Fluorine in PDB 6vh3: 2.20 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7J

The structure of 2.20 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7J, PDB code: 6vh3 was solved by S.Lovell, K.P.Battaile, M.M.Kashipathy, 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)	43.83 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.629, 90.960, 100.030, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 24.5

The binding sites of Fluorine atom in the 2.20 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7J (pdb code 6vh3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the 2.20 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7J, PDB code: 6vh3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the 2.20 A Resolution Structure of Mers 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 2.20 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7J within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:71.6 occ:1.00 F01 A:QYS401 0.0 71.6 1.0 C02 A:QYS401 1.3 70.4 1.0 F03 A:QYS401 2.0 92.6 1.0 C31 A:QYS401 2.3 0.8 1.0 C04 A:QYS401 2.4 61.3 1.0 C30 A:QYS401 3.0 0.4 1.0 CA A:HIS194 3.2 40.1 1.0 C05 A:QYS401 3.2 59.8 1.0 N A:GLN195 3.2 47.2 1.0 CD2 A:HIS194 3.4 49.7 1.0 CG A:HIS194 3.7 52.9 1.0 C A:HIS194 3.7 36.5 1.0 C06 A:QYS401 3.7 65.1 1.0 O A:GLN195 3.8 46.6 1.0 CB A:HIS194 3.9 43.5 1.0 O A:VAL193 4.0 36.6 1.0 N A:HIS194 4.1 40.0 1.0 CB A:ALA171 4.1 52.2 1.0 NE2 A:HIS194 4.2 53.9 1.0 N A:ALA171 4.2 54.6 1.0 CA A:ALA171 4.3 55.9 1.0 CA A:GLN195 4.3 43.4 1.0 C A:VAL193 4.4 36.6 1.0 C A:GLN195 4.5 48.5 1.0 ND1 A:HIS194 4.5 48.4 1.0 CE1 A:HIS194 4.8 53.7 1.0 C A:LEU170 4.8 44.0 1.0 O A:HIS194 4.9 35.3 1.0 CB A:GLN195 4.9 42.7 1.0

Fluorine binding site 2 out of 4 in the 2.20 A Resolution Structure of Mers 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 2.20 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7J within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:92.6 occ:1.00 F03 A:QYS401 0.0 92.6 1.0 C02 A:QYS401 1.3 70.4 1.0 F01 A:QYS401 2.0 71.6 1.0 C31 A:QYS401 2.4 0.8 1.0 C04 A:QYS401 2.4 61.3 1.0 N A:ALA171 2.5 54.6 1.0 C A:LEU170 3.1 44.0 1.0 CA A:ALA171 3.2 55.9 1.0 O A:GLN195 3.2 46.6 1.0 CA A:LEU170 3.2 38.3 1.0 CB A:ALA171 3.3 52.2 1.0 C30 A:QYS401 3.7 0.4 1.0 C05 A:QYS401 3.7 59.8 1.0 N A:GLN195 3.9 47.2 1.0 O A:LEU170 4.0 37.6 1.0 CB A:LEU170 4.0 32.4 1.0 O A:GLU169 4.1 43.8 1.0 C06 A:QYS401 4.1 65.1 1.0 C A:GLN195 4.2 48.5 1.0 CD2 A:LEU170 4.2 39.5 1.0 N A:LEU170 4.4 40.3 1.0 CA A:GLN195 4.5 43.4 1.0 C A:ALA171 4.6 52.1 1.0 C A:GLU169 4.7 38.4 1.0 CD2 A:HIS194 4.8 49.7 1.0 CG A:LEU170 4.8 40.6 1.0 CB A:GLN195 4.8 42.7 1.0 CA A:HIS194 4.9 40.1 1.0 C A:HIS194 4.9 36.5 1.0

Fluorine binding site 3 out of 4 in the 2.20 A Resolution Structure of Mers 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 2.20 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7J within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:78.3 occ:1.00 F01 B:QYS401 0.0 78.3 1.0 C02 B:QYS401 1.4 75.2 1.0 F03 B:QYS401 2.1 77.7 1.0 C04 B:QYS401 2.4 71.2 1.0 C31 B:QYS401 2.5 50.8 1.0 CB B:ALA171 3.0 53.7 1.0 CA B:ALA171 3.4 47.6 1.0 N B:ALA171 3.4 42.6 1.0 CA B:HIS194 3.5 56.8 1.0 ND1 B:HIS194 3.6 78.4 1.0 C05 B:QYS401 3.7 60.0 1.0 C30 B:QYS401 3.8 59.6 1.0 CB B:HIS194 3.9 66.9 1.0 CG B:HIS194 4.0 77.7 1.0 C B:LEU170 4.2 35.5 1.0 C06 B:QYS401 4.2 72.2 1.0 N B:HIS194 4.2 52.6 1.0 N B:GLN195 4.4 48.2 1.0 CE1 B:HIS194 4.4 74.8 1.0 C B:HIS194 4.5 52.8 1.0 O B:VAL193 4.6 48.2 1.0 CA B:LEU170 4.7 37.4 1.0 C B:VAL193 4.7 52.4 1.0 C B:ALA171 4.9 52.3 1.0 CD2 B:HIS194 5.0 69.0 1.0 O B:LEU170 5.0 35.2 1.0

Fluorine binding site 4 out of 4 in the 2.20 A Resolution Structure of Mers 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 2.20 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7J within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:77.7 occ:1.00 F03 B:QYS401 0.0 77.7 1.0 C02 B:QYS401 1.4 75.2 1.0 F01 B:QYS401 2.1 78.3 1.0 C04 B:QYS401 2.4 71.2 1.0 C31 B:QYS401 2.4 50.8 1.0 C05 B:QYS401 2.9 60.0 1.0 C30 B:QYS401 3.1 59.6 1.0 C06 B:QYS401 3.6 72.2 1.0 CA B:HIS194 3.6 56.8 1.0 N B:HIS194 3.6 52.6 1.0 CB B:HIS194 3.9 66.9 1.0 C B:VAL193 4.1 52.4 1.0 ND1 B:HIS194 4.4 78.4 1.0 O B:VAL193 4.5 48.2 1.0 CG B:HIS194 4.6 77.7 1.0 CB B:ALA171 4.8 53.7 1.0 C07 B:QYS401 4.8 63.6 1.0 CA B:VAL193 4.9 55.5 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