List in 7gnd
Chlorine binding site 2 out of 3 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:29.2
occ:1.00
 CL A:RVR408 0.0 29.2 1.0
C A:RVR408 1.7 29.0 1.0
C1 A:RVR408 2.7 29.4 1.0
C5 A:RVR408 2.7 28.7 1.0
CB A:ASP187 3.3 21.3 1.0
CA A:ASP187 3.4 22.0 1.0
CD2 A:HIS41 3.5 24.1 1.0
O A:HIS164 3.7 19.1 1.0
CB A:MET165 3.8 22.6 1.0
NE2 A:HIS41 3.9 25.7 1.0
CB A:HIS164 4.0 14.6 1.0
C2 A:RVR408 4.0 29.9 1.0
C4 A:RVR408 4.0 29.2 1.0
C A:HIS164 4.1 17.9 1.0
C A:ASP187 4.1 23.6 1.0
SD A:MET165 4.1 37.5 1.0
CG A:MET165 4.2 27.1 1.0
CG A:HIS41 4.3 22.4 1.0
O A:HOH535 4.4 16.7 1.0
CE A:MET49 4.4 38.9 1.0
CZ A:PHE181 4.5 16.3 1.0
C3 A:RVR408 4.5 30.6 1.0
CD2 A:HIS164 4.5 13.8 1.0
CA A:HIS164 4.6 15.6 1.0
N A:ASP187 4.6 21.7 1.0
O A:ASP187 4.6 23.6 1.0
N A:MET165 4.6 18.4 1.0
N A:ARG188 4.6 24.8 1.0
CG A:HIS164 4.7 14.1 1.0
CG A:ASP187 4.7 20.8 1.0
O A:VAL186 4.7 22.8 1.0
CA A:MET165 4.8 20.4 1.0
CE1 A:HIS41 4.8 25.5 1.0
CB A:HIS41 4.8 19.6 1.0

Chlorine binding site 3 out of 3 in 7gnd

Go back to Chlorine Binding Sites List in 7gnd
Chlorine binding site 3 out of 3 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mik-Unk-78DBF1B8-1 (Mpro-P2601) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:27.5
occ:0.78
 CL B:RVR404 0.0 27.5 0.8
C B:RVR404 1.7 26.9 0.8
C5 B:RVR404 2.7 26.8 0.8
C1 B:RVR404 2.7 26.9 0.8
CD2 B:HIS41 3.3 30.6 1.0
CB B:ASP187 3.4 20.2 1.0
CA B:ASP187 3.5 20.3 1.0
O B:HIS164 3.6 17.9 1.0
NE2 B:HIS41 3.8 32.4 1.0
CB B:MET165 3.8 21.0 1.0
CB B:HIS164 3.9 14.9 1.0
C2 B:RVR404 4.0 27.4 0.8
C B:HIS164 4.0 16.9 1.0
C4 B:RVR404 4.0 26.9 0.8
C B:ASP187 4.1 23.9 1.0
CG B:MET165 4.2 27.1 1.0
CG B:HIS41 4.3 29.5 1.0
SD B:MET165 4.4 40.9 1.0
CE B:MET49 4.5 53.9 1.0
C3 B:RVR404 4.5 28.0 0.8
CA B:HIS164 4.5 15.1 1.0
N B:ARG188 4.5 25.8 1.0
O B:HOH553 4.5 14.3 1.0
CD2 B:HIS164 4.6 15.5 1.0
N B:MET165 4.6 16.8 1.0
CZ B:PHE181 4.6 17.1 1.0
CG B:HIS164 4.7 15.1 1.0
O B:VAL186 4.7 18.6 1.0
N B:ASP187 4.7 18.5 1.0
O B:ASP187 4.7 24.4 1.0
CA B:MET165 4.7 18.2 1.0
CE1 B:HIS41 4.8 32.7 1.0
CG B:ASP187 4.9 21.0 1.0
CB B:HIS41 4.9 26.2 1.0

Reference:

M.L.Boby, D.Fearon, M.Ferla, M.Filep, L.Koekemoer, M.C.Robinson, The Covid Moonshot Consortium, J.D.Chodera, A.A.Lee, N.London, A.Von Delft, F.Von Delft. Open Science Discovery of Potent Noncovalent Sars-Cov-2 Main Protease Inhibitors Science 2023.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ABO7201
Page generated: Sun Jul 13 02:00:33 2025

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