Fluorine in PDB 8e25: Crystal Structure of Sars-Cov-2 Main Protease M49I Mutant in Complex with Nirmatrelvir

The structure of Crystal Structure of Sars-Cov-2 Main Protease M49I Mutant in Complex with Nirmatrelvir, PDB code: 8e25 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)	72.06 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.859, 100.068, 103.533, 90, 90, 90
R / Rfree (%)	19.4 / 24

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease M49I Mutant in Complex with Nirmatrelvir (pdb code 8e25). 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 Sars-Cov-2 Main Protease M49I Mutant in Complex with Nirmatrelvir, PDB code: 8e25:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease M49I 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 Sars-Cov-2 Main Protease M49I Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:61.0 occ:1.00 F1 A:4WI401 0.0 61.0 1.0 C22 A:4WI401 1.3 61.1 1.0 HE2 A:MET165 2.0 39.2 1.0 F3 A:4WI401 2.1 67.3 1.0 F2 A:4WI401 2.1 64.3 1.0 C21 A:4WI401 2.4 53.0 1.0 HD23 A:LEU167 2.7 33.9 1.0 CE A:MET165 2.8 39.6 1.0 HE1 A:MET165 2.9 39.1 1.0 H16 A:4WI401 3.1 47.4 1.0 O4 A:4WI401 3.1 51.8 1.0 N4 A:4WI401 3.1 46.3 1.0 HE3 A:MET165 3.2 39.1 1.0 HA A:LEU167 3.2 33.9 1.0 HB2 A:GLN192 3.5 44.4 1.0 CD2 A:LEU167 3.6 34.0 1.0 HE22 A:GLN192 3.7 35.6 1.0 O A:GLU166 3.7 31.8 1.0 HB2 A:MET165 3.7 29.1 1.0 HD22 A:LEU167 3.7 33.9 1.0 NE2 A:GLN192 3.9 35.3 1.0 HD3 A:PRO168 3.9 42.6 1.0 HE21 A:GLN192 3.9 35.6 1.0 HB3 A:GLN192 4.0 44.4 1.0 O A:HOH544 4.1 43.2 1.0 CA A:LEU167 4.2 34.0 1.0 HG A:LEU167 4.2 34.2 1.0 HD21 A:LEU167 4.2 33.9 1.0 SD A:MET165 4.2 38.1 1.0 CB A:GLN192 4.2 45.0 1.0 C A:GLU166 4.3 31.9 1.0 HG3 A:MET165 4.3 32.6 1.0 CG A:LEU167 4.4 33.6 1.0 C14 A:4WI401 4.5 44.7 1.0 N A:LEU167 4.5 32.2 1.0 CD A:GLN192 4.5 36.1 1.0 CB A:MET165 4.5 29.0 1.0 CG A:MET165 4.6 32.2 1.0 HA A:GLN189 4.6 40.1 1.0 O A:THR190 4.8 48.6 1.0 CB A:LEU167 4.8 33.7 1.0 H15 A:4WI401 4.8 45.2 1.0 O A:ARG188 4.8 27.9 1.0 H A:GLU166 4.8 27.7 1.0 C13 A:4WI401 4.9 46.9 1.0 CD A:PRO168 4.9 43.1 1.0 HB3 A:MET165 4.9 29.1 1.0 O3 A:4WI401 5.0 49.4 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease M49I 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 Sars-Cov-2 Main Protease M49I Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:64.3 occ:1.00 F2 A:4WI401 0.0 64.3 1.0 C22 A:4WI401 1.3 61.1 1.0 F1 A:4WI401 2.1 61.0 