Fluorine in PDB 8eyj: Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir

The structure of Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir, PDB code: 8eyj was solved by G.D.Noske, A.S.Godoy, G.Oliva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.79 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.646, 101.969, 103.626, 90, 90, 90
R / Rfree (%)	19.3 / 23.4

The binding sites of Fluorine atom in the Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir (pdb code 8eyj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir, PDB code: 8eyj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir


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 Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.9 occ:1.00 F1 A:4WI401 0.0 32.9 1.0 C22 A:4WI401 1.3 29.3 1.0 F3 A:4WI401 2.1 32.5 1.0 F2 A:4WI401 2.1 30.9 1.0 C21 A:4WI401 2.4 27.0 1.0 H16 A:4WI401 2.6 23.3 1.0 HD23 A:LEU167 2.7 20.8 1.0 N4 A:4WI401 2.8 23.2 1.0 O A:GLU166 2.8 16.0 1.0 HA A:LEU167 3.0 22.0 1.0 HB2 A:MET165 3.3 19.1 1.0 O4 A:4WI401 3.4 25.6 1.0 CD2 A:LEU167 3.5 20.8 1.0 HG3 A:MET165 3.5 22.1 1.0 C A:GLU166 3.5 18.9 1.0 HD22 A:LEU167 3.7 20.8 1.0 HG A:LEU167 3.7 20.9 1.0 CA A:LEU167 3.8 22.2 1.0 N A:LEU167 3.9 20.7 1.0 HB2 A:GLN192 3.9 22.2 1.0 SD A:MET165 4.0 27.1 1.0 CG A:MET165 4.0 21.9 1.0 H A:GLU166 4.0 18.9 1.0 CB A:MET165 4.0 18.7 1.0 HD3 A:PRO168 4.0 27.7 1.0 CG A:LEU167 4.1 20.7 1.0 O A:HOH608 4.1 26.4 1.0 C14 A:4WI401 4.1 20.3 1.0 HD21 A:LEU167 4.2 20.8 1.0 N A:GLU166 4.3 18.9 1.0 C13 A:4WI401 4.5 19.1 1.0 HE22 A:GLN192 4.5 21.9 1.0 O3 A:4WI401 4.5 17.9 1.0 H15 A:4WI401 4.5 20.9 1.0 CB A:LEU167 4.5 21.1 1.0 CA A:GLU166 4.5 20.4 1.0 HB3 A:MET165 4.6 19.1 1.0 NE2 A:GLN192 4.6 22.4 1.0 H A:LEU167 4.6 20.6 1.0 H17 A:4WI401 4.7 22.1 1.0 HE21 A:GLN192 4.8 21.9 1.0 C A:MET165 4.8 17.5 1.0 CD A:PRO168 4.8 28.1 1.0 HE2 A:MET165 4.9 31.1 1.0 CB A:GLN192 4.9 22.4 1.0 H26 A:4WI401 4.9 17.9 1.0 HD2 A:PRO168 4.9 27.7 1.0 H29 A:4WI401 4.9 22.6 1.0 HB3 A:LEU167 4.9 21.3 1.0 HG2 A:MET165 4.9 22.1 1.0 C A:LEU167 4.9 23.6 1.0 CD A:GLN192 5.0 21.0 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir


