Fluorine in PDB 6vh2: 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I

The structure of 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I, PDB code: 6vh2 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)	39.07 / 2.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.028, 91.098, 100.777, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 24.8

The binding sites of Fluorine atom in the 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I (pdb code 6vh2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I, PDB code: 6vh2:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:55.9 occ:1.00 F01 A:QZ4401 0.0 55.9 1.0 C02 A:QZ4401 1.4 59.6 1.0 F03 A:QZ4401 2.1 58.9 1.0 C33 A:QZ4401 2.4 50.5 1.0 C04 A:QZ4401 2.5 55.7 1.0 O A:VAL193 2.8 40.9 1.0 C A:VAL193 2.9 46.0 1.0 C32 A:QZ4401 3.1 48.4 1.0 C05 A:QZ4401 3.2 42.5 1.0 N A:HIS194 3.2 44.3 1.0 CA A:HIS194 3.4 45.2 1.0 N A:VAL193 3.5 43.2 1.0 C06 A:QZ4401 3.8 44.9 1.0 CA A:VAL193 3.8 45.4 1.0 N A:GLN195 4.0 44.2 1.0 C A:GLN192 4.1 39.5 1.0 C A:HIS194 4.1 38.4 1.0 O A:LYS191 4.5 36.1 1.0 CA A:GLN192 4.5 37.9 1.0 CB A:HIS194 4.6 49.3 1.0 O A:GLN192 4.7 40.8 1.0 NE2 A:GLN195 4.8 37.1 1.0 O07 A:QZ4401 4.9 47.1 1.0

Fluorine binding site 2 out of 4 in the 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:58.9 occ:1.00 F03 A:QZ4401 0.0 58.9 1.0 C02 A:QZ4401 1.4 59.6 1.0 F01 A:QZ4401 2.1 55.9 1.0 C33 A:QZ4401 2.5 50.5 1.0 C04 A:QZ4401 2.5 55.7 1.0 N A:GLN195 3.3 44.2 1.0 O A:GLN195 3.8 39.6 1.0 O A:VAL193 3.8 40.9 1.0 CA A:HIS194 3.8 45.2 1.0 C32 A:QZ4401 3.8 48.4 1.0 C05 A:QZ4401 3.8 42.5 1.0 C A:HIS194 4.0 38.4 1.0 CA A:LEU170 4.2 39.4 1.0 CD2 A:LEU170 4.2 38.9 1.0 CA A:GLN195 4.2 49.6 1.0 C06 A:QZ4401 4.2 44.9 1.0 N A:ALA171 4.3 47.1 1.0 C A:VAL193 4.3 46.0 1.0 N A:HIS194 4.4 44.3 1.0 CB A:GLN195 4.4 47.2 1.0 C A:GLN195 4.5 54.0 1.0 O A:GLU169 4.5 38.4 1.0 CB A:LEU170 4.7 39.8 1.0 C A:LEU170 4.7 40.6 1.0 CB A:HIS194 4.9 49.3 1.0 NE2 A:GLN195 4.9 37.1 1.0

Fluorine binding site 3 out of 4 in the 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:83.0 occ:1.00 F01 B:QZ4401 0.0 83.0 1.0 C02 B:QZ4401 1.4 73.3 1.0 F03 B:QZ4401 2.1 69.9 1.0 C04 B:QZ4401 2.4 63.0 1.0 C33 B:QZ4401 2.4 67.3 1.0 C05 B:QZ4401 3.0 69.6 1.0 C32 B:QZ4401 3.2 72.5 1.0 C06 B:QZ4401 3.7 72.2 1.0 O07 B:QZ4401 4.8 51.4 1.0 O B:HOH567 4.9 38.4 1.0

Fluorine binding site 4 out of 4 in the 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 2.26 A Resolution Structure of Mers 3CL Protease in Complex with Inhibitor 7I within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:69.9 occ:1.00 F03 B:QZ4401 0.0 69.9 1.0 C02 B:QZ4401 1.4 73.3 1.0 F01 B:QZ4401 2.1 83.0 1.0 C04 B:QZ4401 2.4 63.0 1.0 C33 B:QZ4401 2.4 67.3 1.0 O B:HOH567 2.9 38.4 1.0 O B:LEU170 3.6 39.8 1.0 C05 B:QZ4401 3.7 69.6 1.0 C32 B:QZ4401 3.8 72.5 1.0 CA B:ALA171 3.9 39.5 1.0 C B:LEU170 4.1 32.2 1.0 C06 B:QZ4401 4.2 72.2 1.0 N B:ALA171 4.3 32.7 1.0 OE2 B:GLU169 4.3 48.6 1.0 O B:GLU169 4.5 37.5 1.0 O B:ALA171 4.5 39.0 1.0 C B:ALA171 4.6 41.7 1.0 CG B:GLU169 4.7 36.5 1.0 CB B:ALA171 4.8 40.2 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