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Fluorine in PDB 7ghd: 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 Bar-Com-4E090D3A-57 (Mpro-X3298)

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 Bar-Com-4E090D3A-57 (Mpro-X3298)

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 Bar-Com-4E090D3A-57 (Mpro-X3298):
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 Bar-Com-4E090D3A-57 (Mpro-X3298), PDB code: 7ghd 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) 54.97 / 1.97
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.55, 53.06, 45.338, 90, 102.35, 90
R / Rfree (%) 19.1 / 23.4

Other elements in 7ghd:

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 Bar-Com-4E090D3A-57 (Mpro-X3298) 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 Bar-Com-4E090D3A-57 (Mpro-X3298) (pdb code 7ghd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was 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 Bar-Com-4E090D3A-57 (Mpro-X3298), PDB code: 7ghd:

Fluorine binding site 1 out of 1 in 7ghd

Go back to Fluorine Binding Sites List in 7ghd
Fluorine binding site 1 out of 1 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 Bar-Com-4E090D3A-57 (Mpro-X3298)


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 Bar-Com-4E090D3A-57 (Mpro-X3298) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:77.6
occ:0.88
 F A:Q5K1001 0.0 77.6 0.9
C11 A:Q5K1001 1.4 77.4 0.9
C12 A:Q5K1001 2.3 77.3 0.9
C10 A:Q5K1001 2.3 77.3 0.9
CB A:MET165 3.3 50.5 1.0
CB A:ASP187 3.4 53.6 1.0
O A:HIS164 3.5 47.5 1.0
CA A:ASP187 3.6 53.0 1.0
C13 A:Q5K1001 3.6 77.2 0.9
C9 A:Q5K1001 3.6 77.3 0.9
CG A:MET165 3.6 54.0 1.0
ND1 A:HIS41 3.7 48.0 1.0
SD A:MET165 3.7 63.0 1.0
C A:HIS164 3.8 47.1 1.0
CE1 A:HIS41 3.9 48.7 1.0
CB A:HIS164 3.9 44.4 1.0
C8 A:Q5K1001 4.1 77.3 0.9
N A:MET165 4.2 48.3 1.0
C A:ASP187 4.2 55.2 1.0
CA A:MET165 4.2 49.6 1.0
CA A:HIS164 4.4 45.1 1.0
CE A:MET49 4.5 59.8 1.0
CG A:HIS41 4.5 45.5 1.0
CZ A:PHE181 4.6 45.1 1.0
O A:HOH1117 4.6 41.4 1.0
N A:ARG188 4.7 56.9 1.0
O A:ASP187 4.7 55.0 1.0
NE2 A:HIS41 4.7 48.4 1.0
N A:ASP187 4.8 52.1 1.0
ND1 A:HIS164 4.9 46.3 1.0
CG A:ASP187 4.9 57.1 1.0
O A:VAL186 4.9 52.6 1.0
CG A:HIS164 4.9 45.0 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 20:11:39 2025

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