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 Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:30.9 occ:1.00 F2 A:4WI401 0.0 30.9 1.0 C22 A:4WI401 1.3 29.3 1.0 F1 A:4WI401 2.1 32.9 1.0 F3 A:4WI401 2.2 32.5 1.0 C21 A:4WI401 2.4 27.0 1.0 O4 A:4WI401 2.6 25.6 1.0 HE22 A:GLN192 2.8 21.9 1.0 O A:THR190 3.0 26.6 1.0 HB2 A:GLN192 3.0 22.2 1.0 NE2 A:GLN192 3.2 22.4 1.0 HG3 A:GLN192 3.3 21.9 1.0 H A:THR190 3.5 30.0 1.0 N4 A:4WI401 3.5 23.2 1.0 HD23 A:LEU167 3.6 20.8 1.0 HE21 A:GLN192 3.6 21.9 1.0 CD A:GLN192 3.7 21.0 1.0 CG A:GLN192 3.7 22.0 1.0 CB A:GLN192 3.8 22.4 1.0 H16 A:4WI401 3.8 23.3 1.0 H A:GLN192 3.8 23.5 1.0 O A:ARG188 4.0 19.0 1.0 O A:HOH568 4.1 56.3 1.0 HA A:GLN189 4.2 26.8 1.0 C A:THR190 4.2 29.7 1.0 N A:GLN192 4.2 23.6 1.0 O A:HOH712 4.3 33.9 1.0 N A:THR190 4.4 29.9 1.0 CD2 A:LEU167 4.4 20.8 1.0 HD22 A:LEU167 4.4 20.8 1.0 HA A:LEU167 4.5 22.0 1.0 HD3 A:PRO168 4.5 27.7 1.0 HB3 A:GLN192 4.5 22.2 1.0 CA A:GLN192 4.6 22.1 1.0 SD A:MET165 4.6 27.1 1.0 OE1 A:GLN192 4.6 19.4 1.0 HG2 A:GLN192 4.7 21.9 1.0 O A:GLU166 4.7 16.0 1.0 H15 A:4WI401 4.7 20.9 1.0 HB2 A:MET165 4.7 19.1 1.0 O A:GLN192 4.7 22.9 1.0 C14 A:4WI401 4.7 20.3 1.0 O A:HOH803 4.8 38.5 1.0 HD21 A:LEU167 4.8 20.8 1.0 HA A:ALA191 4.8 27.7 1.0 HG21 A:THR190 4.9 31.9 1.0 C A:ALA191 4.9 24.8 1.0 H28 A:4WI401 4.9 17.9 1.0 H29 A:4WI401 5.0 22.6 1.0 CA A:THR190 5.0 30.9 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir


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 Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.5 occ:1.00 F3 A:4WI401 0.0 32.5 1.0 C22 A:4WI401 1.3 29.3 1.0 F1 A:4WI401 2.1 32.9 1.0 F2 A:4WI401 2.2 30.9 1.0 C21 A:4WI401 2.4 27.0 1.0 HD3 A:PRO168 2.6 27.7 1.0 H16 A:4WI401 2.9 23.3 1.0 O A:HOH608 3.0 26.4 1.0 HA A:LEU167 3.0 22.0 1.0 N4 A:4WI401 3.0 23.2 1.0 O A:HOH803 3.1 38.5 1.0 O A:HOH568 3.1 56.3 1.0 O4 A:4WI401 3.2 25.6 1.0 HD23 A:LEU167 3.2 20.8 1.0 O A:GLU166 3.4 16.0 1.0 CD A:PRO168 3.6 28.1 1.0 H A:GLN192 3.7 23.5 1.0 HB2 A:GLN192 3.8 22.2 1.0 HD2 A:PRO168 3.9 27.7 1.0 CA A:LEU167 3.9 22.2 1.0 H29 A:4WI401 4.0 22.6 1.0 O A:THR190 4.1 26.6 1.0 O A:GLN192 4.1 22.9 1.0 O A:HOH712 4.1 33.9 1.0 HG3 A:PRO168 4.2 28.7 1.0 CD2 A:LEU167 4.2 20.8 1.0 N A:PRO168 4.3 25.8 1.0 C A:GLU166 4.3 18.9 1.0 C14 A:4WI401 4.4 20.3 1.0 C A:LEU167 4.5 23.6 