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Fluorine in PDB 7gjn: 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 Edj-Med-37AAC4BD-4 (Mpro-P0602)

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 Edj-Med-37AAC4BD-4 (Mpro-P0602)

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 Edj-Med-37AAC4BD-4 (Mpro-P0602):
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 Edj-Med-37AAC4BD-4 (Mpro-P0602), PDB code: 7gjn 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) 56.36 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.3, 98.91, 103.14, 90, 90, 90
R / Rfree (%) 23.4 / 27.9

Other elements in 7gjn:

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 Edj-Med-37AAC4BD-4 (Mpro-P0602) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Edj-Med-37AAC4BD-4 (Mpro-P0602) (pdb code 7gjn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine 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 Edj-Med-37AAC4BD-4 (Mpro-P0602), PDB code: 7gjn:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7gjn

Go back to Fluorine Binding Sites List in 7gjn
Fluorine binding site 1 out of 4 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 Edj-Med-37AAC4BD-4 (Mpro-P0602)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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 Edj-Med-37AAC4BD-4 (Mpro-P0602) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:45.2
occ:0.74
 F1 A:QP6404 0.0 45.2 0.7
C7 A:QP6404 1.4 45.6 0.7
C8 A:QP6404 2.3 45.4 0.7
C6 A:QP6404 2.3 46.2 0.7
CD2 A:HIS41 3.1 43.6 1.0
O A:HIS164 3.5 37.9 1.0
CB A:MET165 3.6 40.6 1.0
CB A:ASP187 3.6 43.9 1.0
C5 A:QP6404 3.6 46.6 0.7
C9 A:QP6404 3.6 45.6 0.7
NE2 A:HIS41 3.7 45.2 1.0
CA A:ASP187 3.8 43.7 1.0
C A:HIS164 3.9 37.0 1.0
CG A:HIS41 4.0 43.4 1.0
C4 A:QP6404 4.1 46.2 0.7
CB A:HIS164 4.1 33.7 1.0
CE A:MET165 4.1 45.4 1.0
CG A:MET165 4.3 45.9 1.0
SD A:MET165 4.3 55.6 1.0
C A:ASP187 4.3 44.9 1.0
N A:MET165 4.4 37.6 1.0
CA A:MET165 4.4 39.4 1.0
O A:HOH525 4.6 29.7 1.0
CB A:HIS41 4.6 41.1 1.0
CA A:HIS164 4.6 34.7 1.0
CE1 A:HIS41 4.6 45.7 1.0
O A:ASP187 4.7 45.3 1.0
F A:QP6404 4.7 47.2 0.7
ND1 A:HIS41 4.8 45.6 1.0
C1 A:QP6404 4.9 45.5 0.7
CD2 A:HIS164 4.9 33.6 1.0
N A:ARG188 4.9 45.5 1.0
CG A:HIS164 4.9 33.1 1.0
CZ A:PHE181 4.9 36.9 1.0
CG A:ASP187 5.0 45.8 1.0

Fluorine binding site 2 out of 4 in 7gjn

Go back to Fluorine Binding Sites List in 7gjn
Fluorine binding site 2 out of 4 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 Edj-Med-37AAC4BD-4 (Mpro-P0602)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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 Edj-Med-37AAC4BD-4 (Mpro-P0602) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:47.2
occ:0.74
 F A:QP6404 0.0 47.2 0.7
C5 A:QP6404 1.4 46.6 0.7
C4 A:QP6404 2.3 46.2 0.7
C6 A:QP6404 2.3 46.2 0.7
O1 A:QP6404 2.7 46.2 0.7
N A:GLN189 2.8 49.2 1.0
CA A:GLN189 2.9 52.0 1.0
C A:ARG188 3.0 47.7 1.0
O A:ARG188 3.3 47.3 1.0
CG A:GLN189 3.3 61.8 1.0
CB A:GLN189 3.3 55.5 1.0
C7 A:QP6404 3.6 45.6 0.7
C9 A:QP6404 3.6 45.6 0.7
CA A:ARG188 3.9 46.5 1.0
CE A:MET165 4.0 45.4 1.0
C3 A:QP6404 4.0 46.2 0.7
C8 A:QP6404 4.1 45.4 0.7
O A:DMS403 4.2 62.3 1.0
CD A:GLN189 4.2 68.7 1.0
SD A:MET49 4.2 78.5 1.0
N A:ARG188 4.2 45.5 1.0
C A:GLN189 4.4 53.6 1.0
C1 A:DMS403 4.4 61.6 1.0
O A:MET49 4.4 65.1 1.0
NE2 A:GLN189 4.4 70.4 1.0
CB A:MET49 4.6 68.7 1.0
F1 A:QP6404 4.7 45.2 0.7
CG A:MET49 4.8 71.3 1.0
C A:ASP187 4.8 44.9 1.0
C1 A:QP6404 4.9 45.5 0.7
C2 A:QP6404 5.0 46.0 0.7