1.0 F3 A:4WI401 2.1 67.3 1.0 C21 A:4WI401 2.4 53.0 1.0 H16 A:4WI401 2.4 47.4 1.0 N4 A:4WI401 2.7 46.3 1.0 HD3 A:PRO168 2.8 42.6 1.0 HA A:LEU167 2.8 33.9 1.0 O A:GLU166 3.1 31.8 1.0 O A:HOH544 3.2 43.2 1.0 O A:HOH595 3.2 31.9 1.0 O4 A:4WI401 3.4 51.8 1.0 HD23 A:LEU167 3.5 33.9 1.0 CD A:PRO168 3.6 43.1 1.0 HG3 A:PRO168 3.7 42.9 1.0 CA A:LEU167 3.7 34.0 1.0 H29 A:4WI401 3.7 43.4 1.0 HE2 A:MET165 4.0 39.2 1.0 N A:PRO168 4.0 40.5 1.0 C A:GLU166 4.1 31.9 1.0 C A:LEU167 4.1 35.5 1.0 C14 A:4WI401 4.1 44.7 1.0 CG A:PRO168 4.2 43.7 1.0 HB2 A:GLN192 4.2 44.4 1.0 N A:LEU167 4.3 32.2 1.0 H31 A:4WI401 4.3 43.4 1.0 HD2 A:PRO168 4.4 42.6 1.0 C23 A:4WI401 4.4 43.3 1.0 CD2 A:LEU167 4.5 34.0 1.0 H15 A:4WI401 4.5 45.2 1.0 O A:GLN192 4.6 46.1 1.0 CB A:LEU167 4.8 33.7 1.0 HA A:PRO168 4.8 39.6 1.0 H17 A:4WI401 4.8 42.8 1.0 HG2 A:PRO168 4.8 42.9 1.0 C15 A:4WI401 4.8 43.7 1.0 HD21 A:LEU167 4.8 33.9 1.0 CE A:MET165 4.8 39.6 1.0 HB3 A:LEU167 4.8 33.8 1.0 H A:GLN192 4.9 47.9 1.0 HE1 A:MET165 4.9 39.1 1.0 HB3 A:GLN192 4.9 44.4 1.0 H18 A:4WI401 5.0 42.8 1.0 CA A:PRO168 5.0 39.4 1.0 HG A:LEU167 5.0 34.2 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease M49I 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 Sars-Cov-2 Main Protease M49I Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:67.3 occ:1.00 F3 A:4WI401 0.0 67.3 1.0 C22 A:4WI401 1.3 61.1 1.0 F1 A:4WI401 2.1 61.0 1.0 F2 A:4WI401 2.1 64.3 1.0 C21 A:4WI401 2.4 53.0 1.0 O4 A:4WI401 2.7 51.8 1.0 O A:HOH544 2.8 43.2 1.0 HB2 A:GLN192 3.1 44.4 1.0 O A:THR190 3.1 48.6 1.0 HE22 A:GLN192 3.2 35.6 1.0 HA A:GLN189 3.4 40.1 1.0 N4 A:4WI401 3.5 46.3 1.0 HE2 A:MET165 3.7 39.2 1.0 H16 A:4WI401 3.7 47.4 1.0 NE2 A:GLN192 3.8 35.3 1.0 HE1 A:MET165 3.9 39.1 1.0 CB A:GLN192 4.0 45.0 1.0 H A:GLN192 4.1 47.9 1.0 HD23 A:LEU167 4.1 33.9 1.0 HD3 A:PRO168 4.1 42.6 1.0 HE21 A:GLN192 4.1 35.6 1.0 C A:THR190 4.2 47.3 1.0 CE A:MET165 4.2 39.6 1.0 HG3 A:GLN189 4.2 42.9 1.0 O A:ARG188 4.2 27.9 1.0 HB3 A:GLN192 4.3 44.4 1.0 CA A:GLN189 4.3 39.9 1.0 H A:THR190 4.3 45.3 1.0 N A:THR190 4.4 45.1 1.0 HA A:LEU167 4.5 33.9 1.0 N A:GLN192 4.5 48.5 1.0 C A:GLN189 4.5 44.4 1.0 HE3 A:MET165 4.5 39.1 1.0 H29 A:4WI401 4.6 43.4 1.0 O A:GLN192 4.7 46.1 1.0 H15 A:4WI401 4.7 45.2 1.0 CD A:GLN192 4.7 36.1 1.0 C14 A:4WI401 4.8 44.7 1.0 HG3 A:PRO168 4.8 42.9 1.0 CA A:GLN192 4.8 46.4 1.0 HA A:ALA191 4.8 51.6 1.0 CG A:GLN192 4.8 41.3 1.0 HG3 A:GLN192 