Fluorine in PDB 8cae: Crystal Structure of Sars-Cov-2 Mpro-H172Y Mutant in Complex with Nirmatrelvir

The structure of Crystal Structure of Sars-Cov-2 Mpro-H172Y Mutant in Complex with Nirmatrelvir, PDB code: 8cae was solved by H.El Kilani, R.Hilgenfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.58 / 2.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.208, 53.761, 45.551, 90, 101.59, 90
R / Rfree (%)	17.7 / 25.8

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Mpro-H172Y Mutant in Complex with Nirmatrelvir (pdb code 8cae). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Mpro-H172Y Mutant in Complex with Nirmatrelvir, PDB code: 8cae:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Mpro-H172Y 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 Mpro-H172Y Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:123.7 occ:0.90 F1 A:4WI401 0.0 123.7 0.9 C22 A:4WI401 1.3 106.6 0.9 F2 A:4WI401 2.1 106.5 0.9 F3 A:4WI401 2.1 103.4 0.9 C21 A:4WI401 2.4 95.8 0.9 O A:GLU166 2.6 67.7 1.0 N4 A:4WI401 2.7 97.8 0.9 CD2 A:LEU167 3.1 69.9 1.0 O4 A:4WI401 3.4 88.9 0.9 C A:GLU166 3.5 65.4 1.0 CA A:LEU167 3.6 80.1 1.0 CE A:MET165 3.7 92.1 1.0 CG A:MET165 3.8 64.9 1.0 N A:LEU167 3.9 73.0 1.0 CG A:LEU167 3.9 66.7 1.0 CD A:PRO168 4.0 113.4 1.0 SD A:MET165 4.0 77.5 1.0 C14 A:4WI401 4.1 96.5 0.9 CB A:LEU167 4.3 72.2 1.0 CB A:MET165 4.3 68.4 1.0 C13 A:4WI401 4.4 92.6 0.9 NE2 A:GLN192 4.5 84.9 1.0 N A:GLU166 4.6 60.5 1.0 CA A:GLU166 4.7 63.8 1.0 O3 A:4WI401 4.7 100.4 0.9 C A:LEU167 4.7 94.1 1.0 N A:PRO168 4.8 109.8 1.0 C A:MET165 4.9 66.1 1.0 N3 A:4WI401 4.9 89.8 0.9 O A:THR190 5.0 80.2 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Mpro-H172Y 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 Mpro-H172Y Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:106.5 occ:0.90 F2 A:4WI401 0.0 106.5 0.9 C22 A:4WI401 1.3 106.6 0.9 F1 A:4WI401 2.1 123.7 0.9 F3 A:4WI401 2.1 103.4 0.9 C21 A:4WI401 2.4 95.8 0.9 O4 A:4WI401 2.7 88.9 0.9 NE2 A:GLN192 3.0 84.9 1.0 O A:ARG188 3.2 67.7 1.0 O A:THR190 3.2 80.2 1.0 CE A:MET165 3.4 92.1 1.0 N4 A:4WI401 3.5 97.8 0.9 CD A:GLN192 3.8 78.6 1.0 CG A:GLN192 3.8 76.7 1.0 N A:THR190 4.1 69.0 1.0 CB A:GLN192 4.1 73.0 1.0 SD A:MET165 4.2 77.5 1.0 CD2 A:LEU167 4.3 69.9 1.0 C A:THR190 4.3 78.8 1.0 C A:ARG188 4.4 71.5 1.0 CA A:GLN189 4.5 64.5 1.0 O A:GLU166 4.6 67.7 1.0 C14 A:4WI401 4.8 96.5 0.9 CG A:MET165 4.8 64.9 1.0 C A:GLN189 4.9 64.1 1.0 OE1 A:GLN192 4.9 73.1 1.0 O A:VAL186 4.9 58.1 1.0 CA A:THR190 4.9 73.3 1.0 N A:GLN189 4.9 72.2 1.0 N A:GLN192 5.0 76.7 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Mpro-H172Y 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 Mpro-H172Y Mutant in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:103.4 occ:0.90 F3 A:4WI401 0.0 103.4 0.9 C22 A:4WI401 1.3 106.6 0.9 F2 A:4WI401 2.1 106.5 0.9 F1 A:4WI401 2.1 123.7 0.9 C21 A:4WI401 2.4 95.8 0.9 CD A:PRO168 3.0 113.4 1.0 N4 A:4WI401 3.1 97.8 0.9 O4 A:4WI401 3.1 88.9 0.9 O A:THR190 3.4 80.2 1.0 CG A:PRO168 3.9 120.2 1.0 CD2 A:LEU167 3.9 69.9 1.0 O A:GLU166 3.9 67.7 1.0 CA A:LEU167 4.2 80.1 1.0 N A:PRO168 4.3 109.8 1.0 CB A:GLN192 4.4 73.0 1.0 C A:THR190 4.4 78.8 1.0 N A:GLN192 4.4 76.7 1.0 C14 A:4WI401 4.5 96.5 0.9 CG A:GLN192 4.7 76.7 1.0 C A:LEU167 4.8 94.1 1.0 NE2 A:GLN192 4.8 84.9 1.0 CB A:LEU167 4.8 72.2 1.0 C A:GLU166 4.9 65.4 1.0 CG A:LEU167 4.9 66.7 1.0 N A:THR190 4.9 69.0 1.0 CA A:GLN192 5.0 72.8 1.0

H.El Kilani, R.Hilgenfeld. Crystal Structure of Sars-Cov-2 Mpro-H172Y Mutant in Complex with Nirmatrelvir To Be Published.