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Fluorine in PDB 7gi9: 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 Ral-Tha-2D450E86-26 (Mpro-P0061)

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 Ral-Tha-2D450E86-26 (Mpro-P0061)

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 Ral-Tha-2D450E86-26 (Mpro-P0061):
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 Ral-Tha-2D450E86-26 (Mpro-P0061), PDB code: 7gi9 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) 71.52 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.32, 98.94, 103.49, 90, 90, 90
R / Rfree (%) 23.9 / 28.2

Other elements in 7gi9:

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 Ral-Tha-2D450E86-26 (Mpro-P0061) 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 Ral-Tha-2D450E86-26 (Mpro-P0061) (pdb code 7gi9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 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 Ral-Tha-2D450E86-26 (Mpro-P0061), PDB code: 7gi9:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7gi9

Go back to Fluorine Binding Sites List in 7gi9
Fluorine binding site 1 out of 4 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 Ral-Tha-2D450E86-26 (Mpro-P0061)


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 Ral-Tha-2D450E86-26 (Mpro-P0061) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:51.2
occ:1.00
 F1 A:QDU404 0.0 51.2 1.0
C3 A:QDU404 1.4 50.4 1.0
C4 A:QDU404 2.3 49.1 1.0
C2 A:QDU404 2.3 50.3 1.0
C5 A:QDU404 2.8 47.5 1.0
NE2 A:GLN189 2.9 72.7 1.0
O A:QDU404 3.3 46.3 1.0
C6 A:QDU404 3.3 46.5 1.0
C16 A:QDU404 3.6 49.5 1.0
C1 A:QDU404 3.6 50.3 1.0
CD A:GLN189 3.8 70.7 1.0
CG A:GLN189 3.9 64.5 1.0
C A:QDU404 4.0 50.3 1.0
O A:DMS403 4.2 86.1 1.0
N A:QDU404 4.5 45.3 1.0
O A:HOH679 4.9 56.0 1.0
CE A:MET49 4.9 72.4 1.0

Fluorine binding site 2 out of 4 in 7gi9

Go back to Fluorine Binding Sites List in 7gi9
Fluorine binding site 2 out of 4 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 Ral-Tha-2D450E86-26 (Mpro-P0061)


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 Ral-Tha-2D450E86-26 (Mpro-P0061) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:50.6
occ:1.00
 F A:QDU404 0.0 50.6 1.0
C A:QDU404 1.4 50.3 1.0
C16 A:QDU404 2.3 49.5 1.0
C1 A:QDU404 2.3 50.3 1.0
CA A:ASP187 3.3 44.2 1.0
CB A:ASP187 3.3 43.8 1.0
C2 A:QDU404 3.6 50.3 1.0
CD2 A:HIS41 3.6 41.5 1.0
C4 A:QDU404 3.6 49.1 1.0
CB A:MET165 3.7 38.7 1.0
C A:ASP187 3.8 45.6 1.0
SD A:MET165 3.9 55.0 1.0
O A:HIS164 3.9 37.5 1.0
C3 A:QDU404 4.1 50.4 1.0
CE A:MET165 4.1 50.9 1.0
NE2 A:HIS41 4.2 43.1 1.0
CG A:MET165 4.2 43.4 1.0
N A:ARG188 4.2 46.5 1.0
CG A:HIS41 4.2 40.3 1.0
CE A:MET49 4.4 72.4 1.0
O A:ASP187 4.4 46.3 1.0
C A:HIS164 4.5 36.4 1.0
O A:VAL186 4.5 44.7 1.0
N A:ASP187 4.6 44.0 1.0
CB A:HIS41 4.6 38.4 1.0
CB A:HIS164 4.7 34.4 1.0
CA A:MET165 4.8 37.4 1.0
CG A:ASP187 4.8 44.2 1.0
C5 A:QDU404 4.9 47.5 1.0
O A:HOH536 4.9 29.8 1.0
CE1 A:HIS41 4.9 42.9 1.0
N A:MET165 4.9 36.4 1.0
C A:VAL186 5.0 44.0 1.0
ND1 A:HIS41 5.0 42.1 1.0

Fluorine binding site 3 out of 4 in 7gi9

Go back to Fluorine Binding Sites List in 7gi9
Fluorine binding site 3 out of 4 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 Ral-Tha-2D450E86-26 (Mpro-P0061)


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 Ral-Tha-2D450E86-26 (Mpro-P0061) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:51.4
occ:1.00
 F1 B:QDU403 0.0 51.4 1.0
C3 B:QDU403 1.4 50.9 1.0
C4 B:QDU403 2.3 50.2 1.0
C2 B:QDU403 2.3 50.8 1.0
C5 B:QDU403 2.8 49.1 1.0
O B:HOH575 3.0 54.7 1.0
NE2 B:GLN189 3.2 60.2 1.0
O B:QDU403 3.3 46.6 1.0
C6 B:QDU403 3.4 47.8 1.0
C16 B:QDU403 3.6 50.4 1.0
C1 B:QDU403 3.6 50.5 1.0
C B:QDU403 4.1 50.6 1.0
CD B:GLN189 4.5 60.3 1.0
N B:QDU403 4.5 47.6 1.0

Fluorine binding site 4 out of 4 in 7gi9

Go back to Fluorine Binding Sites List in 7gi9
Fluorine binding site 4 out of 4 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 Ral-Tha-2D450E86-26 (Mpro-P0061)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 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 Ral-Tha-2D450E86-26 (Mpro-P0061) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:50.7
occ:1.00
 F B:QDU403 0.0 50.7 1.0
C B:QDU403 1.4 50.6 1.0
C16 B:QDU403 2.3 50.4 1.0
C1 B:QDU403 2.3 50.5 1.0
CA B:ASP187 3.2 40.3 1.0
CB B:ASP187 3.4 40.8 1.0
C B:ASP187 3.5 43.2 1.0
C2 B:QDU403 3.6 50.8 1.0
C4 B:QDU403 3.6 50.2 1.0
N B:ARG188 3.6 44.8 1.0
CE B:MET49 3.8 60.2 1.0
SD B:MET165 3.8 55.7 1.0
CB B:MET165 3.8 39.1 1.0
CD2 B:HIS41 3.9 43.7 1.0
C3 B:QDU403 4.1 50.9 1.0
O B:ASP187 4.2 43.5 1.0
O B:HIS164 4.2 36.0 1.0
CG B:MET165 4.3 43.8 1.0
O B:VAL186 4.3 37.2 1.0
CE B:MET165 4.4 55.6 1.0
N B:ASP187 4.4 38.3 1.0
NE2 B:HIS41 4.5 45.4 1.0
CG B:HIS41 4.5 42.7 1.0
CA B:ARG188 4.6 47.3 1.0
C B:HIS164 4.7 35.8 1.0
C B:VAL186 4.8 37.5 1.0
CB B:HIS164 4.8 33.8 1.0
O B:ARG188 4.8 48.4 1.0
CG B:ASP187 4.8 42.0 1.0
CB B:HIS41 4.8 40.3 1.0
C5 B:QDU403 4.9 49.1 1.0
C B:ARG188 4.9 48.8 1.0
CA B:MET165 5.0 37.4 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 20:12:13 2025

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