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Fluorine in PDB 9n6m: Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Nirmatrelvir

Enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Nirmatrelvir

All present enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Nirmatrelvir, PDB code: 9n6m was solved by D.Bhandari, A.Kovalevsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.12 / 2.00
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 52.481, 82.473, 91.37, 90, 95.42, 90
R / Rfree (%) 17.8 / 22.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Nirmatrelvir (pdb code 9n6m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Nirmatrelvir, PDB code: 9n6m:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 9n6m

Go back to Fluorine Binding Sites List in 9n6m
Fluorine binding site 1 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion 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 Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:69.1
occ:0.68
 F1 A:4WI401 0.0 69.1 0.7
C22 A:4WI401 1.3 61.5 0.7
F2 A:4WI401 2.2 55.3 0.7
F3 A:4WI401 2.2 69.7 0.7
C21 A:4WI401 2.4 57.8 0.7
O4 A:4WI401 2.6 60.3 0.7
OE1 A:GLN189 3.3 83.4 1.0
N4 A:4WI401 3.6 51.3 0.7
O A:THR190 3.8 50.0 1.0
CE A:MET165 4.1 38.8 0.6
NE2 A:GLN192 4.3 35.3 1.0
N A:THR190 4.3 65.2 1.0
O A:ARG188 4.3 47.5 1.0
CD A:GLN189 4.3 80.8 1.0
CA A:GLN189 4.3 70.9 1.0
CD2 A:LEU167 4.5 48.8 1.0
CG A:GLN192 4.5 37.0 1.0
C14 A:4WI401 4.7 51.2 0.7
C A:THR190 4.8 57.7 1.0
CG A:GLN189 4.8 76.2 1.0
C A:GLN189 4.8 71.3 1.0
CD A:GLN192 4.9 34.0 1.0
CB A:GLN189 5.0 73.1 1.0

Fluorine binding site 2 out of 3 in 9n6m

Go back to Fluorine Binding Sites List in 9n6m
Fluorine binding site 2 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion 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 Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:55.3
occ:0.68
 F2 A:4WI401 0.0 55.3 0.7
C22 A:4WI401 1.3 61.5 0.7
F3 A:4WI401 2.2 69.7 0.7
F1 A:4WI401 2.2 69.1 0.7
C21 A:4WI401 2.4 57.8 0.7
N4 A:4WI401 2.9 51.3 0.7
CD2 A:LEU167 3.0 48.8 1.0
O A:GLU166 3.1 30.2 1.0
O4 A:4WI401 3.2 60.3 0.7
CE A:MET165 3.5 38.8 0.6
CA A:LEU167 3.7 38.6 1.0
CG A:LEU167 3.7 45.8 1.0
CB A:LEU167 3.9 38.4 1.0
C A:GLU166 4.0 35.3 1.0
O A:HOH562 4.2 49.8 1.0
N A:LEU167 4.3 34.1 1.0
C14 A:4WI401 4.4 51.2 0.7
NE2 A:GLN192 4.8 35.3 1.0
CG A:GLN192 4.8 37.0 1.0
O A:GLN192 4.9 51.5 1.0
SD A:MET165 4.9 36.9 0.6
C A:LEU167 5.0 43.0 1.0

Fluorine binding site 3 out of 3 in 9n6m

Go back to Fluorine Binding Sites List in 9n6m
Fluorine binding site 3 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion 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 Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:69.7
occ:0.68
 F3 A:4WI401 0.0 69.7 0.7
C22 A:4WI401 1.3 61.5 0.7
F2 A:4WI401 2.2 55.3 0.7
F1 A:4WI401 2.2 69.1 0.7
C21 A:4WI401 2.4 57.8 0.7
N4 A:4WI401 2.8 51.3 0.7
O A:HOH562 3.3 49.8 1.0
O4 A:4WI401 3.4 60.3 0.7
OE1 A:GLN189 3.8 83.4 1.0
C16 A:4WI401 3.8 47.8 0.7
O A:GLU166 4.0 30.2 1.0
C14 A:4WI401 4.0 51.2 0.7
C15 A:4WI401 4.4 50.8 0.7
C23 A:4WI401 4.7 40.9 0.7
CD A:GLN189 4.8 80.8 1.0
CA A:LEU167 4.8 38.6 1.0

Reference:

D.Bhandari, O.Gerlits, S.Keable, L.Coates, A.Aniana, R.Ghirlando, N.T.Nashed, A.Kovalevsky, J.M.Louis. Characterization of An Unusual Sars-Cov-2 Main Protease Natural Variant Exhibiting Resistance to Nirmatrelvir and Ensitrelvir. Commun Biol V. 8 1061 2025.
ISSN: ESSN 2399-3642
PubMed: 40676153
DOI: 10.1038/S42003-025-08487-W
Page generated: Sat Aug 23 01:56:26 2025

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