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Fluorine in PDB 9cjp: X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir

Enzymatic activity of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir

All present enzymatic activity of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir, PDB code: 9cjp was solved by M.A.Esler, K.Shi, R.S.Harris, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.83 / 1.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.095, 105.665, 53.1, 90, 103.61, 90
R / Rfree (%) 18 / 22.6

Other elements in 9cjp:

The structure of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir also contains other interesting chemical elements:

Bromine (Br) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir (pdb code 9cjp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir, PDB code: 9cjp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 9cjp

Go back to Fluorine Binding Sites List in 9cjp
Fluorine binding site 1 out of 6 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants 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 X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:47.7
occ:1.00
 F1 A:4WI401 0.0 47.7 1.0
C22 A:4WI401 1.3 51.2 1.0
F2 A:4WI401 2.1 63.2 1.0
F3 A:4WI401 2.1 57.4 1.0
C21 A:4WI401 2.3 46.4 1.0
O A:VAL166 2.7 38.0 1.0
N4 A:4WI401 2.9 39.1 1.0
O4 A:4WI401 3.2 51.0 1.0
C A:VAL166 3.4 35.7 1.0
CA A:LEU167 3.6 42.4 1.0
CD2 A:LEU167 3.6 41.4 1.0
CE A:MET165 3.8 51.7 1.0
N A:LEU167 3.8 43.2 1.0
CG A:LEU167 4.1 38.9 1.0
C14 A:4WI401 4.2 46.0 1.0
CG A:MET165 4.2 41.5 1.0
SD A:MET165 4.3 57.8 1.0
CB A:LEU167 4.3 47.4 1.0
CB A:MET165 4.3 46.1 1.0
CD A:PRO168 4.4 49.2 1.0
N A:VAL166 4.5 29.0 1.0
O3 A:4WI401 4.6 48.3 1.0
C13 A:4WI401 4.6 39.2 1.0
C A:LEU167 4.6 44.7 1.0
CA A:VAL166 4.6 33.6 1.0
NE2 A:GLN192 4.6 55.8 1.0
N A:PRO168 4.9 49.4 1.0

Fluorine binding site 2 out of 6 in 9cjp

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

b:63.2
occ:1.00
 F2 A:4WI401 0.0 63.2 1.0
C22 A:4WI401 1.3 51.2 1.0
F1 A:4WI401 2.1 47.7 1.0
F3 A:4WI401 2.1 57.4 1.0
C21 A:4WI401 2.4 46.4 1.0
O4 A:4WI401 2.6 51.0 1.0
O A:THR190 3.1 58.6 1.0
N4 A:4WI401 3.5 39.1 1.0
NE2 A:GLN192 3.7 55.8 1.0
CB A:GLN192 4.1 45.3 1.0
C A:THR190 4.2 56.4 1.0
CG A:GLN192 4.2 49.8 1.0
N A:THR190 4.3 49.0 1.0
N A:GLN192 4.3 56.9 1.0
CD A:GLN192 4.3 52.5 1.0
CD2 A:LEU167 4.4 41.4 1.0
O A:ARG188 4.5 49.9 1.0
CD A:PRO168 4.5 49.2 1.0
O A:VAL166 4.5 38.0 1.0
CE A:MET165 4.7 51.7 1.0
CA A:GLN192 4.8 54.3 1.0
C14 A:4WI401 4.8 46.0 1.0
O A:GLN192 4.8 57.5 1.0
CA A:GLN189 4.9 48.5 1.0
CA A:THR190 4.9 50.7 1.0

Fluorine binding site 3 out of 6 in 9cjp

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

b:57.4
occ:1.00
 F3 A:4WI401 0.0 57.4 1.0
C22 A:4WI401 1.3 51.2 1.0
F1 A:4WI401 2.1 47.7 1.0
F2 A:4WI401 2.1 63.2 1.0
C21 A:4WI401 2.4 46.4 1.0
N4 A:4WI401 2.8 39.1 1.0
O A:VAL166 3.2 38.0 1.0
CD A:PRO168 3.2 49.2 1.0
O4 A:4WI401 3.3 51.0 1.0
CG A:PRO168 3.7 56.1 1.0
CA A:LEU167 3.7 42.4 1.0
N A:PRO168 3.8 49.4 1.0
C A:LEU167 4.1 44.7 1.0
C A:VAL166 4.1 35.7 1.0
C14 A:4WI401 4.2 46.0 1.0
N A:LEU167 4.4 43.2 1.0
CD2 A:LEU167 4.6 41.4 1.0
C16 A:4WI401 4.6 51.6 1.0
O A:THR190 4.7 58.6 1.0
CA A:PRO168 4.7 39.3 1.0
CB A:LEU167 4.8 47.4 1.0
C15 A:4WI401 4.9 46.9 1.0
CB A:PRO168 4.9 52.2 1.0
C23 A:4WI401 4.9 37.5 1.0

