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Fluorine in PDB 7gd2: 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-0F94FC3D-3 (Mpro-X10862)

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-0F94FC3D-3 (Mpro-X10862)

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-0F94FC3D-3 (Mpro-X10862):
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-0F94FC3D-3 (Mpro-X10862), PDB code: 7gd2 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) 55.58 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.545, 53.266, 44.619, 90, 101.79, 90
R / Rfree (%) 18.6 / 21.2

Other elements in 7gd2:

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-0F94FC3D-3 (Mpro-X10862) also contains other interesting chemical elements:

Bromine (Br) 2 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 Bar-Com-0F94FC3D-3 (Mpro-X10862) (pdb code 7gd2). 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 Bar-Com-0F94FC3D-3 (Mpro-X10862), PDB code: 7gd2:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7gd2

Go back to Fluorine Binding Sites List in 7gd2
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 Bar-Com-0F94FC3D-3 (Mpro-X10862)


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-0F94FC3D-3 (Mpro-X10862) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:40.0
occ:0.40
 F A:M26404 0.0 40.0 0.4
F A:M26404 0.0 43.2 0.5
C10 A:M26404 1.4 39.8 0.4
C10 A:M26404 1.4 43.0 0.5
C11 A:M26404 2.3 39.7 0.4
C9 A:M26404 2.3 39.7 0.4
C9 A:M26404 2.4 42.9 0.5
C11 A:M26404 2.4 42.9 0.5
CB A:ASN142 3.3 36.0 1.0
CG A:ASN142 3.4 42.4 1.0
OD1 A:ASN142 3.5 45.4 1.0
C A:M26404 3.5 43.6 0.4
C8 A:M26404 3.6 39.6 0.4
C12 A:M26404 3.6 39.6 0.4
C8 A:M26404 3.6 42.7 0.5
C12 A:M26404 3.6 42.8 0.5
C A:M26404 3.7 48.8 0.5
O A:M26404 3.9 43.8 0.4
CA A:ASN142 3.9 33.5 1.0
O A:M26404 4.0 48.8 0.5
C7 A:M26404 4.1 39.5 0.4
C7 A:M26404 4.1 42.6 0.5
ND2 A:ASN142 4.2 44.5 1.0
N A:ASN142 4.3 33.4 1.0
C5 A:M26404 5.0 39.7 0.4

Fluorine binding site 2 out of 2 in 7gd2

Go back to Fluorine Binding Sites List in 7gd2
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 Bar-Com-0F94FC3D-3 (Mpro-X10862)


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 Bar-Com-0F94FC3D-3 (Mpro-X10862) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:43.2
occ:0.50
 F A:M26404 0.0 43.2 0.5
F A:M26404 0.0 40.0 0.4
C10 A:M26404 1.3 39.8 0.4
C10 A:M26404 1.4 43.0 0.5
C11 A:M26404 2.3 39.7 0.4
C9 A:M26404 2.3 39.7 0.4
C11 A:M26404 2.3 42.9 0.5
C9 A:M26404 2.3 42.9 0.5
CB A:ASN142 3.3 36.0 1.0
CG A:ASN142 3.4 42.4 1.0
OD1 A:ASN142 3.5 45.4 1.0
C A:M26404 3.5 43.6 0.4
C12 A:M26404 3.6 39.6 0.4
C8 A:M26404 3.6 39.6 0.4
C8 A:M26404 3.6 42.7 0.5
C12 A:M26404 3.6 42.8 0.5
C A:M26404 3.7 48.8 0.5
O A:M26404 3.9 43.8 0.4
CA A:ASN142 3.9 33.5 1.0
O A:M26404 4.1 48.8 0.5
C7 A:M26404 4.1 39.5 0.4
C7 A:M26404 4.1 42.6 0.5
ND2 A:ASN142 4.2 44.5 1.0
N A:ASN142 4.3 33.4 1.0
C5 A:M26404 5.0 39.7 0.4
C5 A:M26404 5.0 42.9 0.5

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: Fri Aug 2 07:34:37 2024

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