Fluorine in PDB 9cjq: X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir

The structure of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir, PDB code: 9cjq was solved by M.A.Esler, K.Shi, R.S.Harris, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.33 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.022, 106.994, 116.522, 90, 99.34, 90
R / Rfree (%)	22.1 / 25.8

The structure of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir (pdb code 9cjq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir, PDB code: 9cjq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:49.5 occ:1.00 F28 A:7YY401 0.0 49.5 1.0 C27 A:7YY401 1.4 43.7 1.0 NE2 A:GLN189 2.2 59.3 1.0 C29 A:7YY401 2.3 41.1 1.0 C26 A:7YY401 2.4 43.3 1.0 C25 A:7YY401 2.8 40.9 1.0 CD A:GLN189 3.2 58.8 1.0 C30 A:7YY401 3.6 39.9 1.0 C34 A:7YY401 3.6 43.4 1.0 CA A:GLN189 3.7 59.6 1.0 CB A:GLN189 3.7 61.2 1.0 CG A:GLN189 3.9 61.6 1.0 N A:GLN189 4.0 59.1 1.0 OE1 A:GLN189 4.0 58.8 1.0 C32 A:7YY401 4.1 41.8 1.0 N24 A:7YY401 4.3 49.4 1.0 C A:ARG188 4.4 57.2 1.0 O A:ARG188 4.5 55.7 1.0 O36 A:7YY401 4.6 40.1 1.0 F31 A:7YY401 4.7 51.0 1.0 NE2 A:HIS41 4.7 54.7 1.0 CB A:MET165 4.7 48.3 1.0 C35 A:7YY401 4.9 45.6 1.0 CE1 A:HIS41 4.9 54.6 1.0

Fluorine binding site 2 out of 12 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:51.0 occ:1.00 F31 A:7YY401 0.0 51.0 1.0 C30 A:7YY401 1.3 39.9 1.0 C32 A:7YY401 2.3 41.8 1.0 C29 A:7YY401 2.4 41.1 1.0 F33 A:7YY401 2.7 45.6 1.0 CE A:MET165 3.1 50.8 1.0 CA A:ASP187 3.1 50.9 1.0 CB A:ASP187 3.2 50.1 1.0 C A:ASP187 3.2 53.8 1.0 ND1 A:HIS41 3.3 51.9 1.0 N A:ARG188 3.6 54.5 1.0 CG A:HIS41 3.6 50.1 1.0 C27 A:7YY401 3.6 43.7 1.0 C34 A:7YY401 3.6 43.4 1.0 O A:ASP187 3.7 59.3 1.0 CB A:HIS41 3.8 47.4 1.0 CE1 A:HIS41 3.8 54.6 1.0 C26 A:7YY401 4.1 43.3 1.0 CD2 A:HIS41 4.3 51.8 1.0 OH A:TYR54 4.3 41.0 1.0 CA A:ARG188 4.3 57.3 1.0 O A:HOH516 4.4 38.4 1.0 NE2 A:HIS41 4.4 54.7 1.0 N A:ASP187 4.6 50.9 1.0 CG A:ASP187 4.6 51.5 1.0 F28 A:7YY401 4.7 49.5 1.0 C A:ARG188 4.8 57.2 1.0 SD A:MET165 4.8 52.6 1.0 CB A:MET165 4.8 48.3 1.0 O A:VAL186 4.9 50.9 1.0

