Fluorine in PDB 7gs5: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28, PDB code: 7gs5 was solved by C.-Y.Huang, A.Metz, M.Sharpe, A.Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.94 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.92, 99.96, 104.43, 90, 90, 90
R / Rfree (%)	19.9 / 24.7

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28 (pdb code 7gs5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28, PDB code: 7gs5:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:45.7 occ:0.84 F A:0TI401 0.0 45.7 0.8 C5 A:0TI401 1.4 47.7 0.8 C4 A:0TI401 2.3 39.8 0.8 C A:0TI401 2.3 48.9 0.8 C2 A:DMS403 3.1 66.1 1.0 NE2 A:GLN189 3.3 58.3 1.0 C1 A:0TI401 3.6 47.4 0.8 C3 A:0TI401 3.6 47.6 0.8 O A:DMS403 4.0 61.4 1.0 C2 A:0TI401 4.1 43.3 0.8 OE1 A:GLN189 4.1 76.8 1.0 CD A:GLN189 4.1 74.5 1.0 S A:DMS403 4.1 70.8 1.0 CB A:MET165 4.2 27.4 1.0 O A:HIS164 4.4 28.6 1.0 CE A:MET165 4.5 53.5 1.0 CA A:MET165 4.7 26.1 1.0 C6 A:0TI401 5.0 52.4 0.8

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:90.8 occ:0.94 F B:0TI401 0.0 90.8 0.9 C5 B:0TI401 1.4 75.3 0.9 C B:0TI401 2.3 73.6 0.9 C4 B:0TI401 2.3 70.3 0.9 C1 B:0TI401 3.6 79.2 0.9 C3 B:0TI401 3.6 67.0 0.9 C2 B:0TI401 4.1 67.8 0.9 CB B:MET165 4.7 41.4 1.0 CA B:MET165 4.9 37.0 1.0 O B:HIS164 5.0 42.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-28 within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:52.4 occ:0.81 F B:0TI402 0.0 52.4 0.8 C5 B:0TI402 1.4 56.6 0.8 C B:0TI402 2.3 40.1 0.8 C4 B:0TI402 2.3 50.1 0.8 NH2 B:ARG188 3.2 64.1 1.0 CA B:TYR54 3.3 53.1 1.0 CB B:TYR54 3.3 52.6 1.0 N B:TYR54 3.3 65.9 1.0 CG B:PRO52 3.5 87.9 1.0 O B:PRO52 3.5 80.5 1.0 C1 B:0TI402 3.6 43.0 0.8 C3 B:0TI402 3.6 57.2 0.8 CZ B:ARG188 3.7 79.3 1.0 NH1 B:ARG188 3.8 76.4 1.0 CD2 B:TYR54 4.0 41.1 1.0 C B:PRO52 4.0 84.8 1.0 C B:ASN53 4.1 81.5 1.0 C2 B:0TI402 4.1 42.2 0.8 CB B:PRO52 4.1 95.3 1.0 CG B:TYR54 4.1 49.9 1.0 CD1 B:LEU57 4.2 63.1 1.0 CD B:PRO52 4.6 93.9 1.0 NE B:ARG188 4.6 77.4 1.0 CA B:ASN53 4.6 83.7 1.0 CA B:PRO52 4.6 91.8 1.0 N B:ASN53 4.7 74.0 1.0 O B:ASN53 4.7 73.5 1.0 C B:TYR54 4.8 61.4 1.0

C.Y.Huang, A.Metz, R.Lange, N.Artico, C.Potot, J.Hazemann, M.Muller, M.Dos Santos, A.Chambovey, D.Ritz, D.Eris, S.Meyer, G.Bourquin, M.Sharpe, A.Mac Sweeney. Fragment-Based Screening Targeting An Open Form of the Sars-Cov-2 Main Protease Binding Pocket. Acta Crystallogr D Struct V. 80 123 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38289714
DOI: 10.1107/S2059798324000329