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Fluorine in PDB 7gdf: 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 Jag-Ucb-A3EF7265-23 (Mpro-X10995)

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 Jag-Ucb-A3EF7265-23 (Mpro-X10995)

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 Jag-Ucb-A3EF7265-23 (Mpro-X10995):
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 Jag-Ucb-A3EF7265-23 (Mpro-X10995), PDB code: 7gdf 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 / 1.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.471, 53.31, 44.703, 90, 101.59, 90
R / Rfree (%) 18.4 / 23.1

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 Jag-Ucb-A3EF7265-23 (Mpro-X10995) (pdb code 7gdf). 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 Jag-Ucb-A3EF7265-23 (Mpro-X10995), PDB code: 7gdf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7gdf

Go back to Fluorine Binding Sites List in 7gdf
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 Jag-Ucb-A3EF7265-23 (Mpro-X10995)


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 Jag-Ucb-A3EF7265-23 (Mpro-X10995) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:58.8
occ:0.80
 F2 A:M6U404 0.0 58.8 0.8
C14 A:M6U404 1.3 58.4 0.8
F1 A:M6U404 2.1 58.8 0.8
F A:M6U404 2.2 58.3 0.8
C13 A:M6U404 2.3 57.5 0.8
C A:ASP187 2.8 34.9 1.0
C12 A:M6U404 2.8 57.1 0.8
N A:ARG188 2.8 37.6 1.0
CA A:ASP187 3.0 32.4 1.0
SD A:MET165 3.3 54.3 1.0
N2 A:M6U404 3.4 56.5 0.8
O A:ASP187 3.5 34.5 1.0
C A:ARG188 3.5 42.3 1.0
O A:ARG188 3.5 42.0 1.0
CG A:MET165 3.5 41.3 1.0
CA A:ARG188 3.6 40.6 1.0
CB A:ASP187 3.6 30.7 1.0
O A:VAL186 4.1 33.0 1.0
N A:GLN189 4.1 44.0 1.0
C11 A:M6U404 4.2 56.7 0.8
N A:ASP187 4.3 32.1 1.0
CE A:MET49 4.5 69.8 1.0
C9 A:M6U404 4.6 55.6 0.8
C A:VAL186 4.7 32.8 1.0
CB A:MET165 4.7 36.1 1.0
C10 A:M6U404 4.9 56.3 0.8
CA A:GLN189 4.9 45.9 1.0
CE A:MET165 4.9 53.0 1.0
OH A:TYR54 4.9 38.3 1.0

Fluorine binding site 2 out of 3 in 7gdf

Go back to Fluorine Binding Sites List in 7gdf
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 Jag-Ucb-A3EF7265-23 (Mpro-X10995)


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 Jag-Ucb-A3EF7265-23 (Mpro-X10995) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:58.3
occ:0.80
 F A:M6U404 0.0 58.3 0.8
C14 A:M6U404 1.3 58.4 0.8
F1 A:M6U404 2.1 58.8 0.8
F2 A:M6U404 2.2 58.8 0.8
C13 A:M6U404 2.4 57.5 0.8
CE A:MET49 2.8 69.8 1.0
N2 A:M6U404 3.2 56.5 0.8
C12 A:M6U404 3.2 57.1 0.8
O A:ASP187 3.3 34.5 1.0
C A:ASP187 3.4 34.9 1.0
SD A:MET49 3.4 72.5 1.0
OH A:TYR54 3.4 38.3 1.0
CB A:HIS41 3.5 30.1 1.0
CB A:ASP187 3.6 30.7 1.0
CG A:HIS41 3.7 33.2 1.0
ND1 A:HIS41 3.8 36.0 1.0
CA A:ASP187 3.8 32.4 1.0
N A:ARG188 4.0 37.6 1.0
C9 A:M6U404 4.3 55.6 0.8
C11 A:M6U404 4.4 56.7 0.8
CA A:ARG188 4.5 40.6 1.0
CD2 A:HIS41 4.6 34.8 1.0
CE1 A:HIS41 4.6 36.5 1.0
CG A:ASP187 4.7 30.8 1.0
CZ A:TYR54 4.8 37.3 1.0
C A:ARG188 4.8 42.3 1.0
O A:HOH579 4.8 20.1 1.0
C10 A:M6U404 4.9 56.3 0.8
CG A:MET49 4.9 62.8 1.0
CA A:HIS41 4.9 29.4 1.0
CG A:MET165 4.9 41.3 1.0
OD2 A:ASP187 5.0 31.6 1.0

Fluorine binding site 3 out of 3 in 7gdf

Go back to Fluorine Binding Sites List in 7gdf
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 Jag-Ucb-A3EF7265-23 (Mpro-X10995)


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 Jag-Ucb-A3EF7265-23 (Mpro-X10995) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:58.8
occ:0.80
 F1 A:M6U404 0.0 58.8 0.8
C14 A:M6U404 1.3 58.4 0.8
F2 A:M6U404 2.1 58.8 0.8
F A:M6U404 2.1 58.3 0.8
C13 A:M6U404 2.4 57.5 0.8
N2 A:M6U404 2.6 56.5 0.8
CG A:MET165 3.0 41.3 1.0
ND1 A:HIS41 3.2 36.0 1.0
CB A:ASP187 3.6 30.7 1.0
C12 A:M6U404 3.6 57.1 0.8
CE1 A:HIS41 3.6 36.5 1.0
O A:HIS164 3.7 31.1 1.0
CA A:ASP187 3.8 32.4 1.0
SD A:MET165 3.9 54.3 1.0
CG A:HIS41 3.9 33.2 1.0
C9 A:M6U404 4.0 55.6 0.8
C A:ASP187 4.2 34.9 1.0
CB A:MET165 4.2 36.1 1.0
C A:HIS164 4.3 30.7 1.0
CB A:HIS41 4.4 30.1 1.0
NE2 A:HIS41 4.4 36.3 1.0
CA A:MET165 4.5 34.0 1.0
CD2 A:HIS41 4.5 34.8 1.0
O A:HOH579 4.6 20.1 1.0
O A:ASP187 4.6 34.5 1.0
CB A:HIS164 4.6 27.8 1.0
N A:MET165 4.7 32.1 1.0
N A:ARG188 4.7 37.6 1.0
C11 A:M6U404 4.7 56.7 0.8
C8 A:M6U404 4.8 54.2 0.8
C10 A:M6U404 4.9 56.3 0.8
CE A:MET49 4.9 69.8 1.0
O A:M6U404 5.0 52.2 0.8
CG A:ASP187 5.0 30.8 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: Tue Jul 15 20:10:38 2025

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