Fluorine in PDB 7gro: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11, PDB code: 7gro 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)	56.68 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.62, 99.49, 103.93, 90, 90, 90
R / Rfree (%)	19.2 / 23.2

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11 also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11 (pdb code 7gro). 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-11, PDB code: 7gro:
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-11


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-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:46.5 occ:0.74 F14 A:Y3N401 0.0 46.5 0.7 C13 A:Y3N401 1.4 52.2 0.7 F16 A:Y3N401 2.2 55.8 0.7 F15 A:Y3N401 2.2 54.1 0.7 C12 A:Y3N401 2.4 44.3 0.7 C11 A:Y3N401 2.6 33.1 0.7 O A:HOH645 3.2 32.5 1.0 O A:HOH743 3.5 38.6 1.0 CE1 A:HIS41 3.5 27.0 1.0 C05 A:Y3N401 3.7 42.7 0.7 ND1 A:HIS41 3.7 25.4 1.0 C2 A:DMS405 3.9 50.3 1.0 O A:HOH623 3.9 27.6 1.0 C08 A:Y3N401 4.0 29.3 0.7 NE2 A:HIS41 4.0 24.5 1.0 C1 A:DMS405 4.1 47.3 1.0 N04 A:Y3N401 4.3 46.5 0.7 CG A:HIS41 4.3 20.5 1.0 CD2 A:HIS41 4.5 21.1 1.0 O03 A:Y3N401 4.7 46.8 0.7 C06 A:Y3N401 4.7 45.1 0.7 C02 A:Y3N401 4.8 54.2 0.7 C09 A:Y3N401 4.8 28.4 0.7 O A:HIS164 4.9 20.7 1.0 C07 A:Y3N401 4.9 42.6 0.7 SD A:MET49 4.9 40.2 1.0 S A:DMS405 4.9 69.2 1.0 CG A:MET49 4.9 41.5 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11


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-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:54.1 occ:0.74 F15 A:Y3N401 0.0 54.1 0.7 C13 A:Y3N401 1.4 52.2 0.7 F14 A:Y3N401 2.2 46.5 0.7 F16 A:Y3N401 2.2 55.8 0.7 C12 A:Y3N401 2.3 44.3 0.7 O A:HOH645 2.9 32.5 1.0 C05 A:Y3N401 3.0 42.7 0.7 N04 A:Y3N401 3.1 46.5 0.7 C11 A:Y3N401 3.3 33.1 0.7 O A:HOH660 3.7 27.9 1.0 C02 A:Y3N401 3.8 54.2 0.7 C06 A:Y3N401 4.3 45.1 0.7 O03 A:Y3N401 4.3 46.8 0.7 C08 A:Y3N401 4.5 29.3 0.7 O A:HOH703 4.5 42.2 1.0 C01 A:Y3N401 4.6 53.4 0.7 O A:HOH743 4.7 38.6 1.0 C1 A:DMS405 4.8 47.3 1.0 C07 A:Y3N401 4.9 42.6 0.7

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11


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-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:55.8 occ:0.74 F16 A:Y3N401 0.0 55.8 0.7 C13 A:Y3N401 1.4 52.2 0.7 F14 A:Y3N401 2.2 46.5 0.7 F15 A:Y3N401 2.2 54.1 0.7 C12 A:Y3N401 2.4 44.3 0.7 O03 A:Y3N401 2.7 46.8 0.7 C02 A:Y3N401 2.8 54.2 0.7 N04 A:Y3N401 2.9 46.5 0.7 C05 A:Y3N401 2.9 42.7 0.7 C2 A:DMS405 3.0 50.3 1.0 C11 A:Y3N401 3.4 33.1 0.7 C1 A:DMS405 3.6 47.3 1.0 C01 A:Y3N401 3.8 53.4 0.7 S A:DMS405 3.9 69.2 1.0 CG A:MET49 4.0 41.5 1.0 O A:DMS405 4.1 69.7 1.0 C06 A:Y3N401 4.2 45.1 0.7 C08 A:Y3N401 4.6 29.3 0.7 O A:HOH645 4.7 32.5 1.0 SD A:MET49 4.7 40.2 1.0 O A:HOH743 4.8 38.6 1.0 C07 A:Y3N401 4.9 42.6 0.7 CB A:MET49 5.0 38.5 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