Fluorine binding site 3 out of 12 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:45.6 occ:1.00 F33 A:7YY401 0.0 45.6 1.0 C32 A:7YY401 1.4 41.8 1.0 C30 A:7YY401 2.3 39.9 1.0 C34 A:7YY401 2.4 43.4 1.0 F31 A:7YY401 2.7 51.0 1.0 CB A:HIS41 3.1 47.4 1.0 O A:HIS164 3.3 44.5 1.0 CG A:HIS41 3.4 50.1 1.0 C29 A:7YY401 3.6 41.1 1.0 C26 A:7YY401 3.6 43.3 1.0 SG A:CYS145 3.7 43.3 1.0 CD2 A:HIS41 3.9 51.8 1.0 C A:HIS164 3.9 44.0 1.0 O A:HOH516 4.1 38.4 1.0 C27 A:7YY401 4.1 43.7 1.0 ND1 A:HIS41 4.1 51.9 1.0 CL2 A:7YY401 4.2 44.0 1.0 CA A:HIS164 4.3 42.9 1.0 CB A:HIS164 4.3 44.0 1.0 CD2 A:HIS164 4.4 45.1 1.0 CA A:HIS41 4.6 46.3 1.0 CG A:HIS164 4.6 43.9 1.0 CE A:MET165 4.7 50.8 1.0 NE2 A:HIS41 4.7 54.7 1.0 N A:MET165 4.8 44.5 1.0 CE1 A:HIS41 4.8 54.6 1.0 CB A:PRO39 4.9 41.8 1.0 C25 A:7YY401 4.9 40.9 1.0 CB A:MET165 4.9 48.3 1.0 N A:HIS41 4.9 44.7 1.0 N24 A:7YY401 4.9 49.4 1.0 CB A:CYS145 5.0 42.9 1.0

Fluorine binding site 4 out of 12 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:42.3 occ:1.00 F28 B:7YY401 0.0 42.3 1.0 C27 B:7YY401 1.4 38.0 1.0 C29 B:7YY401 2.3 32.5 1.0 C26 B:7YY401 2.4 32.5 1.0 C25 B:7YY401 2.8 37.2 1.0 O B:HOH520 3.0 35.0 1.0 CG B:GLN189 3.1 51.3 1.0 CA B:GLN189 3.2 51.5 1.0 CB B:GLN189 3.3 52.7 1.0 C30 B:7YY401 3.6 39.2 1.0 C34 B:7YY401 3.6 30.1 1.0 O B:HOH524 3.8 44.7 1.0 O B:HOH533 3.9 33.6 1.0 CD B:GLN189 3.9 55.5 1.0 NE2 B:GLN189 3.9 48.5 1.0 N B:GLN189 4.0 49.0 1.0 C32 B:7YY401 4.1 33.9 1.0 O B:ARG188 4.1 51.9 1.0 N24 B:7YY401 4.3 41.1 1.0 C B:ARG188 4.3 48.1 1.0 CB B:MET165 4.4 41.1 1.0 C B:GLN189 4.4 51.5 1.0 O36 B:7YY401 4.5 40.2 1.0 F31 B:7YY401 4.7 51.5 1.0 N B:THR190 4.8 51.8 1.0 OE1 B:GLN189 4.9 61.2 1.0 C35 B:7YY401 4.9 36.5 1.0 NE2 B:HIS41 5.0 45.9 1.0

Fluorine binding site 5 out of 12 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:51.5 occ:1.00 F31 B:7YY401 0.0 51.5 1.0 C30 B:7YY401 1.3 39.2 1.0 C32 B:7YY401 2.3 33.9 1.0 C29 B:7YY401 2.4 32.5 1.0 F33 B:7YY401 2.7 38.0 1.0 CA B:ASP187 3.1 44.6 1.0 C B:ASP187 3.3 46.9 1.0 CB B:ASP187 3.3 42.5 1.0 N B:ARG188 3.4 46.2 1.0 ND1 B:HIS41 3.4 44.7 1.0 C27 B:7YY401 3.6 38.0 1.0 C34 B:7YY401 3.6 30.1 1.0 CE1 B:HIS41 3.8 45.9 1.0 CG B:HIS41 3.9 43.9 1.0 O B:ASP187 3.9 54.9 1.0 SD B:MET165 3.9 62.5 1.0 C26 B:7YY401 4.1 32.5 1.0 CA B:ARG188 4.2 47.9 1.0 NE2 B:HIS41 4.3 45.9 1.0 C B:ARG188 4.4 48.1 1.0 CB B:HIS41 4.4 42.7 1.0 CD2 B:HIS41 4.4 44.6 1.0 O B:ARG188 4.4 51.9 1.0 N B:ASP187 4.5 44.1 1.0 CB B:MET165 4.5 41.1 1.0 O B:VAL186 4.6 45.0 1.0 OH B:TYR54 4.7 47.0 1.0 F28 B:7YY401 4.7 42.3 1.0 CG B:ASP187 4.7 43.0 1.0 CG B:MET165 4.7 41.2 1.0 N B:GLN189 4.9 49.0 1.0 CD2 B:HIS164 5.0 38.3 1.0 CB B:HIS164 5.0 38.0 1.0 C B:VAL186 5.0 44.8 1.0

