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Fluorine in PDB 9eev: Crystal Structure of the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332)

Enzymatic activity of Crystal Structure of the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332)

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332):
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332), PDB code: 9eev was solved by G.Neilsen, K.A.Kirby, S.G.Sarafianos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.02 / 2.40
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 44.947, 53.204, 113.698, 90, 101.12, 90
R / Rfree (%) 21.7 / 25.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332) (pdb code 9eev). 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 the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332), PDB code: 9eev:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 9eev

Go back to Fluorine Binding Sites List in 9eev
Fluorine binding site 1 out of 3 in the Crystal Structure of the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332)


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 the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:78.4
occ:0.00
 F1 A:4WI401 0.0 78.4 0.0
C22 A:4WI401 1.4 81.9 0.0
F2 A:4WI401 2.2 83.3 0.0
F3 A:4WI401 2.3 88.6 0.8
C21 A:4WI401 2.4 83.4 0.8
O4 A:4WI401 2.7 84.7 0.8
O A:THR190 2.9 81.6 1.0
NE2 A:GLN192 3.1 67.3 1.0
CD A:GLN192 3.4 69.8 1.0
CG A:GLN192 3.4 61.8 1.0
N4 A:4WI401 3.5 85.5 0.8
CD2 A:LEU167 3.8 81.1 1.0
CB A:GLN192 3.9 64.8 1.0
O A:ARG188 4.0 62.1 1.0
C A:THR190 4.1 75.2 1.0
OE1 A:GLN192 4.2 66.2 1.0
N A:GLN192 4.3 72.6 1.0
N A:THR190 4.3 77.5 1.0
CE A:MET165 4.4 75.5 1.0
O A:VAL166 4.6 88.1 1.0
CD A:PRO168 4.7 97.4 1.0
CA A:GLN192 4.7 76.7 1.0
C14 A:4WI401 4.7 85.1 0.8
CA A:LEU167 4.9 87.6 1.0
SD A:MET165 4.9 90.8 1.0
CA A:THR190 4.9 76.2 1.0
C19 A:4WI401 4.9 74.4 0.8
C A:ALA191 4.9 77.1 1.0

Fluorine binding site 2 out of 3 in 9eev

Go back to Fluorine Binding Sites List in 9eev
Fluorine binding site 2 out of 3 in the Crystal Structure of the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332)


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 the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:83.3
occ:0.00
 F2 A:4WI401 0.0 83.3 0.0
C22 A:4WI401 1.4 81.9 0.0
F3 A:4WI401 2.2 88.6 0.8
F1 A:4WI401 2.2 78.4 0.0
C21 A:4WI401 2.4 83.4 0.8
O A:THR190 2.9 81.6 1.0
N4 A:4WI401 3.1 85.5 0.8
O4 A:4WI401 3.1 84.7 0.8
CD A:PRO168 3.2 97.4 1.0
C A:THR190 3.6 75.2 1.0
CG A:PRO168 4.0 99.4 1.0
N A:GLN192 4.0 72.6 1.0
N A:PRO168 4.0 98.3 1.0
CA A:ALA191 4.1 81.9 1.0
N A:ALA191 4.1 83.3 1.0
O A:VAL166 4.3 88.1 1.0
N A:THR190 4.4 77.5 1.0
C14 A:4WI401 4.4 85.1 0.8
CA A:LEU167 4.4 87.6 1.0
C A:ALA191 4.5 77.1 1.0
C A:LEU167 4.6 96.8 1.0
CD2 A:LEU167 4.6 81.1 1.0
CB A:PRO168 4.6 92.9 1.0
CA A:THR190 4.6 76.2 1.0
CG A:GLN192 4.6 61.8 1.0
C23 A:4WI401 4.7 74.9 0.8
CB A:GLN192 4.9 64.8 1.0
CA A:PRO168 4.9 94.4 1.0

Fluorine binding site 3 out of 3 in 9eev

Go back to Fluorine Binding Sites List in 9eev
Fluorine binding site 3 out of 3 in the Crystal Structure of the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332)


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 the Sars-Cov-2 Omicron NSP5 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:88.6
occ:0.80
 F3 A:4WI401 0.0 88.6 0.8
C22 A:4WI401 1.4 81.9 0.0
F2 A:4WI401 2.2 83.3 0.0
F1 A:4WI401 2.3 78.4 0.0
C21 A:4WI401 2.3 83.4 0.8
O A:VAL166 2.5 88.1 1.0
N4 A:4WI401 2.5 85.5 0.8
CA A:LEU167 2.9 87.6 1.0
C A:VAL166 3.2 83.8 1.0
CD2 A:LEU167 3.3 81.1 1.0
N A:LEU167 3.4 81.4 1.0
O4 A:4WI401 3.4 84.7 0.8
CD A:PRO168 3.6 97.4 1.0
C A:LEU167 3.6 96.8 1.0
N A:PRO168 3.8 98.3 1.0
C14 A:4WI401 3.9 85.1 0.8
CB A:LEU167 4.0 86.7 1.0
CG A:LEU167 4.2 83.0 1.0
O3 A:4WI401 4.2 86.8 0.8
C23 A:4WI401 4.4 74.9 0.8
C13 A:4WI401 4.4 85.2 0.8
CA A:VAL166 4.4 81.6 1.0
N A:VAL166 4.5 80.2 1.0
O A:LEU167 4.6 94.6 1.0
O A:THR190 4.6 81.6 1.0
C15 A:4WI401 4.8 81.2 0.8
CB A:MET165 4.8 60.9 1.0
CG A:PRO168 4.9 99.4 1.0
CE A:MET165 4.9 75.5 1.0
CA A:PRO168 5.0 94.4 1.0

Reference:

G.Neilsen, S.Lan, R.L.Slack, Z.C.Lorson, A.Emanuelli Castaner, R.Lee, K.G.Edwards, H.Zhang, J.Lee, W.A.Cantara, M.E.Cilento, H.Zhang, R.De, F.Amblard, P.R.Tedbury, K.A.Kirby, R.F.Schinazi, S.G.Sarafianos. Strategy to Overcome A Nirmatrelvir Resistance Mechanism in the Sars-Cov-2 NSP5 Protease. Sci Adv V. 11 V8875 2025.
ISSN: ESSN 2375-2548
PubMed: 40479048
DOI: 10.1126/SCIADV.ADV8875
Page generated: Wed Jul 16 11:07:14 2025

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