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Fluorine in PDB 8h6n: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (T21I) in Complex with Protease Inhibitor Nirmatrelvir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (T21I) in Complex with Protease Inhibitor Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (T21I) 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 (T21I) in Complex with Protease Inhibitor Nirmatrelvir, PDB code: 8h6n 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) 27.97 / 1.65
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.697, 63.904, 106.117, 90, 90, 90
R / Rfree (%) 19.3 / 21.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (T21I) in Complex with Protease Inhibitor Nirmatrelvir (pdb code 8h6n). 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 (T21I) in Complex with Protease Inhibitor Nirmatrelvir, PDB code: 8h6n:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8h6n

Go back to Fluorine Binding Sites List in 8h6n
Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (T21I) 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 (T21I) in Complex with Protease Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:41.6
occ:1.00
 F1 A:4WI401 0.0 41.6 1.0
C22 A:4WI401 1.4 32.0 1.0
F2 A:4WI401 2.2 42.0 1.0
F3 A:4WI401 2.3 36.6 1.0
C21 A:4WI401 2.4 26.3 1.0
O A:HOH577 3.0 42.7 1.0
O A:HOH667 3.1 43.3 1.0
N4 A:4WI401 3.1 18.9 1.0
O4 A:4WI401 3.2 30.6 1.0
O A:GLU166 3.5 22.1 1.0
CD A:PRO168 3.8 28.0 1.0
O A:GLN192 4.0 31.5 1.0
CA A:LEU167 4.1 24.3 1.0
CD2 A:LEU167 4.1 28.6 1.0
N A:GLN192 4.2 31.5 1.0
O A:THR190 4.2 28.9 1.0
C A:GLU166 4.4 18.4 1.0
C14 A:4WI401 4.4 18.0 1.0
N A:PRO168 4.6 28.1 1.0
CG A:PRO168 4.6 31.8 1.0
CB A:GLN192 4.7 30.5 1.0
N A:LEU167 4.7 18.4 1.0
C A:LEU167 4.7 31.2 1.0
CE A:MET165 4.7 30.6 1.0
C A:GLN192 4.8 30.6 1.0
CA A:GLN192 4.8 34.1 1.0
C17 A:4WI401 4.8 21.9 1.0
CB A:LEU167 4.9 24.7 1.0
CG A:LEU167 5.0 24.6 1.0

Fluorine binding site 2 out of 3 in 8h6n

Go back to Fluorine Binding Sites List in 8h6n
Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (T21I) 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 (T21I) in Complex with Protease Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:42.0
occ:1.00
 F2 A:4WI401 0.0 42.0 1.0
C22 A:4WI401 1.4 32.0 1.0
F1 A:4WI401 2.2 41.6 1.0
F3 A:4WI401 2.2 36.6 1.0
C21 A:4WI401 2.4 26.3 1.0
O A:GLU166 2.6 22.1 1.0
N4 A:4WI401 2.7 18.9 1.0
CE A:MET165 2.9 30.6 1.0
CD2 A:LEU167 3.3 28.6 1.0
O4 A:4WI401 3.4 30.6 1.0
C A:GLU166 3.4 18.4 1.0
CA A:LEU167 3.8 24.3 1.0
N A:LEU167 3.9 18.4 1.0
CG A:LEU167 4.0 24.6 1.0
C14 A:4WI401 4.1 18.0 1.0
CG A:MET165 4.1 22.9 1.0
O A:HOH667 4.2 43.3 1.0
SD A:MET165 4.3 29.8 1.0
N A:GLU166 4.4 17.5 1.0
CB A:MET165 4.4 19.8 1.0
CB A:LEU167 4.4 24.7 1.0
C13 A:4WI401 4.5 24.1 1.0
O3 A:4WI401 4.5 21.6 1.0
CA A:GLU166 4.5 15.8 1.0
NE2 A:GLN192 4.8 25.4 1.0
CB A:GLN192 4.9 30.5 1.0
CD A:PRO168 4.9 28.0 1.0
C A:LEU167 5.0 31.2 1.0

Fluorine binding site 3 out of 3 in 8h6n

Go back to Fluorine Binding Sites List in 8h6n
Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Mutant (T21I) 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 (T21I) in Complex with Protease Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:36.6
occ:1.00
 F3 A:4WI401 0.0 36.6 1.0
C22 A:4WI401 1.4 32.0 1.0
F2 A:4WI401 2.2 42.0 1.0
F1 A:4WI401 2.3 41.6 1.0
C21 A:4WI401 2.3 26.3 1.0
O4 A:4WI401 2.7 30.6 1.0
O A:THR190 2.9 28.9 1.0
CE A:MET165 3.2 30.6 1.0
NE2 A:GLN192 3.3 25.4 1.0
N4 A:4WI401 3.6 18.9 1.0
CD A:GLN192 3.8 24.5 1.0
CB A:GLN192 3.8 30.5 1.0
CG A:GLN192 3.8 25.8 1.0
O A:ARG188 3.8 21.4 1.0
N A:GLN192 4.0 31.5 1.0
C A:THR190 4.0 31.0 1.0
N A:THR190 4.3 24.5 1.0
CD2 A:LEU167 4.3 28.6 1.0
O A:HOH577 4.4 42.7 1.0
CA A:GLN192 4.5 34.1 1.0
O A:GLU166 4.7 22.1 1.0
C A:ALA191 4.7 27.6 1.0
OE1 A:GLN192 4.7 28.1 1.0
C14 A:4WI401 4.8 18.0 1.0
O A:GLN192 4.8 31.5 1.0
CA A:THR190 4.9 29.4 1.0
CA A:ALA191 4.9 33.0 1.0
N A:ALA191 4.9 32.2 1.0
SD A:MET165 4.9 29.8 1.0
C A:ARG188 5.0 20.7 1.0
CA A:GLN189 5.0 23.3 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 05:11:56 2025

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