5.0 40.8 1.0 HE22 A:GLN189 5.0 50.5 1.0 CD2 A:LEU167 5.0 34.0 1.0 O A:GLU166 5.0 31.8 1.0 CA A:THR190 5.0 46.9 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease M49I 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 Sars-Cov-2 Main Protease M49I Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:78.5 occ:1.00 F1 B:4WI401 0.0 78.5 1.0 C22 B:4WI401 1.3 70.9 1.0 F3 B:4WI401 2.1 68.9 1.0 F2 B:4WI401 2.1 78.4 1.0 C21 B:4WI401 2.4 64.7 1.0 H16 B:4WI401 3.0 54.4 1.0 N4 B:4WI401 3.0 53.4 1.0 O4 B:4WI401 3.2 68.6 1.0 HD3 B:PRO168 3.3 38.2 1.0 O B:HOH548 3.4 46.1 1.0 O B:THR190 3.6 50.7 1.0 H29 B:4WI401 3.7 45.6 1.0 H B:GLN192 3.8 35.6 1.0 HA B:LEU167 3.9 32.4 1.0 HE21 B:GLN189 3.9 65.0 1.0 HG3 B:PRO168 4.0 39.2 1.0 HE22 B:GLN189 4.0 65.2 1.0 O B:GLU166 4.1 30.0 1.0 HB2 B:GLN192 4.2 33.8 1.0 HD23 B:LEU167 4.2 32.4 1.0 HE3 B:MET165 4.2 39.9 1.0 CD B:PRO168 4.2 38.0 1.0 H31 B:4WI401 4.3 45.6 1.0 HG3 B:GLN192 4.3 32.9 1.0 C14 B:4WI401 4.3 47.8 1.0 NE2 B:GLN189 4.4 66.5 1.0 C23 B:4WI401 4.4 45.4 1.0 H15 B:4WI401 4.4 48.1 1.0 O B:GLN192 4.5 36.8 1.0 HA B:ALA191 4.5 40.7 1.0 CG B:PRO168 4.6 39.7 1.0 N B:GLN192 4.6 36.2 1.0 HE1 B:MET165 4.6 39.8 1.0 HE22 B:GLN192 4.6 30.7 1.0 HD2 B:PRO168 4.8 38.2 1.0 CE B:MET165 4.8 40.5 1.0 C B:THR190 4.8 50.4 1.0 CA B:LEU167 4.9 31.7 1.0 C15 B:4WI401 4.9 46.1 1.0 CB B:GLN192 4.9 34.5 1.0 HG2 B:PRO168 4.9 39.2 1.0 H B:THR190 4.9 59.5 1.0 H20 B:4WI401 4.9 44.4 1.0 N B:PRO168 5.0 37.6 1.0 H21 B:4WI401 5.0 44.5 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease M49I 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 Sars-Cov-2 Main Protease M49I Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:78.4 occ:1.00 F2 B:4WI401 0.0 78.4 1.0 C22 B:4WI401 1.3 70.9 1.0 F3 B:4WI401 2.1 68.9 1.0 F1 B:4WI401 2.1 78.5 1.0 C21 B:4WI401 2.4 64.7 1.0 HE22 B:GLN192 2.5 30.7 1.0 O4 B:4WI401 2.6 68.6 1.0 HE1 B:MET165 2.8 39.8 1.0 HE3 B:MET165 2.8 39.9 1.0 HG3 B:GLN192 2.9 32.9 1.0 O B:THR190 3.1 50.7 1.0 NE2 B:GLN192 3.2 30.3 1.0 CE B:MET165 3.2 40.5 1.0 HB2 B:GLN192 3.3 33.8 1.0 N4 B:4WI401 3.6 53.4 1.0 CG B:GLN192 3.6 32.6 1.0 HE21 B:GLN192 3.7 30.7 1.0 H B:THR190 3.7 59.5 1.0 CD B:GLN192 3.7 31.7 1.0 H16 B:4WI401 3.8 54.4 1.0 HE2 B:MET165 3.8 39.8 1.0 HD23 B:LEU167 3.9 32.4 1.0 CB B:GLN192 3.9 34.5 1.0 H B:GLN192 4.0 35.6 1.0 O B:ARG188 4.1 39.0 1.0 HE22 B:GLN189 4.2 65.2 1.0 C B:THR190 4.3 50.4 1.0 N