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Fluorine in PDB 7gkl: 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 Sam-Unk-2684B532-12 (Mpro-P0925)

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 Sam-Unk-2684B532-12 (Mpro-P0925)

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 Sam-Unk-2684B532-12 (Mpro-P0925):
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 Sam-Unk-2684B532-12 (Mpro-P0925), PDB code: 7gkl 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) 71.72 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.34, 99.58, 103.38, 90, 90, 90
R / Rfree (%) 23.9 / 27.7

Other elements in 7gkl:

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 Sam-Unk-2684B532-12 (Mpro-P0925) also contains other interesting chemical elements:

Chlorine (Cl) 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 Sam-Unk-2684B532-12 (Mpro-P0925) (pdb code 7gkl). 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 Sam-Unk-2684B532-12 (Mpro-P0925), PDB code: 7gkl:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7gkl

Go back to Fluorine Binding Sites List in 7gkl
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 Sam-Unk-2684B532-12 (Mpro-P0925)


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 Sam-Unk-2684B532-12 (Mpro-P0925) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:48.8
occ:0.73
 F2 A:QXX408 0.0 48.8 0.7
C A:QXX408 1.3 48.9 0.7
F A:QXX408 2.1 49.4 0.7
F1 A:QXX408 2.1 49.2 0.7
C1 A:QXX408 2.4 48.2 0.7
C2 A:QXX408 2.7 47.6 0.7
O A:HOH635 3.6 47.2 1.0
C5 A:QXX408 3.7 48.1 0.7
O A:HOH692 3.9 61.8 1.0
N A:ASN142 4.0 47.3 1.0
C3 A:QXX408 4.1 47.4 0.7
N1 A:QXX408 4.2 48.6 0.7
CB A:ASN142 4.2 50.8 1.0
CA A:ASN142 4.3 47.6 1.0
O B:HOH579 4.3 61.8 1.0
C A:LEU141 4.5 46.8 1.0
C4 A:QXX408 4.8 47.8 0.7
ND2 A:ASN142 5.0 58.9 1.0
OE1 A:GLU166 5.0 54.8 1.0
N A:QXX408 5.0 47.5 0.7
C6 A:QXX408 5.0 49.2 0.7
OE2 A:GLU166 5.0 60.3 1.0

Fluorine binding site 2 out of 3 in 7gkl

Go back to Fluorine Binding Sites List in 7gkl
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 Sam-Unk-2684B532-12 (Mpro-P0925)


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 Sam-Unk-2684B532-12 (Mpro-P0925) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:49.2
occ:0.73
 F1 A:QXX408 0.0 49.2 0.7
C A:QXX408 1.3 48.9 0.7
F2 A:QXX408 2.1 48.8 0.7
F A:QXX408 2.2 49.4 0.7
C1 A:QXX408 2.4 48.2 0.7
O A:HOH692 2.9 61.8 1.0
N1 A:QXX408 3.0 48.6 0.7
C5 A:QXX408 3.0 48.1 0.7
C6 A:QXX408 3.2 49.2 0.7
O A:QXX408 3.3 49.0 0.7
C2 A:QXX408 3.4 47.6 0.7
C7 A:QXX408 4.3 49.7 0.7
C4 A:QXX408 4.3 47.8 0.7
C3 A:QXX408 4.6 47.4 0.7
CB A:GLU166 4.6 44.0 1.0
N A:QXX408 5.0 47.5 0.7
ND2 A:ASN142 5.0 58.9 1.0

Fluorine binding site 3 out of 3 in 7gkl

Go back to Fluorine Binding Sites List in 7gkl
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 Sam-Unk-2684B532-12 (Mpro-P0925)


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 Sam-Unk-2684B532-12 (Mpro-P0925) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:49.4
occ:0.73
 F A:QXX408 0.0 49.4 0.7
C A:QXX408 1.3 48.9 0.7
F2 A:QXX408 2.1 48.8 0.7
F1 A:QXX408 2.2 49.2 0.7
C1 A:QXX408 2.4 48.2 0.7
N1 A:QXX408 2.9 48.6 0.7
C5 A:QXX408 3.0 48.1 0.7
ND2 A:ASN142 3.1 58.9 1.0
CB A:ASN142 3.2 50.8 1.0
CA A:ASN142 3.3 47.6 1.0
C2 A:QXX408 3.5 47.6 0.7
CG A:ASN142 3.6 57.4 1.0
N A:ASN142 3.8 47.3 1.0
C6 A:QXX408 3.8 49.2 0.7
C4 A:QXX408 4.3 47.8 0.7
O A:QXX408 4.5 49.0 0.7
C A:LEU141 4.5 46.8 1.0
C7 A:QXX408 4.6 49.7 0.7
C3 A:QXX408 4.6 47.4 0.7
O A:HOH596 4.7 64.2 1.0
C A:ASN142 4.7 46.1 1.0
O A:HOH635 4.7 47.2 1.0
O A:LEU141 4.8 46.5 1.0
OD1 A:ASN142 4.8 60.7 1.0
O A:HOH692 4.9 61.8 1.0
N A:QXX408 5.0 47.5 0.7

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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