1.0 CG A:PRO168 4.5 29.1 1.0 N A:GLN192 4.5 23.6 1.0 HD21 A:LEU167 4.5 20.8 1.0 N A:LEU167 4.6 20.7 1.0 H31 A:4WI401 4.6 22.6 1.0 H15 A:4WI401 4.6 20.9 1.0 HD22 A:LEU167 4.7 20.8 1.0 C23 A:4WI401 4.7 22.7 1.0 CB A:GLN192 4.7 22.4 1.0 HG3 A:GLN192 4.8 21.9 1.0 HA A:ALA191 4.8 27.7 1.0 CB A:LEU167 4.8 21.1 1.0 HE22 A:GLN192 4.9 21.9 1.0 HB3 A:LEU167 4.9 21.3 1.0 HG A:LEU167 4.9 20.9 1.0 C A:GLN192 4.9 23.4 1.0 CG A:LEU167 4.9 20.7 1.0 CA A:GLN192 5.0 22.1 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:35.8 occ:1.00 F1 B:4WI401 0.0 35.8 1.0 C22 B:4WI401 1.3 35.3 1.0 F3 B:4WI401 2.1 42.7 1.0 F2 B:4WI401 2.1 37.1 1.0 HE2 B:MET165 2.3 29.6 1.0 C21 B:4WI401 2.4 31.6 1.0 HE3 B:MET165 2.4 29.5 1.0 HD23 B:LEU167 2.7 26.7 1.0 H16 B:4WI401 2.7 26.1 1.0 O B:GLU166 2.7 25.4 1.0 CE B:MET165 2.7 30.7 1.0 N4 B:4WI401 2.9 25.3 1.0 HA B:LEU167 2.9 25.7 1.0 HE1 B:MET165 3.2 29.6 1.0 HB2 B:MET165 3.3 20.1 1.0 O4 B:4WI401 3.3 31.7 1.0 C B:GLU166 3.5 25.8 1.0 CD2 B:LEU167 3.5 27.2 1.0 HG3 B:MET165 3.7 22.1 1.0 HG B:LEU167 3.7 26.1 1.0 HD22 B:LEU167 3.7 26.7 1.0 CA B:LEU167 3.7 25.6 1.0 N B:LEU167 3.9 24.5 1.0 CG B:LEU167 4.1 25.7 1.0 H B:GLU166 4.1 21.7 1.0 CB B:MET165 4.1 20.4 1.0 CG B:MET165 4.1 21.1 1.0 HB2 B:GLN192 4.2 36.7 1.0 SD B:MET165 4.2 27.1 1.0 C14 B:4WI401 4.2 23.3 1.0 HD21 B:LEU167 4.3 26.7 1.0 HD3 B:PRO168 4.3 34.3 1.0 N B:GLU166 4.3 21.9 1.0 O B:HOH683 4.4 25.7 1.0 CB B:LEU167 4.5 25.4 1.0 OE1 B:GLN192 4.5 30.4 1.0 CA B:GLU166 4.5 23.9 1.0 O B:HOH680 4.6 45.9 1.0 C13 B:4WI401 4.6 24.4 1.0 HB3 B:MET165 4.6 20.1 1.0 H B:LEU167 4.7 25.1 1.0 H15 B:4WI401 4.7 23.9 1.0 H17 B:4WI401 4.7 24.0 1.0 O3 B:4WI401 4.7 20.8 1.0 HD2 B:PRO168 4.7 34.2 1.0 C B:MET165 4.8 19.5 1.0 C B:LEU167 4.8 27.3 1.0 HB3 B:LEU167 4.9 25.5 1.0 H26 B:4WI401 4.9 23.5 1.0 CD B:PRO168 4.9 35.3 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:37.1 occ:1.00 F2 B:4WI401 0.0 37.1 1.0 C22 B:4WI401 1.3 35.3 1.0 F3 B:4WI401 2.1 42.7 1.0 F1 B:4WI401 2.1 35.8 1.0 C21 B:4WI401 2.4 31.6 1.0 H16 B:4WI401 2.8 26.1 1.0 O B:HOH680 2.8 45.9 1.0 HD3 B:PRO168 2.9 34.3 1.0 N4 B:4WI401 2.9 25.3 1.0 HA B:LEU167 3.0 25.7 1.0 O B:HOH683 3.1 25.7 1.0 O4 B:4WI401 3.2 31.7 1.0 O B:GLU166 3.2 25.4 1.0 HD23 B:LEU167 