Fluorine in PDB 8dcz: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir, PDB code: 8dcz was solved by E.M.Lewandowski, Y.Hu, H.Tan, J.Wang, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.28 / 2.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.566, 53.786, 114.76, 90, 100.53, 90
R / Rfree (%) 19.2 / 25.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir (pdb code 8dcz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir, PDB code: 8dcz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8dcz

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Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant 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 Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:49.1
occ:1.00
 F1 A:4WI401 0.0 49.1 1.0
C22 A:4WI401 1.3 47.9 1.0
F2 A:4WI401 2.1 57.7 1.0
F3 A:4WI401 2.1 44.9 1.0
C21 A:4WI401 2.4 41.9 1.0
N4 A:4WI401 2.8 36.2 1.0
O A:GLU166 3.1 24.5 1.0
O4 A:4WI401 3.4 42.0 1.0
N A:PRO168 3.4 31.4 1.0
C A:LEU167 3.6 31.1 1.0
CD A:PRO168 3.7 30.6 1.0
C23 A:4WI401 3.8 31.7 1.0
CA A:PRO168 3.8 30.4 1.0
CG A:PRO168 3.9 30.6 1.0
O A:LEU167 3.9 32.3 1.0
C14 A:4WI401 4.0 31.5 1.0
C A:GLU166 4.2 26.5 1.0
CA A:LEU167 4.2 29.7 1.0
C15 A:4WI401 4.3 31.4 1.0
C17 A:4WI401 4.4 31.3 1.0
OH A:TYR165 4.4 35.9 1.0
CB A:PRO168 4.4 30.8 1.0
N A:LEU167 4.6 26.9 1.0
CZ A:TYR165 4.7 33.5 1.0
CE1 A:TYR165 4.9 31.8 1.0

Fluorine binding site 2 out of 6 in 8dcz

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Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant 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 Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:57.7
occ:1.00
 F2 A:4WI401 0.0 57.7 1.0
C22 A:4WI401 1.3 47.9 1.0
F1 A:4WI401 2.1 49.1 1.0
F3 A:4WI401 2.1 44.9 1.0
OH A:TYR165 2.3 35.9 1.0
C21 A:4WI401 2.4 41.9 1.0
CZ A:TYR165 2.7 33.5 1.0
O A:GLU166 2.9 24.5 1.0
N4 A:4WI401 3.0 36.2 1.0
CE1 A:TYR165 3.1 31.8 1.0
O4 A:4WI401 3.2 42.0 1.0
CD A:PRO168 3.4 30.6 1.0
CE2 A:TYR165 3.5 32.8 1.0
O A:THR190 3.6 35.8 1.0
CA A:LEU167 3.6 29.7 1.0
N A:PRO168 3.8 31.4 1.0
C A:LEU167 3.8 31.1 1.0
C A:GLU166 3.9 26.5 1.0
CG A:PRO168 4.0 30.6 1.0
CD1 A:TYR165 4.2 30.1 1.0
N A:LEU167 4.2 26.9 1.0
C A:THR190 4.4 35.5 1.0
CA A:ALA191 4.4 36.5 1.0
C14 A:4WI401 4.4 31.5 1.0
CD2 A:TYR165 4.5 31.0 1.0
N A:GLN192 4.6 34.4 1.0
O A:LEU167 4.6 32.3 1.0
N A:ALA191 4.7 36.0 1.0
CA A:PRO168 4.8 30.4 1.0
CG A:TYR165 4.8 27.7 1.0
CB A:LEU167 4.8 30.0 1.0
C A:ALA191 5.0 36.5 1.0

Fluorine binding site 3 out of 6 in 8dcz

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Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant 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 Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:44.9
occ:1.00
 F3 A:4WI401 0.0 44.9 1.0
C22 A:4WI401 1.3 47.9 1.0
F1 A:4WI401 2.1 49.1 1.0
F2 A:4WI401 2.1 57.7 1.0
C21 A:4WI401 2.4 41.9 1.0
O4 A:4WI401 2.7 42.0 1.0
O A:THR190 3.3 35.8 1.0
C A:THR190 3.4 35.5 1.0
N A:ALA191 3.5 36.0 1.0
CA A:ALA191 3.5 36.5 1.0
N4 A:4WI401 3.6 36.2 1.0
OH A:TYR165 3.7 35.9 1.0
CG A:PRO168 3.8 30.6 1.0
CD A:PRO168 4.1 30.6 1.0
CB A:ALA191 4.3 37.2 1.0
N A:THR190 4.3 35.6 1.0
CA A:THR190 4.3 36.8 1.0
CZ A:TYR165 4.4 33.5 1.0
N A:PRO168 4.5 31.4 1.0
C A:ALA191 4.6 36.5 1.0
CE1 A:TYR165 4.6 31.8 1.0
O A:GLU166 4.6 24.5 1.0
C14 A:4WI401 4.8 31.5 1.0
C23 A:4WI401 4.8 31.7 1.0
N A:GLN192 4.8 34.4 1.0
CB A:PRO168 4.8 30.8 1.0
CA A:PRO168 4.9 30.4 1.0