Fluorine binding site 4 out of 6 in 9cjp

Go back to Fluorine Binding Sites List in 9cjp
Fluorine binding site 4 out of 6 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants 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 X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:40.8
occ:1.00
 F1 B:4WI401 0.0 40.8 1.0
C22 B:4WI401 1.3 30.1 1.0
F3 B:4WI401 2.1 37.3 1.0
F2 B:4WI401 2.1 38.6 1.0
C21 B:4WI401 2.4 28.7 1.0
N4 B:4WI401 2.9 25.4 1.0
O B:VAL166 2.9 28.2 1.0
O4 B:4WI401 3.2 35.7 1.0
CD2 B:LEU167 3.5 35.9 1.0
C B:VAL166 3.6 30.8 1.0
CE B:MET165 3.6 40.0 1.0
CA B:LEU167 3.7 29.1 1.0
N B:LEU167 3.9 27.4 1.0
CG B:LEU167 4.0 35.0 1.0
SD B:MET165 4.1 42.9 1.0
CG B:MET165 4.1 36.5 1.0
C14 B:4WI401 4.2 27.3 1.0
CB B:MET165 4.2 26.2 1.0
NE2 B:GLN192 4.3 28.6 1.0
CB B:LEU167 4.4 34.3 1.0
O3 B:4WI401 4.5 29.0 1.0
N B:VAL166 4.5 23.5 1.0
C13 B:4WI401 4.5 31.1 1.0
CD B:PRO168 4.6 40.9 1.0
CA B:VAL166 4.7 27.6 1.0
C B:LEU167 4.8 39.5 1.0
CB B:GLN192 4.8 31.8 1.0
CD B:GLN192 4.8 29.2 1.0

Fluorine binding site 5 out of 6 in 9cjp

Go back to Fluorine Binding Sites List in 9cjp
Fluorine binding site 5 out of 6 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants 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 X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:38.6
occ:1.00
 F2 B:4WI401 0.0 38.6 1.0
C22 B:4WI401 1.3 30.1 1.0
F3 B:4WI401 2.1 37.3 1.0
F1 B:4WI401 2.1 40.8 1.0
C21 B:4WI401 2.3 28.7 1.0
O4 B:4WI401 2.6 35.7 1.0
O B:THR190 3.1 34.4 1.0
NE2 B:GLN192 3.3 28.6 1.0
N4 B:4WI401 3.5 25.4 1.0
CB B:GLN192 3.7 31.8 1.0
CG B:GLN192 3.9 32.0 1.0
CD B:GLN192 3.9 29.2 1.0
N B:GLN192 4.2 36.1 1.0
C B:THR190 4.2 29.7 1.0
CD2 B:LEU167 4.3 35.9 1.0
N B:THR190 4.4 33.1 1.0
O B:ARG188 4.5 34.6 1.0
CA B:GLN192 4.5 38.3 1.0
CE B:MET165 4.6 40.0 1.0
O B:GLN192 4.6 46.4 1.0
O B:VAL166 4.7 28.2 1.0
C14 B:4WI401 4.8 27.3 1.0
CD B:PRO168 4.8 40.9 1.0
OE1 B:GLN192 4.9 31.7 1.0
C B:GLN192 5.0 39.4 1.0
CA B:GLN189 5.0 24.2 1.0

Fluorine binding site 6 out of 6 in 9cjp

Go back to Fluorine Binding Sites List in 9cjp
Fluorine binding site 6 out of 6 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants 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 X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:37.3
occ:1.00
 F3 B:4WI401 0.0 37.3 1.0
C22 B:4WI401 1.3 30.1 1.0
F2 B:4WI401 2.1 38.6 1.0
F1 B:4WI401 2.1 40.8 1.0
C21 B:4WI401 2.4 28.7 1.0
N4 B:4WI401 2.9 25.4 1.0
O4 B:4WI401 3.3 35.7 1.0
O B:VAL166 3.3 28.2 1.0
CD B:PRO168 3.3 40.9 1.0
CA B:LEU167 3.8 29.1 1.0
CG B:PRO168 3.9 44.1 1.0
N B:PRO168 4.0 41.1 1.0
C B:VAL166 4.2 30.8 1.0
C B:LEU167 4.2 39.5 1.0
C14 B:4WI401 4.3 27.3 1.0
CD2 B:LEU167 4.4 35.9 1.0
N B:LEU167 4.4 27.4 1.0
O B:THR190 4.6 34.4 1.0
O B:GLN192 4.6 46.4 1.0
C16 B:4WI401 4.7 31.1 1.0
CB B:LEU167 4.7 34.3 1.0
CG B:LEU167 4.9 35.0 1.0
C15 B:4WI401 4.9 25.7 1.0

Reference:

M.A.Esler, K.Shi, R.S.Harris, H.Aihara. X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir To Be Published.
Page generated: Wed Jul 16 10:42:51 2025

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