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Fluorine in PDB 7gbq: 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 Jan-Ghe-83B26C96-23 (Mpro-X10396)

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 Jan-Ghe-83B26C96-23 (Mpro-X10396)

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 Jan-Ghe-83B26C96-23 (Mpro-X10396):
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 Jan-Ghe-83B26C96-23 (Mpro-X10396), PDB code: 7gbq 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) 56.01 / 1.72
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.061, 53.663, 44.297, 90, 100.83, 90
R / Rfree (%) 18.2 / 22.6

Other elements in 7gbq:

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 Jan-Ghe-83B26C96-23 (Mpro-X10396) 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 Jan-Ghe-83B26C96-23 (Mpro-X10396) (pdb code 7gbq). 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 Jan-Ghe-83B26C96-23 (Mpro-X10396), PDB code: 7gbq:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7gbq

Go back to Fluorine Binding Sites List in 7gbq
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 Jan-Ghe-83B26C96-23 (Mpro-X10396)


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 Jan-Ghe-83B26C96-23 (Mpro-X10396) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:22.8
occ:1.00
 F A:KYU404 0.0 22.8 1.0
C7 A:KYU404 1.4 23.0 1.0
F1 A:KYU404 2.2 24.5 1.0
C8 A:KYU404 2.3 23.0 1.0
C6 A:KYU404 2.4 21.7 1.0
N1 A:KYU404 2.7 20.3 1.0
C13 A:KYU404 2.8 23.1 1.0
O A:HOH502 2.9 23.1 1.0
O A:HOH633 3.4 30.1 1.0
O A:KYU404 3.4 22.1 1.0
C9 A:KYU404 3.5 23.3 1.0
NE2 A:HIS41 3.6 19.4 1.0
SG A:CYS145 3.9 20.9 1.0
C5 A:KYU404 4.1 19.6 1.0
O A:HOH753 4.1 48.7 1.0
CD2 A:HIS41 4.1 18.1 1.0
CE1 A:HIS41 4.1 19.6 1.0
C12 A:KYU404 4.2 23.5 1.0
O A:HIS164 4.2 13.7 1.0
O A:HOH829 4.4 48.4 1.0
O A:HOH836 4.6 42.7 1.0
O A:HOH650 4.6 25.2 1.0
C10 A:KYU404 4.7 23.7 1.0
C4 A:KYU404 4.8 19.5 1.0
CG A:HIS41 4.8 17.2 1.0
ND1 A:HIS41 4.9 19.7 1.0
O A:HOH693 4.9 50.1 1.0
C11 A:KYU404 5.0 23.7 1.0

Fluorine binding site 2 out of 2 in 7gbq

Go back to Fluorine Binding Sites List in 7gbq
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 Jan-Ghe-83B26C96-23 (Mpro-X10396)


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 Jan-Ghe-83B26C96-23 (Mpro-X10396) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:24.5
occ:1.00
 F1 A:KYU404 0.0 24.5 1.0
C7 A:KYU404 1.4 23.0 1.0
F A:KYU404 2.2 22.8 1.0
C6 A:KYU404 2.4 21.7 1.0
C8 A:KYU404 2.4 23.0 1.0
C9 A:KYU404 2.8 23.3 1.0
N1 A:KYU404 3.0 20.3 1.0
O A:HOH693 3.0 50.1 1.0
O A:HOH753 3.1 48.7 1.0
O A:KYU404 3.2 22.1 1.0
O A:HOH836 3.3 42.7 1.0
C13 A:KYU404 3.6 23.1 1.0
O A:HOH502 3.7 23.1 1.0
O A:HOH839 4.0 46.2 1.0
O A:HOH717 4.1 31.3 1.0
C10 A:KYU404 4.2 23.7 1.0
C A:KYU404 4.3 18.8 1.0
C5 A:KYU404 4.3 19.6 1.0
O A:HOH829 4.6 48.4 1.0
OE1 A:GLN189 4.6 34.7 1.0
C12 A:KYU404 4.8 23.5 1.0
C1 A:KYU404 4.8 19.1 1.0
C11 A:KYU404 5.0 23.7 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 07:33:54 2024

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