Fluorine binding site 4 out of 6 in 8dcz

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Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:44.1
occ:1.00
 F1 B:4WI401 0.0 44.1 1.0
C22 B:4WI401 1.3 41.7 1.0
F3 B:4WI401 2.1 40.3 1.0
F2 B:4WI401 2.1 49.5 1.0
C21 B:4WI401 2.4 39.9 1.0
N4 B:4WI401 2.8 35.4 1.0
O4 B:4WI401 3.3 38.9 1.0
O B:GLU166 3.3 24.4 1.0
N B:PRO168 3.6 33.0 1.0
C23 B:4WI401 3.7 31.8 1.0
C B:LEU167 3.8 32.5 1.0
CD B:PRO168 3.8 33.1 1.0
O B:HOH516 3.9 28.4 1.0
CA B:PRO168 3.9 33.3 1.0
CG B:PRO168 4.0 34.7 1.0
C14 B:4WI401 4.0 32.1 1.0
O B:LEU167 4.1 33.0 1.0
C15 B:4WI401 4.2 31.9 1.0
C17 B:4WI401 4.3 32.5 1.0
C B:GLU166 4.4 27.1 1.0
CA B:LEU167 4.4 30.6 1.0
CB B:PRO168 4.5 34.5 1.0
OH B:TYR165 4.6 30.3 1.0
N B:LEU167 4.9 29.8 1.0
CZ B:TYR165 4.9 30.9 1.0

Fluorine binding site 5 out of 6 in 8dcz

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Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:49.5
occ:1.00
 F2 B:4WI401 0.0 49.5 1.0
C22 B:4WI401 1.3 41.7 1.0
F1 B:4WI401 2.1 44.1 1.0
F3 B:4WI401 2.1 40.3 1.0
C21 B:4WI401 2.4 39.9 1.0
OH B:TYR165 2.5 30.3 1.0
CZ B:TYR165 2.8 30.9 1.0
O B:GLU166 2.9 24.4 1.0
N4 B:4WI401 2.9 35.4 1.0
CE1 B:TYR165 3.2 30.3 1.0
O4 B:4WI401 3.3 38.9 1.0
CD B:PRO168 3.3 33.1 1.0
CA B:LEU167 3.6 30.6 1.0
N B:PRO168 3.6 33.0 1.0
CE2 B:TYR165 3.7 30.9 1.0
C B:LEU167 3.7 32.5 1.0
O B:THR190 3.8 37.8 1.0
C B:GLU166 3.8 27.1 1.0
CG B:PRO168 4.0 34.7 1.0
N B:LEU167 4.2 29.8 1.0
CD1 B:TYR165 4.3 29.8 1.0
C14 B:4WI401 4.3 32.1 1.0
C B:THR190 4.5 36.9 1.0
O B:LEU167 4.5 33.0 1.0
CA B:ALA191 4.5 38.2 1.0
CD2 B:TYR165 4.6 29.2 1.0
O B:HOH516 4.6 28.4 1.0
CA B:PRO168 4.6 33.3 1.0
N B:GLN192 4.8 34.4 1.0
N B:ALA191 4.8 37.2 1.0
CB B:LEU167 4.8 29.9 1.0
CG B:TYR165 4.9 28.2 1.0

Fluorine binding site 6 out of 6 in 8dcz

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Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:40.3
occ:1.00
 F3 B:4WI401 0.0 40.3 1.0
C22 B:4WI401 1.3 41.7 1.0
F1 B:4WI401 2.1 44.1 1.0
F2 B:4WI401 2.1 49.5 1.0
C21 B:4WI401 2.4 39.9 1.0
O4 B:4WI401 2.7 38.9 1.0
O B:HOH516 2.7 28.4 1.0
O B:THR190 3.3 37.8 1.0
C B:THR190 3.4 36.9 1.0
N B:ALA191 3.4 37.2 1.0
CA B:ALA191 3.5 38.2 1.0
N4 B:4WI401 3.6 35.4 1.0
OH B:TYR165 3.7 30.3 1.0
CG B:PRO168 3.9 34.7 1.0
CD B:PRO168 4.1 33.1 1.0
CB B:ALA191 4.3 39.0 1.0
N B:THR190 4.3 35.0 1.0
CA B:THR190 4.3 36.6 1.0
CZ B:TYR165 4.5 30.9 1.0
N B:PRO168 4.5 33.0 1.0
CE1 B:TYR165 4.6 30.3 1.0
C B:ALA191 4.7 36.8 1.0
O B:GLU166 4.7 24.4 1.0
C14 B:4WI401 4.8 32.1 1.0
C23 B:4WI401 4.8 31.8 1.0
N B:GLN192 4.9 34.4 1.0
C B:GLN189 4.9 33.9 1.0
CB B:PRO168 4.9 34.5 1.0
CA B:PRO168 5.0 33.3 1.0

Reference:

Y.Hu, E.M.Lewandowski, H.Tan, X.Zhang, R.T.Morgan, X.Zhang, L.M.C.Jacobs, S.G.Butler, M.V.Gongora, J.Choy, X.Deng, Y.Chen, J.Wang. Naturally Occurring Mutations of Sars-Cov-2 Main Protease Confer Drug Resistance to Nirmatrelvir. Biorxiv 2022.
ISSN: ISSN 2692-8205
PubMed: 36119652
DOI: 10.1101/2022.06.28.497978
Page generated: Fri Aug 2 17:27:09 2024

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