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Fluorine in PDB 7gil: 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 Ral-Tha-2D450E86-6 (Mpro-P0108)

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 Ral-Tha-2D450E86-6 (Mpro-P0108)

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 Ral-Tha-2D450E86-6 (Mpro-P0108):
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 Ral-Tha-2D450E86-6 (Mpro-P0108), PDB code: 7gil 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) 71.01 / 2.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.19, 98.26, 102.73, 90, 90, 90
R / Rfree (%) 23.6 / 28.7

Other elements in 7gil:

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 Ral-Tha-2D450E86-6 (Mpro-P0108) 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 Ral-Tha-2D450E86-6 (Mpro-P0108) (pdb code 7gil). 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 Ral-Tha-2D450E86-6 (Mpro-P0108), PDB code: 7gil:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7gil

Go back to Fluorine Binding Sites List in 7gil
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 Ral-Tha-2D450E86-6 (Mpro-P0108)


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 Ral-Tha-2D450E86-6 (Mpro-P0108) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:64.2
occ:1.00
 F A:QH6404 0.0 64.2 1.0
C A:QH6404 1.4 64.1 1.0
C1 A:QH6404 2.4 63.7 1.0
C16 A:QH6404 2.4 64.2 1.0
CL A:QH6404 2.9 65.0 1.0
C A:ARG188 3.1 53.9 1.0
O A:ARG188 3.2 53.5 1.0
N A:GLN189 3.3 55.9 1.0
CE A:MET49 3.4 78.0 1.0
C2 A:QH6404 3.6 63.1 1.0
C15 A:QH6404 3.6 63.5 1.0
CE A:MET165 3.6 60.9 1.0
N A:ARG188 3.7 50.5 1.0
CA A:GLN189 3.7 58.6 1.0
CA A:ARG188 3.7 52.2 1.0
OE1 A:GLN189 4.0 77.0 1.0
CG A:GLN189 4.1 67.9 1.0
C3 A:QH6404 4.1 63.0 1.0
C A:ASP187 4.1 49.4 1.0
CB A:GLN189 4.4 61.5 1.0
CG A:MET49 4.4 78.8 1.0
CD A:GLN189 4.5 75.8 1.0
O A:ASP187 4.6 49.4 1.0
SD A:MET49 4.6 82.3 1.0
SD A:MET165 4.7 60.6 1.0
CA A:ASP187 4.7 47.9 1.0
O A:DMS403 4.8 86.0 1.0
S A:DMS403 4.9 86.3 1.0
O A:MET49 4.9 73.3 1.0

Fluorine binding site 2 out of 2 in 7gil

Go back to Fluorine Binding Sites List in 7gil
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 Ral-Tha-2D450E86-6 (Mpro-P0108)


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 Ral-Tha-2D450E86-6 (Mpro-P0108) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:90.7
occ:1.00
 F B:QH6403 0.0 90.7 1.0
C B:QH6403 1.4 90.7 1.0
C1 B:QH6403 2.4 90.6 1.0
C16 B:QH6403 2.4 90.7 1.0
C B:ARG188 2.9 64.2 1.0
CL B:QH6403 2.9 91.0 1.0
O B:ARG188 3.0 64.1 1.0
N B:ARG188 3.2 59.4 1.0
N B:GLN189 3.3 65.7 1.0
CA B:ARG188 3.3 62.1 1.0
CE B:MET49 3.6 94.9 1.0
C2 B:QH6403 3.6 90.5 1.0
C15 B:QH6403 3.6 90.5 1.0
C B:ASP187 3.7 56.9 1.0
CA B:GLN189 3.8 67.2 1.0
C3 B:QH6403 4.1 90.3 1.0
O B:ASP187 4.2 57.6 1.0
CA B:ASP187 4.3 53.2 1.0
CG B:MET49 4.4 97.3 1.0
SD B:MET165 4.4 59.3 1.0
CE B:MET165 4.6 56.4 1.0
CB B:GLN189 4.6 69.5 1.0
O B:HOH592 4.6 52.5 1.0
SD B:MET49 4.6 98.5 1.0
OE1 B:GLN189 4.7 81.5 1.0
O B:VAL186 4.7 50.1 1.0
CB B:ARG188 4.9 64.4 1.0
NE2 B:GLN192 4.9 59.3 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 20:12:56 2025

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