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Fluorine in PDB 7gfc: 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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616)

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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616)

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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616):
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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616), PDB code: 7gfc 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) 55.67 / 2.23
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.79, 53.422, 44.876, 90, 101.89, 90
R / Rfree (%) 18.5 / 25.3

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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616) (pdb code 7gfc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616), PDB code: 7gfc:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7gfc

Go back to Fluorine Binding Sites List in 7gfc
Fluorine binding site 1 out of 3 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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616)


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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:46.7
occ:0.70
 F A:O87404 0.0 46.7 0.7
C A:O87404 1.3 46.4 0.7
F1 A:O87404 2.1 46.9 0.7
F2 A:O87404 2.1 46.8 0.7
C1 A:O87404 2.3 45.3 0.7
C2 A:O87404 2.8 45.0 0.7
O A:ASP187 2.9 46.6 1.0
C A:ASP187 3.0 46.8 1.0
OH A:TYR54 3.0 53.0 1.0
CB A:ASP187 3.4 44.0 1.0
CB A:HIS41 3.5 38.1 1.0
C6 A:O87404 3.5 44.4 0.7
CA A:ASP187 3.5 44.8 1.0
N A:ARG188 3.6 48.8 1.0
ND1 A:HIS41 3.8 42.5 1.0
CG A:HIS41 3.9 40.3 1.0
CA A:ARG188 4.1 50.9 1.0
C3 A:O87404 4.2 44.6 0.7
CG A:ASP187 4.3 44.9 1.0
CZ A:TYR54 4.4 52.7 1.0
OD2 A:ASP187 4.5 46.5 1.0
C A:ARG188 4.5 52.4 1.0
C5 A:O87404 4.6 43.6 0.7
O A:HOH521 4.6 24.8 1.0
CE1 A:HIS41 4.8 42.7 1.0
CA A:HIS41 4.8 37.9 1.0
N A:GLN189 4.9 54.2 1.0
C4 A:O87404 4.9 44.2 0.7
CD2 A:HIS41 4.9 41.2 1.0
N A:ASP187 4.9 44.1 1.0

Fluorine binding site 2 out of 3 in 7gfc

Go back to Fluorine Binding Sites List in 7gfc
Fluorine binding site 2 out of 3 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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616)


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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:46.9
occ:0.70
 F1 A:O87404 0.0 46.9 0.7
C A:O87404 1.3 46.4 0.7
F A:O87404 2.1 46.7 0.7
F2 A:O87404 2.1 46.8 0.7
C1 A:O87404 2.3 45.3 0.7
C A:ARG188 2.9 52.4 1.0
N A:GLN189 2.9 54.2 1.0
C2 A:O87404 3.0 45.0 0.7
CA A:ARG188 3.1 50.9 1.0
N A:ARG188 3.2 48.8 1.0
C6 A:O87404 3.3 44.4 0.7
C A:ASP187 3.4 46.8 1.0
O A:ARG188 3.4 51.9 1.0
O A:ASP187 3.7 46.6 1.0
CA A:GLN189 3.7 56.0 1.0
O A:MET49 4.0 69.5 1.0
CB A:GLN189 4.1 58.4 1.0
CA A:ASP187 4.3 44.8 1.0
C3 A:O87404 4.3 44.6 0.7
C5 A:O87404 4.6 43.6 0.7
CE A:MET165 4.6 50.2 1.0
CB A:ARG188 4.6 53.3 1.0
OH A:TYR54 4.7 53.0 1.0
CB A:ASP187 4.9 44.0 1.0
C4 A:O87404 5.0 44.2 0.7

Fluorine binding site 3 out of 3 in 7gfc

Go back to Fluorine Binding Sites List in 7gfc
Fluorine binding site 3 out of 3 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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 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 Eri-Ucb-A0B0DBCB-4 (Mpro-X11616) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:46.8
occ:0.70
 F2 A:O87404 0.0 46.8 0.7
C A:O87404 1.3 46.4 0.7
F1 A:O87404 2.1 46.9 0.7
F A:O87404 2.1 46.7 0.7
C1 A:O87404 2.4 45.3 0.7
C6 A:O87404 2.7 44.4 0.7
C2 A:O87404 3.6 45.0 0.7
CE A:MET165 3.7 50.2 1.0
C A:ASP187 3.7 46.8 1.0
N A:ARG188 3.8 48.8 1.0
CA A:ASP187 3.8 44.8 1.0
SD A:MET165 3.9 50.0 1.0
CB A:MET165 4.0 41.5 1.0
ND1 A:HIS41 4.0 42.5 1.0
CB A:ASP187 4.1 44.0 1.0
C5 A:O87404 4.1 43.6 0.7
O A:ASP187 4.3 46.6 1.0
C A:ARG188 4.3 52.4 1.0
O A:ARG188 4.3 51.9 1.0
CA A:ARG188 4.5 50.9 1.0
CE1 A:HIS41 4.6 42.7 1.0
O A:HIS164 4.6 38.4 1.0
CG A:HIS41 4.6 40.3 1.0
CG A:MET165 4.6 44.2 1.0
N A:GLN189 4.7 54.2 1.0
C3 A:O87404 4.8 44.6 0.7
C10 A:O87404 4.8 41.5 0.7
CB A:HIS41 4.8 38.1 1.0
C4 A:O87404 4.9 44.2 0.7
N A:O87404 5.0 42.2 0.7
O A:VAL186 5.0 44.8 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: Fri Aug 2 07:36:20 2024

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