Fluorine binding site 6 out of 12 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:38.0 occ:1.00 F33 B:7YY401 0.0 38.0 1.0 C32 B:7YY401 1.4 33.9 1.0 C30 B:7YY401 2.3 39.2 1.0 C34 B:7YY401 2.4 30.1 1.0 F31 B:7YY401 2.7 51.5 1.0 O B:HIS164 3.3 38.7 1.0 CB B:HIS41 3.4 42.7 1.0 CG B:HIS41 3.4 43.9 1.0 C29 B:7YY401 3.6 32.5 1.0 C26 B:7YY401 3.6 32.5 1.0 CD2 B:HIS41 3.8 44.6 1.0 SG B:CYS145 3.8 41.2 1.0 C B:HIS164 3.8 38.4 1.0 ND1 B:HIS41 3.9 44.7 1.0 C27 B:7YY401 4.1 38.0 1.0 CB B:HIS164 4.1 38.0 1.0 CA B:HIS164 4.2 37.5 1.0 CD2 B:HIS164 4.3 38.3 1.0 NE2 B:HIS41 4.4 45.9 1.0 CL2 B:7YY401 4.4 39.4 1.0 CG B:HIS164 4.5 37.7 1.0 CE1 B:HIS41 4.5 45.9 1.0 CB B:MET165 4.6 41.1 1.0 N B:MET165 4.7 38.8 1.0 CA B:HIS41 4.8 43.6 1.0 C25 B:7YY401 4.9 37.2 1.0 CA B:MET165 5.0 39.9 1.0 CB B:ASP187 5.0 42.5 1.0 N24 B:7YY401 5.0 41.1 1.0

Fluorine binding site 7 out of 12 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:36.0 occ:1.00 F28 C:7YY401 0.0 36.0 1.0 C27 C:7YY401 1.4 29.9 1.0 C29 C:7YY401 2.3 20.9 1.0 C26 C:7YY401 2.4 26.2 1.0 C25 C:7YY401 2.8 23.9 1.0 CG C:GLN189 3.2 40.6 1.0 CA C:GLN189 3.2 37.1 1.0 CB C:GLN189 3.2 30.9 1.0 C30 C:7YY401 3.6 27.1 1.0 C34 C:7YY401 3.6 25.6 1.0 N C:GLN189 3.8 33.4 1.0 CD C:GLN189 3.9 43.1 1.0 NE2 C:GLN189 4.0 33.7 1.0 C32 C:7YY401 4.1 27.6 1.0 O C:ARG188 4.1 39.8 1.0 C C:ARG188 4.2 31.5 1.0 O C:HOH517 4.2 21.5 1.0 N24 C:7YY401 4.3 27.6 1.0 CB C:MET165 4.3 27.5 1.0 C C:GLN189 4.4 37.4 1.0 O36 C:7YY401 4.5 33.6 1.0 F31 C:7YY401 4.7 33.9 1.0 N C:THR190 4.8 36.1 1.0 NE2 C:HIS41 4.9 26.3 1.0 OE1 C:GLN189 4.9 46.2 1.0 SD C:MET165 4.9 46.2 1.0 C35 C:7YY401 4.9 31.7 1.0

