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Fluorine in PDB 7gkn: 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-611D11E7-4 (Mpro-P0978)

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-611D11E7-4 (Mpro-P0978)

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-611D11E7-4 (Mpro-P0978):
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-611D11E7-4 (Mpro-P0978), PDB code: 7gkn 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) 71.51 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.3, 99, 103.4, 90, 90, 90
R / Rfree (%) 23.8 / 27.4

Other elements in 7gkn:

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-611D11E7-4 (Mpro-P0978) 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 Edj-Med-611D11E7-4 (Mpro-P0978) (pdb code 7gkn). 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 Edj-Med-611D11E7-4 (Mpro-P0978), PDB code: 7gkn:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7gkn

Go back to Fluorine Binding Sites List in 7gkn
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 Edj-Med-611D11E7-4 (Mpro-P0978)


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-611D11E7-4 (Mpro-P0978) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:49.2
occ:1.00
 F A:QYI407 0.0 49.2 1.0
C17 A:QYI407 1.4 48.3 1.0
C18 A:QYI407 2.3 47.5 1.0
C16 A:QYI407 2.3 47.8 1.0
ND2 A:ASN142 3.1 56.0 1.0
O A:DMS410 3.6 114.7 1.0
C15 A:QYI407 3.6 47.1 1.0
C19 A:QYI407 3.6 46.2 1.0
CG A:ASN142 4.1 53.5 1.0
C14 A:QYI407 4.1 46.2 1.0
C1 A:DMS410 4.3 114.8 1.0
CB A:ASN142 4.4 45.5 1.0
S A:DMS410 4.5 114.7 1.0
O A:HOH645 4.6 47.8 1.0
C11 A:QYI407 4.8 45.6 1.0
CA A:ASN142 5.0 41.4 1.0

Fluorine binding site 2 out of 2 in 7gkn

Go back to Fluorine Binding Sites List in 7gkn
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 Edj-Med-611D11E7-4 (Mpro-P0978)


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-611D11E7-4 (Mpro-P0978) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:56.7
occ:1.00
 F B:QYI404 0.0 56.7 1.0
C17 B:QYI404 1.4 56.3 1.0
C18 B:QYI404 2.3 55.7 1.0
C16 B:QYI404 2.3 56.2 1.0
C15 B:QYI404 3.6 56.0 1.0
C19 B:QYI404 3.6 55.2 1.0
C14 B:QYI404 4.1 55.4 1.0
O B:HOH601 4.2 54.6 1.0
O B:HOH582 4.4 54.6 1.0
CB B:ASN142 4.7 50.6 1.0
C11 B:QYI404 4.8 54.6 1.0
CG B:ASN142 5.0 56.0 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 20:14:35 2025

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