Fluorine in PDB 7grn: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-10

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-10:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-10, PDB code: 7grn 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)	56.46 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.31, 99.63, 103.69, 90, 90, 90
R / Rfree (%)	24.6 / 30.1

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-10 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-10 (pdb code 7grn). 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-10, PDB code: 7grn:
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-10


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-10 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:33.2 occ:0.79 F01 B:Y0W502 0.0 33.2 0.8 C02 B:Y0W502 1.3 33.8 0.8 F04 B:Y0W502 2.2 34.3 0.8 F03 B:Y0W502 2.2 33.8 0.8 C05 B:Y0W502 2.3 35.3 0.8 C18 B:Y0W502 2.9 35.7 0.8 CB B:MET165 3.1 30.8 1.0 O B:HIS164 3.1 31.2 1.0 O B:HOH725 3.4 33.0 1.0 C06 B:Y0W502 3.4 35.6 0.8 CE B:MET165 3.6 30.0 1.0 CD2 B:HIS41 3.9 33.5 1.0 CA B:MET165 3.9 31.4 1.0 NE2 B:HIS41 3.9 33.4 1.0 C B:HIS164 3.9 31.1 1.0 O B:HOH706 4.0 34.2 1.0 C17 B:Y0W502 4.2 36.9 0.8 CG B:MET165 4.2 29.8 1.0 SD B:MET165 4.2 29.6 1.0 N B:MET165 4.4 30.9 1.0 C07 B:Y0W502 4.5 36.6 0.8 CG B:HIS41 4.6 34.3 1.0 CE1 B:HIS41 4.6 33.7 1.0 O B:HOH716 4.7 31.0 1.0 C08 B:Y0W502 4.9 37.3 0.8 CE B:MET49 4.9 37.2 1.0 CA B:ASP187 4.9 32.6 1.0 CB B:HIS164 4.9 29.6 1.0 ND1 B:HIS41 5.0 34.7 1.0 CA B:HIS164 5.0 30.5 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-10


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-10 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:33.8 occ:0.79 F03 B:Y0W502 0.0 33.8 0.8 C02 B:Y0W502 1.4 33.8 0.8 F04 B:Y0W502 2.2 34.3 0.8 F01 B:Y0W502 2.2 33.2 0.8 C05 B:Y0W502 2.4 35.3 0.8 C06 B:Y0W502 2.8 35.6 0.8 O B:ARG188 3.2 35.1 1.0 O B:HOH716 3.5 31.0 1.0 CE B:MET165 3.6 30.0 1.0 C B:ARG188 3.7 36.2 1.0 N B:ARG188 3.7 34.8 1.0 C18 B:Y0W502 3.7 35.7 0.8 O B:HOH669 3.8 33.5 1.0 SD B:MET165 3.8 29.6 1.0 CB B:MET165 4.0 30.8 1.0 C07 B:Y0W502 4.2 36.6 0.8 N B:GLN189 4.2 36.9 1.0 CA B:ARG188 4.2 35.6 1.0 CE B:MET49 4.3 37.2 1.0 C B:ASP187 4.3 33.9 1.0 CA B:ASP187 4.4 32.6 1.0 O B:VAL186 4.5 31.2 1.0 CG B:MET165 4.6 29.8 1.0 CA B:GLN189 4.6 36.8 1.0 NE2 B:GLN192 4.7 32.6 1.0 OE1 B:GLN189 4.7 36.1 1.0 O B:HOH706 4.8 34.2 1.0 C17 B:Y0W502 4.8 36.9 0.8 O B:HOH725 4.9 33.0 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-10


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-10 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:34.3 occ:0.79 F04 B:Y0W502 0.0 34.3 0.8 C02 B:Y0W502 1.4 33.8 0.8 F01 B:Y0W502 2.2 33.2 0.8 F03 B:Y0W502 2.2 33.8 0.8 C05 B:Y0W502 2.4 35.3 0.8 C18 B:Y0W502 2.9 35.7 0.8 CE B:MET49 3.1 37.2 1.0 C B:ASP187 3.3 33.9 1.0 N B:ARG188 3.3 34.8 1.0 CA B:ASP187 3.3 32.6 1.0 C06 B:Y0W502 3.5 35.6 0.8 CB B:ASP187 3.5 32.5 1.0 CD2 B:HIS41 3.8 33.5 1.0 O B:ASP187 3.9 34.3 1.0 CE B:MET165 4.0 30.0 1.0 CA B:ARG188 4.1 35.6 1.0 CG B:HIS41 4.2 34.3 1.0 SD B:MET49 4.2 37.9 1.0 C17 B:Y0W502 4.2 36.9 0.8 C B:ARG188 4.3 36.2 1.0 CB B:HIS41 4.3 35.0 1.0 O B:ARG188 4.4 35.1 1.0 NE2 B:HIS41 4.5 33.4 1.0 N B:ASP187 4.7 31.6 1.0 C07 B:Y0W502 4.7 36.6 0.8 O B:VAL186 4.7 31.2 1.0 N B:GLN189 4.8 36.9 1.0 OH B:TYR54 4.9 34.5 1.0 O B:HIS164 4.9 31.2 1.0 CB B:MET165 4.9 30.8 1.0 CG B:ASP187 4.9 32.2 1.0 ND1 B:HIS41 5.0 34.7 1.0 C08 B:Y0W502 5.0 37.3 0.8

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