B:GLN192 4.4 36.2 1.0 HE21 B:GLN189 4.4 65.0 1.0 HG2 B:GLN192 4.5 32.8 1.0 HA B:GLN189 4.5 59.6 1.0 N B:THR190 4.5 61.3 1.0 HD3 B:PRO168 4.6 38.2 1.0 HB3 B:GLN192 4.6 33.8 1.0 NE2 B:GLN189 4.7 66.5 1.0 SD B:MET165 4.7 38.2 1.0 HA B:LEU167 4.7 32.4 1.0 HB2 B:MET165 4.7 32.4 1.0 HG21 B:THR190 4.7 54.4 1.0 CA B:GLN192 4.7 33.6 1.0 CD2 B:LEU167 4.8 32.5 1.0 HG23 B:THR190 4.8 54.3 1.0 H25 B:4WI401 4.8 38.3 1.0 H15 B:4WI401 4.8 48.1 1.0 C14 B:4WI401 4.8 47.8 1.0 HD22 B:LEU167 4.8 32.4 1.0 OE1 B:GLN192 4.8 30.0 1.0 HA B:ALA191 4.9 40.7 1.0 O B:GLU166 4.9 30.0 1.0 O B:GLN192 4.9 36.8 1.0 H29 B:4WI401 5.0 45.6 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease M49I 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 Sars-Cov-2 Main Protease M49I Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:68.9 occ:1.00 F3 B:4WI401 0.0 68.9 1.0 C22 B:4WI401 1.3 70.9 1.0 F2 B:4WI401 2.1 78.4 1.0 F1 B:4WI401 2.1 78.5 1.0 C21 B:4WI401 2.4 64.7 1.0 HE3 B:MET165 2.4 39.9 1.0 H16 B:4WI401 2.5 54.4 1.0 HD23 B:LEU167 2.7 32.4 1.0 HA B:LEU167 2.8 32.4 1.0 N4 B:4WI401 2.8 53.4 1.0 O B:GLU166 2.9 30.0 1.0 CE B:MET165 3.0 40.5 1.0 HE1 B:MET165 3.1 39.8 1.0 HE2 B:MET165 3.1 39.8 1.0 O4 B:4WI401 3.4 68.6 1.0 HD3 B:PRO168 3.4 38.2 1.0 C B:GLU166 3.6 30.9 1.0 CD2 B:LEU167 3.7 32.5 1.0 CA B:LEU167 3.7 31.7 1.0 HB2 B:MET165 3.7 32.4 1.0 HB2 B:GLN192 3.8 33.8 1.0 O B:HOH548 3.8 46.1 1.0 N B:LEU167 3.9 31.9 1.0 HD22 B:LEU167 4.0 32.4 1.0 HG B:LEU167 4.1 32.2 1.0 HD21 B:LEU167 4.2 32.4 1.0 C14 B:4WI401 4.2 47.8 1.0 CG B:LEU167 4.3 32.2 1.0 HE22 B:GLN192 4.3 30.7 1.0 CD B:PRO168 4.3 38.0 1.0 H B:GLU166 4.4 29.7 1.0 H20 B:4WI401 4.5 44.4 1.0 CB B:LEU167 4.5 31.8 1.0 HG3 B:GLN192 4.6 32.9 1.0 CB B:MET165 4.6 32.4 1.0 H15 B:4WI401 4.6 48.1 1.0 N B:GLU166 4.6 29.2 1.0 C B:LEU167 4.6 35.0 1.0 SD B:MET165 4.7 38.2 1.0 CB B:GLN192 4.7 34.5 1.0 H29 B:4WI401 4.7 45.6 1.0 NE2 B:GLN192 4.7 30.3 1.0 HD2 B:PRO168 4.7 38.2 1.0 H B:LEU167 4.7 31.6 1.0 HB3 B:LEU167 4.8 31.9 1.0 O B:GLN192 4.8 36.8 1.0 C13 B:4WI401 4.8 45.7 1.0 CA B:GLU166 4.8 32.1 1.0 O3 B:4WI401 4.8 44.8 1.0 H B:GLN192 4.8 35.6 1.0 N B:PRO168 4.8 37.6 1.0 HG3 B:MET165 4.9 35.5 1.0 O B:THR190 4.9 50.7 1.0 HB3 B:MET165 5.0 32.4 1.0 CG B:MET165 5.0 35.9 1.0 CG B:GLN192 5.0 32.6 1.0

G.D.Noske, A.S.Godoy, G.Oliva. Crystal Structure of Sars-Cov-2 Main Protease N142S Mutant in Complex with Nirmatrelvir To Be Published.