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Fluorine in PDB 8h7w: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (S144A) in Complex with Protease Inhibitor Nirmatrelvir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (S144A) in Complex with Protease Inhibitor Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (S144A) in Complex with Protease Inhibitor Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (S144A) in Complex with Protease Inhibitor Nirmatrelvir, PDB code: 8h7w 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) 27.76 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.497, 63.83, 105.101, 90, 90, 90
R / Rfree (%) 16.8 / 19.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (S144A) in Complex with Protease Inhibitor Nirmatrelvir (pdb code 8h7w). 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) Mutant (S144A) in Complex with Protease Inhibitor Nirmatrelvir, PDB code: 8h7w:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8h7w

Go back to Fluorine Binding Sites List in 8h7w
Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (S144A) in Complex with Protease 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) Mutant (S144A) in Complex with Protease Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:36.8
occ:0.98
 F1 A:4WI401 0.0 36.8 1.0
C22 A:4WI401 1.4 28.1 1.0
F2 A:4WI401 2.2 31.9 1.0
F3 A:4WI401 2.3 30.5 1.0
C21 A:4WI401 2.4 20.7 1.0
O A:HOH660 3.0 39.1 1.0
N4 A:4WI401 3.1 16.7 1.0
O4 A:4WI401 3.2 25.6 1.0
O A:HOH663 3.2 32.9 1.0
O A:GLU166 3.4 18.1 1.0
CD A:PRO168 3.9 21.0 1.0
CA A:LEU167 4.0 14.8 1.0
CD2 A:LEU167 4.1 21.0 1.0
O A:GLN192 4.1 25.3 1.0
N A:GLN192 4.3 26.0 1.0
C A:GLU166 4.3 16.7 1.0
O A:THR190 4.4 25.1 1.0
C14 A:4WI401 4.4 12.8 1.0
N A:PRO168 4.6 24.2 1.0
N A:LEU167 4.6 15.5 1.0
C A:LEU167 4.7 20.0 1.0
CB A:GLN192 4.7 18.6 1.0
C17 A:4WI401 4.7 16.0 1.0
CG A:PRO168 4.7 23.7 1.0
CE A:MET165 4.8 28.9 1.0
C A:GLN192 4.9 20.7 1.0
CG A:LEU167 4.9 18.0 1.0
CB A:LEU167 4.9 16.3 1.0
CA A:GLN192 4.9 20.4 1.0

Fluorine binding site 2 out of 3 in 8h7w

Go back to Fluorine Binding Sites List in 8h7w
Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (S144A) in Complex with Protease 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) Mutant (S144A) in Complex with Protease Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:31.9
occ:0.98
 F2 A:4WI401 0.0 31.9 1.0
C22 A:4WI401 1.4 28.1 1.0
F1 A:4WI401 2.2 36.8 1.0
F3 A:4WI401 2.2 30.5 1.0
C21 A:4WI401 2.3 20.7 1.0
O A:GLU166 2.7 18.1 1.0
N4 A:4WI401 2.7 16.7 1.0
CE A:MET165 2.9 28.9 1.0
CD2 A:LEU167 3.4 21.0 1.0
O4 A:4WI401 3.4 25.6 1.0
C A:GLU166 3.4 16.7 1.0
CA A:LEU167 3.9 14.8 1.0
CG A:LEU167 3.9 18.0 1.0
N A:LEU167 3.9 15.5 1.0
C14 A:4WI401 4.1 12.8 1.0
SD A:MET165 4.1 27.4 1.0
N A:GLU166 4.2 13.4 1.0
CB A:MET165 4.3 15.7 1.0
CG A:MET165 4.3 17.9 1.0
O A:HOH663 4.4 32.9 1.0
C13 A:4WI401 4.4 15.2 1.0
O3 A:4WI401 4.4 16.8 1.0
CB A:LEU167 4.5 16.3 1.0
CA A:GLU166 4.5 15.0 1.0
NE2 A:GLN192 4.7 19.5 1.0
C A:MET165 4.8 14.3 1.0
CB A:GLN192 4.9 18.6 1.0

Fluorine binding site 3 out of 3 in 8h7w

Go back to Fluorine Binding Sites List in 8h7w
Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (S144A) in Complex with Protease 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) Mutant (S144A) in Complex with Protease Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.5
occ:0.98
 F3 A:4WI401 0.0 30.5 1.0
C22 A:4WI401 1.4 28.1 1.0
F2 A:4WI401 2.2 31.9 1.0
F1 A:4WI401 2.3 36.8 1.0
C21 A:4WI401 2.3 20.7 1.0
O4 A:4WI401 2.6 25.6 1.0
O A:THR190 3.0 25.1 1.0
NE2 A:GLN192 3.2 19.5 1.0
CE A:MET165 3.3 28.9 1.0
N4 A:4WI401 3.6 16.7 1.0
CB A:GLN192 3.7 18.6 1.0
CG A:GLN192 3.8 19.2 1.0
CD A:GLN192 3.8 19.5 1.0
O A:ARG188 3.9 17.6 1.0
N A:GLN192 4.0 26.0 1.0
C A:THR190 4.1 26.0 1.0
CD2 A:LEU167 4.3 21.0 1.0
O A:HOH660 4.3 39.1 1.0
N A:THR190 4.4 19.3 1.0
CA A:GLN192 4.4 20.4 1.0
O A:GLU166 4.7 18.1 1.0
C A:ALA191 4.7 25.2 1.0
OE1 A:GLN192 4.7 20.5 1.0
O A:GLN192 4.7 25.3 1.0
C14 A:4WI401 4.8 12.8 1.0
CA A:ALA191 4.9 27.9 1.0
SD A:MET165 4.9 27.4 1.0
CA A:THR190 4.9 27.0 1.0
N A:ALA191 4.9 24.8 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 05:12:27 2025

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