Fluorine in PDB 7grv: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18, PDB code: 7grv 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)	56.82 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.76, 100.04, 104.28, 90, 90, 90
R / Rfree (%)	19.3 / 23.6

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18 also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18 (pdb code 7grv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18, PDB code: 7grv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18


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-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:42.1 occ:0.76 F12 A:Y0C401 0.0 42.1 0.8 C11 A:Y0C401 1.4 46.5 0.8 C06 A:Y0C401 2.4 41.7 0.8 C10 A:Y0C401 2.4 46.2 0.8 C05 A:Y0C401 2.8 43.5 0.8 ND1 A:HIS41 3.1 28.9 1.0 CE1 A:HIS41 3.2 30.4 1.0 CG A:HIS41 3.3 30.2 1.0 NE2 A:HIS41 3.5 29.6 1.0 CD2 A:HIS41 3.5 25.4 1.0 O A:HOH644 3.5 38.0 1.0 C07 A:Y0C401 3.6 43.2 0.8 C09 A:Y0C401 3.7 43.9 0.8 O A:HOH586 3.7 33.6 1.0 S04 A:Y0C401 3.8 39.5 0.8 CB A:HIS41 4.0 27.3 1.0 N13 A:Y0C401 4.1 39.1 0.8 C08 A:Y0C401 4.1 47.8 0.8 O A:HOH501 4.3 60.8 1.0 O A:HOH504 4.4 51.1 1.0 O A:HIS41 4.7 34.0 1.0 O A:HIS164 4.8 25.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18


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-18 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:55.8 occ:0.78 F12 B:Y0C401 0.0 55.8 0.8 C11 B:Y0C401 1.4 49.0 0.8 C06 B:Y0C401 2.4 47.4 0.8 C10 B:Y0C401 2.4 43.9 0.8 C05 B:Y0C401 2.8 46.6 0.8 O B:HOH631 3.3 39.6 1.0 C07 B:Y0C401 3.7 39.8 0.8 C09 B:Y0C401 3.7 43.2 0.8 N13 B:Y0C401 3.7 40.6 0.8 ND1 B:HIS41 3.8 26.9 1.0 CE1 B:HIS41 4.0 31.0 1.0 O B:HOH555 4.0 33.8 1.0 S04 B:Y0C401 4.1 51.5 0.8 C08 B:Y0C401 4.2 40.3 0.8 CG B:HIS41 4.2 26.9 1.0 NE2 B:HIS41 4.4 29.1 1.0 CD2 B:HIS41 4.5 29.5 1.0 OE1 B:GLN189 4.6 55.3 1.0 CB B:HIS41 4.8 24.6 1.0 NE2 B:GLN189 5.0 68.1 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