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Fluorine in PDB 8h5p: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir, PDB code: 8h5p was solved by M.Lin, X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.90 / 1.67
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.65, 63.81, 105.761, 90, 90, 90
R / Rfree (%) 18 / 20.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir (pdb code 8h5p). 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 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir, PDB code: 8h5p:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8h5p

Go back to Fluorine Binding Sites List in 8h5p
Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor 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 (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:36.0
occ:1.00
 F1 A:4WI401 0.0 36.0 1.0
C22 A:4WI401 1.4 33.7 1.0
F2 A:4WI401 2.2 34.1 1.0
F3 A:4WI401 2.3 35.5 1.0
C21 A:4WI401 2.4 29.7 1.0
N4 A:4WI401 3.1 24.1 1.0
O A:HOH648 3.2 36.9 1.0
O A:HOH658 3.2 41.8 1.0
O4 A:4WI401 3.2 29.9 1.0
O A:VAL166 3.5 23.1 1.0
CD A:PRO168 3.6 30.6 1.0
CA A:LEU167 3.9 26.3 1.0
CD2 A:LEU167 4.1 29.4 1.0
O A:GLN192 4.2 33.2 1.0
O A:THR190 4.3 33.7 1.0
N A:PRO168 4.3 30.7 1.0
C A:VAL166 4.4 23.8 1.0
CG A:PRO168 4.4 33.8 1.0
C A:LEU167 4.4 29.7 1.0
C14 A:4WI401 4.5 25.7 1.0
N A:LEU167 4.6 24.0 1.0
C16 A:4WI401 4.7 27.0 1.0
N A:GLN192 4.7 34.9 1.0
CB A:LEU167 4.8 27.5 1.0
CB A:GLN192 4.8 29.1 1.0
CE A:MET165 4.9 35.1 1.0
CG A:LEU167 4.9 24.4 1.0

Fluorine binding site 2 out of 3 in 8h5p

Go back to Fluorine Binding Sites List in 8h5p
Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor 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 (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.1
occ:1.00
 F2 A:4WI401 0.0 34.1 1.0
C22 A:4WI401 1.4 33.7 1.0
F1 A:4WI401 2.2 36.0 1.0
F3 A:4WI401 2.2 35.5 1.0
C21 A:4WI401 2.3 29.7 1.0
N4 A:4WI401 2.8 24.1 1.0
O A:VAL166 2.8 23.1 1.0
CE A:MET165 3.0 35.1 1.0
O4 A:4WI401 3.4 29.9 1.0
CD2 A:LEU167 3.4 29.4 1.0
C A:VAL166 3.5 23.8 1.0
CA A:LEU167 3.8 26.3 1.0
CG A:MET165 3.8 25.9 1.0
N A:LEU167 3.9 24.0 1.0
CB A:MET165 4.0 24.8 1.0
CG A:LEU167 4.0 24.4 1.0
C14 A:4WI401 4.1 25.7 1.0
SD A:MET165 4.2 34.6 1.0
O A:HOH648 4.3 36.9 1.0
O3 A:4WI401 4.4 24.1 1.0
N A:VAL166 4.4 21.8 1.0
C13 A:4WI401 4.4 25.7 1.0
CB A:LEU167 4.4 27.5 1.0
CA A:VAL166 4.6 22.5 1.0
NE2 A:GLN192 4.7 27.4 1.0
CD A:PRO168 4.9 30.6 1.0
C A:LEU167 4.9 29.7 1.0
CB A:GLN192 5.0 29.1 1.0

Fluorine binding site 3 out of 3 in 8h5p

Go back to Fluorine Binding Sites List in 8h5p
Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor 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 (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.5
occ:1.00
 F3 A:4WI401 0.0 35.5 1.0
C22 A:4WI401 1.4 33.7 1.0
F2 A:4WI401 2.2 34.1 1.0
F1 A:4WI401 2.3 36.0 1.0
C21 A:4WI401 2.4 29.7 1.0
O4 A:4WI401 2.7 29.9 1.0
O A:THR190 3.0 33.7 1.0
NE2 A:GLN192 3.2 27.4 1.0
CE A:MET165 3.3 35.1 1.0
N4 A:4WI401 3.7 24.1 1.0
CB A:GLN192 3.7 29.1 1.0
CD A:GLN192 3.7 29.8 1.0
CG A:GLN192 3.7 31.1 1.0
O A:ARG188 4.0 27.8 1.0
C A:THR190 4.2 36.8 1.0
O A:HOH658 4.2 41.8 1.0
N A:GLN192 4.2 34.9 1.0
CD2 A:LEU167 4.2 29.4 1.0
N A:THR190 4.3 31.2 1.0
CA A:GLN192 4.5 28.9 1.0
OE1 A:GLN192 4.7 27.0 1.0
O A:GLN192 4.7 33.2 1.0
O A:VAL166 4.8 23.1 1.0
C14 A:4WI401 4.8 25.7 1.0
CA A:THR190 4.9 35.9 1.0
C A:ALA191 5.0 35.4 1.0
C A:GLN192 5.0 30.9 1.0

Reference:

Y.Duan, H.Zhou, X.Liu, S.Iketani, M.Lin, X.Zhang, Q.Bian, H.Wang, H.Sun, S.J.Hong, B.Culbertson, H.Mohri, M.I.Luck, Y.Zhu, X.Liu, Y.Lu, X.Yang, K.Yang, Y.Sabo, A.Chavez, S.P.Goff, Z.Rao, D.D.Ho, H.Yang. Molecular Mechanisms of Sars-Cov-2 Resistance to Nirmatrelvir. Nature 2023.
ISSN: ESSN 1476-4687
PubMed: 37696289
DOI: 10.1038/S41586-023-06609-0
Page generated: Wed Jul 16 05:11:38 2025

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