Fluorine binding site 3 out of 4 in 7gjn

Go back to Fluorine Binding Sites List in 7gjn
Fluorine binding site 3 out of 4 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 Edj-Med-37AAC4BD-4 (Mpro-P0602)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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 Edj-Med-37AAC4BD-4 (Mpro-P0602) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:45.5
occ:0.52
 F1 B:QP6404 0.0 45.5 0.5
C7 B:QP6404 1.4 45.0 0.5
C6 B:QP6404 2.3 44.8 0.5
C8 B:QP6404 2.3 44.4 0.5
CD2 B:HIS41 3.2 49.4 1.0
CB B:MET165 3.5 45.4 1.0
O B:HIS164 3.5 43.2 1.0
C5 B:QP6404 3.6 45.0 0.5
C9 B:QP6404 3.6 44.2 0.5
CB B:ASP187 3.7 49.8 1.0
CA B:ASP187 3.7 50.9 1.0
NE2 B:HIS41 3.8 50.5 1.0
C B:HIS164 3.9 43.0 1.0
CG B:MET165 4.0 50.9 1.0
SD B:MET165 4.1 63.1 1.0
C4 B:QP6404 4.1 44.6 0.5
CG B:HIS41 4.1 48.4 1.0
C B:ASP187 4.1 54.8 1.0
CB B:HIS164 4.2 42.6 1.0
O B:ASP187 4.3 55.5 1.0
CA B:MET165 4.4 43.3 1.0
N B:MET165 4.4 42.8 1.0
CA B:HIS164 4.6 42.1 1.0
CB B:HIS41 4.6 46.6 1.0
F B:QP6404 4.7 45.2 0.5
CE B:MET165 4.7 61.5 1.0
O B:HOH508 4.8 35.2 1.0
CE1 B:HIS41 4.8 50.7 1.0
N B:ARG188 4.8 57.2 1.0
C1 B:QP6404 4.9 43.4 0.5
O B:VAL186 4.9 48.2 1.0
C B:QP6404 5.0 43.2 0.5
N B:ASP187 5.0 48.9 1.0
ND1 B:HIS41 5.0 50.2 1.0

Fluorine binding site 4 out of 4 in 7gjn

Go back to Fluorine Binding Sites List in 7gjn
Fluorine binding site 4 out of 4 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 Edj-Med-37AAC4BD-4 (Mpro-P0602)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 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 Edj-Med-37AAC4BD-4 (Mpro-P0602) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:45.2
occ:0.52
 F B:QP6404 0.0 45.2 0.5
C5 B:QP6404 1.4 45.0 0.5
C6 B:QP6404 2.3 44.8 0.5
C4 B:QP6404 2.4 44.6 0.5
O1 B:QP6404 2.6 44.7 0.5
N B:GLN189 2.9 63.7 1.0
C B:ARG188 3.0 62.2 1.0
CA B:GLN189 3.1 65.2 1.0
O B:ARG188 3.2 62.0 1.0
CB B:GLN189 3.5 67.3 1.0
C7 B:QP6404 3.6 45.0 0.5
C9 B:QP6404 3.6 44.2 0.5
OE1 B:GLN189 3.7 78.1 1.0
CA B:ARG188 3.9 60.2 1.0
C3 B:QP6404 4.0 44.3 0.5
C8 B:QP6404 4.1 44.4 0.5
N B:ARG188 4.1 57.2 1.0
CD B:GLN189 4.3 76.4 1.0
CG B:GLN189 4.5 71.1 1.0
C B:GLN189 4.5 66.1 1.0
C B:ASP187 4.5 54.8 1.0
O B:ASP187 4.6 55.5 1.0
F1 B:QP6404 4.7 45.5 0.5
C1 B:QP6404 4.9 43.4 0.5
C2 B:QP6404 4.9 43.7 0.5
N B:THR190 4.9 65.9 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: Tue Jul 15 20:13:27 2025

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