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Fluorine in PDB 7gm4: 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 Alp-Pos-6F6AE286-5 (Mpro-P2080)

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 Alp-Pos-6F6AE286-5 (Mpro-P2080)

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 Alp-Pos-6F6AE286-5 (Mpro-P2080):
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 Alp-Pos-6F6AE286-5 (Mpro-P2080), PDB code: 7gm4 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) 33.97 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.946, 100.546, 104.545, 90, 90, 90
R / Rfree (%) 23 / 26.4

Other elements in 7gm4:

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 Alp-Pos-6F6AE286-5 (Mpro-P2080) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

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 Alp-Pos-6F6AE286-5 (Mpro-P2080) (pdb code 7gm4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 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 Alp-Pos-6F6AE286-5 (Mpro-P2080), PDB code: 7gm4:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7gm4

Go back to Fluorine Binding Sites List in 7gm4
Fluorine binding site 1 out of 2 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 Alp-Pos-6F6AE286-5 (Mpro-P2080)


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 Alp-Pos-6F6AE286-5 (Mpro-P2080) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:29.8
occ:0.94
 F A:RGQ407 0.0 29.8 0.9
C11 A:RGQ407 1.4 29.6 0.9
C10 A:RGQ407 2.3 29.2 0.9
C12 A:RGQ407 2.3 29.6 0.9
O A:HOH644 2.9 34.5 1.0
C13 A:RGQ407 3.6 29.4 0.9
C9 A:RGQ407 3.6 29.0 0.9
C14 A:RGQ407 4.1 29.2 0.9
N A:ASN142 4.3 27.4 1.0
OE2 A:GLU166 4.4 36.1 1.0
C A:RGQ407 4.6 34.0 0.9
N B:SER1 4.7 29.4 1.0
CA A:LEU141 4.7 27.0 1.0
C A:LEU141 4.8 27.2 1.0
OE1 A:GLU166 4.8 34.3 1.0
C8 A:RGQ407 4.8 28.9 0.9
CD A:GLU166 4.8 33.1 1.0
CB A:ASN142 4.8 29.9 1.0
CA A:ASN142 5.0 27.4 1.0

Fluorine binding site 2 out of 2 in 7gm4

Go back to Fluorine Binding Sites List in 7gm4
Fluorine binding site 2 out of 2 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 Alp-Pos-6F6AE286-5 (Mpro-P2080)


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 Alp-Pos-6F6AE286-5 (Mpro-P2080) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F405

b:38.9
occ:0.94
 F B:RGQ405 0.0 38.9 0.9
C11 B:RGQ405 1.4 39.0 0.9
C10 B:RGQ405 2.3 38.9 0.9
C12 B:RGQ405 2.3 39.0 0.9
O A:HOH592 2.9 31.6 1.0
C13 B:RGQ405 3.6 38.9 0.9
C9 B:RGQ405 3.6 38.8 0.9
C14 B:RGQ405 4.1 38.9 0.9
N B:ASN142 4.2 30.6 1.0
OE2 B:GLU166 4.4 36.7 1.0
N A:SER1 4.4 31.0 1.0
CA B:LEU141 4.6 29.8 1.0
C B:LEU141 4.7 30.2 1.0
OE1 B:GLU166 4.7 33.6 1.0
C8 B:RGQ405 4.8 38.6 0.9
CD B:GLU166 4.8 34.4 1.0
CB B:ASN142 4.9 33.2 1.0
CA B:ASN142 5.0 31.2 1.0
O B:PHE140 5.0 28.8 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 20:15:00 2025

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