3.5 26.7 1.0 CD B:PRO168 3.7 35.3 1.0 CA B:LEU167 3.9 25.6 1.0 HD2 B:PRO168 4.0 34.2 1.0 H29 B:4WI401 4.0 24.3 1.0 HE3 B:MET165 4.2 29.5 1.0 C B:GLU166 4.2 25.8 1.0 H B:GLN192 4.2 42.2 1.0 HE2 B:MET165 4.2 29.6 1.0 N B:PRO168 4.3 31.1 1.0 C14 B:4WI401 4.3 23.3 1.0 C B:LEU167 4.4 27.3 1.0 CD2 B:LEU167 4.4 27.2 1.0 HB2 B:GLN192 4.4 36.7 1.0 N B:LEU167 4.5 24.5 1.0 O B:GLN192 4.6 34.2 1.0 H15 B:4WI401 4.6 23.9 1.0 CE B:MET165 4.6 30.7 1.0 H31 B:4WI401 4.6 24.3 1.0 O B:THR190 4.7 46.5 1.0 C23 B:4WI401 4.7 24.6 1.0 HD21 B:LEU167 4.8 26.7 1.0 HE1 B:MET165 4.8 29.6 1.0 H17 B:4WI401 4.8 24.0 1.0 HG3 B:PRO168 4.9 35.0 1.0 HG3 B:GLN189 4.9 37.5 1.0 CB B:LEU167 4.9 25.4 1.0 CG B:PRO168 4.9 35.2 1.0 HD22 B:LEU167 4.9 26.7 1.0 HA B:GLN189 4.9 33.3 1.0 HB3 B:LEU167 5.0 25.5 1.0 HG B:LEU167 5.0 26.1 1.0 C15 B:4WI401 5.0 23.7 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:42.7 occ:1.00 F3 B:4WI401 0.0 42.7 1.0 C22 B:4WI401 1.3 35.3 1.0 F1 B:4WI401 2.1 35.8 1.0 F2 B:4WI401 2.1 37.1 1.0 C21 B:4WI401 2.3 31.6 1.0 O4 B:4WI401 2.5 31.7 1.0 HE3 B:MET165 2.9 29.5 1.0 HE1 B:MET165 3.0 29.6 1.0 HE2 B:MET165 3.1 29.6 1.0 CE B:MET165 3.2 30.7 1.0 O B:THR190 3.3 46.5 1.0 OE1 B:GLN192 3.4 30.4 1.0 N4 B:4WI401 3.5 25.3 1.0 HA B:GLN189 3.6 33.3 1.0 HG3 B:GLN192 3.6 34.2 1.0 O B:HOH680 3.6 45.9 1.0 HB2 B:GLN192 3.6 36.7 1.0 HD23 B:LEU167 3.7 26.7 1.0 H16 B:4WI401 3.8 26.1 1.0 O B:ARG188 3.9 25.0 1.0 H B:GLN192 3.9 42.2 1.0 CD B:GLN192 4.0 30.0 1.0 H B:THR190 4.0 38.1 1.0 CG B:GLN192 4.1 35.0 1.0 CB B:GLN192 4.3 36.8 1.0 HA B:LEU167 4.4 25.7 1.0 N B:THR190 4.4 36.9 1.0 CA B:GLN189 4.5 33.3 1.0 HG3 B:GLN189 4.5 37.5 1.0 C B:THR190 4.5 44.5 1.0 O B:GLU166 4.5 25.4 1.0 CD2 B:LEU167 4.5 27.2 1.0 HD3 B:PRO168 4.6 34.3 1.0 N B:GLN192 4.6 42.8 1.0 HD22 B:LEU167 4.6 26.7 1.0 C B:GLN189 4.7 35.4 1.0 HB2 B:MET165 4.7 20.1 1.0 H15 B:4WI401 4.7 23.9 1.0 H28 B:4WI401 4.7 23.6 1.0 C14 B:4WI401 4.8 23.3 1.0 C B:ARG188 4.9 29.4 1.0 HG21 B:THR190 4.9 50.0 1.0 CA B:GLN192 5.0 38.3 1.0 SD B:MET165 5.0 27.1 1.0 O B:GLN192 5.0 34.2 1.0 HD21 B:LEU167 5.0 26.7 1.0

G.D.Noske, A.S.Godoy, G.Oliva. Crystal Structure of Uncleaved Sars-Cov-2 Main Protease C145S Mutant in Complex with Nirmatrelvir To Be Published.