Fluorine binding site 8 out of 12 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:33.9 occ:1.00 F31 C:7YY401 0.0 33.9 1.0 C30 C:7YY401 1.3 27.1 1.0 C32 C:7YY401 2.3 27.6 1.0 C29 C:7YY401 2.4 20.9 1.0 F33 C:7YY401 2.7 33.5 1.0 CA C:ASP187 3.2 28.7 1.0 CB C:ASP187 3.3 20.8 1.0 ND1 C:HIS41 3.3 29.4 1.0 C C:ASP187 3.3 27.7 1.0 N C:ARG188 3.5 26.8 1.0 C27 C:7YY401 3.6 29.9 1.0 C34 C:7YY401 3.6 25.6 1.0 CG C:HIS41 3.7 30.0 1.0 CE1 C:HIS41 3.8 29.4 1.0 O C:ASP187 4.0 38.7 1.0 SD C:MET165 4.0 46.2 1.0 C26 C:7YY401 4.1 26.2 1.0 CB C:HIS41 4.1 26.6 1.0 O C:HOH522 4.3 22.9 1.0 CA C:ARG188 4.3 28.0 1.0 CD2 C:HIS41 4.4 24.4 1.0 NE2 C:HIS41 4.4 26.3 1.0 OH C:TYR54 4.4 34.7 1.0 CB C:MET165 4.5 27.5 1.0 N C:ASP187 4.6 25.6 1.0 C C:ARG188 4.6 31.5 1.0 CG C:ASP187 4.7 29.3 1.0 F28 C:7YY401 4.7 36.0 1.0 O C:VAL186 4.8 37.7 1.0 CG C:MET165 4.8 24.9 1.0 CD2 C:HIS164 4.8 19.5 1.0 O C:ARG188 4.8 39.8 1.0 CB C:HIS164 4.9 24.0 1.0 O C:HIS164 4.9 33.1 1.0

Fluorine binding site 9 out of 12 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:33.5 occ:1.00 F33 C:7YY401 0.0 33.5 1.0 C32 C:7YY401 1.4 27.6 1.0 C30 C:7YY401 2.3 27.1 1.0 C34 C:7YY401 2.4 25.6 1.0 F31 C:7YY401 2.7 33.9 1.0 O C:HIS164 3.1 33.1 1.0 CB C:HIS41 3.3 26.6 1.0 CG C:HIS41 3.4 30.0 1.0 C29 C:7YY401 3.6 20.9 1.0 C26 C:7YY401 3.6 26.2 1.0 SG C:CYS145 3.6 35.7 1.0 C C:HIS164 3.8 25.7 1.0 CD2 C:HIS41 3.8 24.4 1.0 ND1 C:HIS41 4.0 29.4 1.0 C27 C:7YY401 4.1 29.9 1.0 O C:HOH522 4.1 22.9 1.0 CA C:HIS164 4.1 28.6 1.0 CB C:HIS164 4.2 24.0 1.0 CL2 C:7YY401 4.2 45.8 1.0 CD2 C:HIS164 4.4 19.5 1.0 CG C:HIS164 4.5 19.6 1.0 NE2 C:HIS41 4.5 26.3 1.0 CE1 C:HIS41 4.6 29.4 1.0 CB C:MET165 4.7 27.5 1.0 N C:MET165 4.7 21.6 1.0 CA C:HIS41 4.8 26.9 1.0 CB C:PRO39 4.9 26.5 1.0 C25 C:7YY401 4.9 23.9 1.0 N24 C:7YY401 5.0 27.6 1.0 CA C:MET165 5.0 32.4 1.0

Fluorine binding site 10 out of 12 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ D:F401 b:36.1 occ:1.00 F28 D:7YY401 0.0 36.1 1.0 C27 D:7YY401 1.4 31.2 1.0 NE2 D:GLN189 2.1 50.8 1.0 C29 D:7YY401 2.3 29.8 1.0 C26 D:7YY401 2.4 23.0 1.0 C25 D:7YY401 2.8 27.1 1.0 CD D:GLN189 3.1 47.9 1.0 O D:HOH522 3.3 33.8 1.0 C30 D:7YY401 3.6 29.7 1.0 CB D:GLN189 3.6 44.4 1.0 C34 D:7YY401 3.6 27.4 1.0 CA D:GLN189 3.7 38.4 1.0 CG D:GLN189 3.8 43.1 1.0 O D:HOH536 3.8 28.1 1.0 O D:HOH523 3.8 39.2 1.0 OE1 D:GLN189 4.0 50.2 1.0 N D:GLN189 4.1 32.0 1.0 C32 D:7YY401 4.1 29.1 1.0 N24 D:7YY401 4.3 41.1 1.0 C D:ARG188 4.5 33.7 1.0 NE2 D:HIS41 4.6 35.8 1.0 O D:ARG188 4.6 46.5 1.0 F31 D:7YY401 4.7 39.1 1.0 O36 D:7YY401 4.8 35.5 1.0 CB D:MET165 4.8 27.7 1.0 CE1 D:HIS41 4.8 34.8 1.0

M.A.Esler, K.Shi, R.S.Harris, H.Aihara. X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Ensitrelvir To Be Published.