Fluorine in PDB 7gre: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-1

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-1:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-1, PDB code: 7gre was solved by C.-Y.Huang, A.Metz, M.Sharpe, A.M.Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.82 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.79, 99.93, 104.2, 90, 90, 90
R / Rfree (%)	20.6 / 24.9

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-1 also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-1 (pdb code 7gre). 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-1, PDB code: 7gre:
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-1


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-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:57.9 occ:0.83 F01 A:XWH501 0.0 57.9 0.8 C02 A:XWH501 1.4 54.0 0.8 F04 A:XWH501 2.2 49.8 0.8 F03 A:XWH501 2.2 47.0 0.8 C05 A:XWH501 2.4 43.9 0.8 N15 A:XWH501 3.2 42.4 0.8 C06 A:XWH501 3.4 37.7 0.8 N14 A:XWH501 4.3 41.4 0.8 C07 A:XWH501 4.4 37.2 0.8 O A:HOH818 4.5 38.4 1.0

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


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-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:47.0 occ:0.83 F03 A:XWH501 0.0 47.0 0.8 C02 A:XWH501 1.4 54.0 0.8 F04 A:XWH501 2.2 49.8 0.8 F01 A:XWH501 2.2 57.9 0.8 C05 A:XWH501 2.4 43.9 0.8 C06 A:XWH501 3.0 37.7 0.8 N15 A:XWH501 3.6 42.4 0.8 OD1 A:ASN142 3.6 36.9 1.0 O A:HOH818 3.7 38.4 1.0 CG A:ASN142 4.0 39.8 1.0 C07 A:XWH501 4.3 37.2 0.8 ND2 A:ASN142 4.5 40.8 1.0 N14 A:XWH501 4.5 41.4 0.8 CB A:ASN142 4.7 29.7 1.0 O A:HOH614 4.9 31.2 1.0

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


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-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:49.8 occ:0.83 F04 A:XWH501 0.0 49.8 0.8 C02 A:XWH501 1.4 54.0 0.8 F01 A:XWH501 2.2 57.9 0.8 F03 A:XWH501 2.2 47.0 0.8 C05 A:XWH501 2.3 43.9 0.8 N15 A:XWH501 2.8 42.4 0.8 C06 A:XWH501 3.6 37.7 0.8 CG A:ASN142 3.8 39.8 1.0 ND2 A:ASN142 4.0 40.8 1.0 CB A:ASN142 4.1 29.7 1.0 N14 A:XWH501 4.1 41.4 0.8 OD1 A:ASN142 4.1 36.9 1.0 C07 A:XWH501 4.5 37.2 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