Fluorine in PDB 6xmk: 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J

All present enzymatic activity of 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J:
3.4.22.69;

The structure of 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J, PDB code: 6xmk was solved by S.Lovell, M.M.Kashipathy, K.P.Battaile, A.D.Rathnayake, J.Zheng, Y.Kim, H.N.Nguyen, K.O.Chang, W.C.Groutas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.61 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.354, 98.631, 58.802, 90.00, 107.79, 90.00
R / Rfree (%)	17.9 / 21.2

The binding sites of Fluorine atom in the 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J (pdb code 6xmk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J, PDB code: 6xmk:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:70.7 occ:1.00 F01 A:QYS401 0.0 70.7 1.0 C02 A:QYS401 1.4 60.5 1.0 F03 A:QYS401 2.1 66.9 1.0 C31 A:QYS401 2.4 45.4 1.0 C04 A:QYS401 2.4 47.4 1.0 CB A:ALA191 3.3 35.7 1.0 C30 A:QYS401 3.7 37.4 1.0 C05 A:QYS401 3.7 47.3 1.0 CA A:ALA191 3.9 29.9 1.0 CG A:PRO168 4.0 37.3 1.0 C06 A:QYS401 4.2 46.5 1.0 N A:ALA191 4.4 34.5 1.0 CB A:PRO168 4.5 30.0 1.0 CD A:PRO168 4.7 30.9 1.0 CA A:PRO168 4.9 33.6 1.0

Fluorine binding site 2 out of 4 in the 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:66.9 occ:1.00 F03 A:QYS401 0.0 66.9 1.0 C02 A:QYS401 1.4 60.5 1.0 F01 A:QYS401 2.1 70.7 1.0 C31 A:QYS401 2.4 45.4 1.0 C04 A:QYS401 2.4 47.4 1.0 C05 A:QYS401 3.2 47.3 1.0 C30 A:QYS401 3.3 37.4 1.0 C06 A:QYS401 3.8 46.5 1.0 NE2 A:GLN189 4.9 40.5 1.0 C07 A:QYS401 5.0 34.0 1.0

Fluorine binding site 3 out of 4 in the 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:72.7 occ:1.00 F01 B:QYS401 0.0 72.7 1.0 C02 B:QYS401 1.3 62.1 1.0 F03 B:QYS401 2.1 73.1 1.0 C31 B:QYS401 2.4 53.7 1.0 C04 B:QYS401 2.4 58.6 1.0 CB B:ALA191 3.6 54.1 1.0 C30 B:QYS401 3.7 51.7 1.0 C05 B:QYS401 3.7 52.6 1.0 CA B:ALA191 3.9 53.5 1.0 CB B:PRO168 4.2 39.8 1.0 C06 B:QYS401 4.2 49.7 1.0 CG B:PRO168 4.4 47.0 1.0 N B:ALA191 4.4 50.2 1.0 CD B:PRO168 4.5 47.4 1.0 CA B:PRO168 4.6 43.3 1.0 N B:PRO168 4.9 41.5 1.0 C B:THR190 5.0 48.0 1.0 O B:HOH604 5.0 41.7 1.0

Fluorine binding site 4 out of 4 in the 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 1.70 A Resolution Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 7J within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:73.1 occ:1.00 F03 B:QYS401 0.0 73.1 1.0 C02 B:QYS401 1.3 62.1 1.0 F01 B:QYS401 2.1 72.7 1.0 C31 B:QYS401 2.4 53.7 1.0 C04 B:QYS401 2.4 58.6 1.0 C30 B:QYS401 3.0 51.7 1.0 C05 B:QYS401 3.1 52.6 1.0 C06 B:QYS401 3.6 49.7 1.0 C07 B:QYS401 4.8 47.1 1.0

A.D.Rathnayake, J.Zheng, Y.Kim, K.D.Perera, S.Mackin, D.K.Meyerholz, M.M.Kashipathy, K.P.Battaile, S.Lovell, S.Perlman, W.C.Groutas, K.O.Chang. 3C-Like Protease Inhibitors Block Coronavirus Replication in Vitro and Improve Survival in Mers-Cov-Infected Mice. Sci Transl Med V. 12 2020.
ISSN: ESSN 1946-6242
PubMed: 32747425
DOI: 10.1126/SCITRANSLMED.ABC5332