Fluorine in PDB 7sgh: Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N

Enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N:
3.4.22.69;

Protein crystallography data

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N, PDB code: 7sgh was solved by M.Westberg, D.Fernandez, M.Z.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.89 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.538, 102.523, 102.487, 90, 91.59, 90
R / Rfree (%) 19.5 / 23.2

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N (pdb code 7sgh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N, PDB code: 7sgh:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 7sgh

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Fluorine binding site 1 out of 12 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:65.8
occ:1.00
 F1 A:99W401 0.0 65.8 1.0
C10 A:99W401 1.3 65.8 1.0
C9 A:99W401 2.4 58.7 1.0
C11 A:99W401 2.4 72.1 1.0
N2 A:99W401 2.8 43.1 1.0
O A:HOH668 3.5 61.3 1.0
C12 A:99W401 3.6 72.0 1.0
C14 A:99W401 3.6 64.5 1.0
C8 A:99W401 3.9 33.6 1.0
NE2 A:GLN189 4.1 29.2 1.0
C13 A:99W401 4.1 67.2 1.0
CB A:GLN189 4.3 28.1 1.0
CD A:GLN189 4.4 29.7 1.0
O A:GLN189 4.4 27.5 1.0
CG A:GLN189 4.7 30.1 1.0
F3 A:99W401 4.7 69.1 1.0
F2 A:99W401 4.7 76.9 1.0
OE1 A:GLN189 4.8 28.9 1.0
CA A:GLN189 4.9 26.1 1.0

Fluorine binding site 2 out of 12 in 7sgh

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Fluorine binding site 2 out of 12 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:76.9
occ:1.00
 F2 A:99W401 0.0 76.9 1.0
C12 A:99W401 1.4 72.0 1.0
C13 A:99W401 2.3 67.2 1.0
C11 A:99W401 2.3 72.1 1.0
O A:THR190 3.0 29.9 1.0
N A:GLN192 3.0 26.3 1.0
CA A:ALA191 3.3 31.3 1.0
C14 A:99W401 3.6 64.5 1.0
C10 A:99W401 3.6 65.8 1.0
C A:ALA191 3.6 26.5 1.0
C A:THR190 3.7 30.5 1.0
O A:GLN192 3.8 29.9 1.0
N A:ALA191 3.8 29.7 1.0
CG A:PRO168 3.9 41.0 1.0
CD A:PRO168 4.1 42.9 1.0
CA A:GLN192 4.1 27.1 1.0
C9 A:99W401 4.1 58.7 1.0
CB A:GLN192 4.3 27.5 1.0
O A:GLN189 4.4 27.5 1.0
C A:GLN192 4.4 28.8 1.0
CG A:GLN192 4.5 28.1 1.0
CB A:ALA191 4.6 32.0 1.0
C A:GLN189 4.6 28.3 1.0
F3 A:99W401 4.7 69.1 1.0
F1 A:99W401 4.7 65.8 1.0
O A:ALA191 4.7 25.8 1.0
NE2 A:GLN192 4.9 29.3 1.0
N A:THR190 4.9 27.6 1.0
CA A:THR190 4.9 29.8 1.0

Fluorine binding site 3 out of 12 in 7sgh

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Fluorine binding site 3 out of 12 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:69.1
occ:1.00
 F3 A:99W401 0.0 69.1 1.0
C14 A:99W401 1.3 64.5 1.0
C13 A:99W401 2.3 67.2 1.0
C9 A:99W401 2.4 58.7 1.0
CE A:MET165 2.7 34.6 1.0
N2 A:99W401 2.7 43.1 1.0
C8 A:99W401 2.9 33.6 1.0
C7 A:99W401 3.0 27.4 1.0
O A:GLU166 3.3 19.1 1.0
N1 A:99W401 3.5 23.9 1.0
O2 A:99W401 3.5 23.4 1.0
C12 A:99W401 3.6 72.0 1.0
C10 A:99W401 3.6 65.8 1.0
CB A:MET165 3.8 22.7 1.0
C11 A:99W401 4.1 72.1 1.0
SD A:MET165 4.3 39.0 1.0
C A:GLU166 4.4 22.6 1.0
C2 A:99W401 4.4 24.6 1.0
CG A:MET165 4.5 27.1 1.0
O A:ARG188 4.5 20.2 1.0
N A:GLU166 4.5 17.8 1.0
C6 A:99W401 4.6 26.8 1.0
CG A:GLN189 4.6 30.1 1.0
F2 A:99W401 4.7 76.9 1.0
F1 A:99W401 4.7 65.8 1.0
CA A:GLN189 4.7 26.1 1.0
C4 A:99W401 4.8 26.4 1.0
CA A:MET165 4.8 17.7 1.0
NE2 A:GLN192 4.9 29.3 1.0

Fluorine binding site 4 out of 12 in 7sgh

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Fluorine binding site 4 out of 12 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:61.2
occ:1.00
 F1 B:99W401 0.0 61.2 1.0
C10 B:99W401 1.3 60.5 1.0
C11 B:99W401 2.3 61.6 1.0
C9 B:99W401 2.4 56.2 1.0
N2 B:99W401 2.9 46.0 1.0
C7 B:99W401 3.1 32.3 1.0
C8 B:99W401 3.3 34.9 1.0
N1 B:99W401 3.3 27.8 1.0
SD B:MET165 3.4 45.1 1.0
CB B:MET165 3.5 26.7 1.0
C12 B:99W401 3.6 65.3 1.0
O B:GLU166 3.6 23.1 1.0
C14 B:99W401 3.6 58.8 1.0
O2 B:99W401 3.6 28.1 1.0
CG B:MET165 4.0 30.0 1.0
O B:ARG188 4.0 23.7 1.0
C13 B:99W401 4.1 62.7 1.0
C2 B:99W401 4.2 28.4 1.0
C6 B:99W401 4.2 28.0 1.0
C4 B:99W401 4.4 29.0 1.0
CG B:GLN189 4.4 29.3 1.0
CE B:MET165 4.5 42.9 1.0
N B:GLU166 4.5 20.0 1.0
CA B:GLN189 4.6 27.5 1.0
C B:GLU166 4.6 23.5 1.0
O B:HOH540 4.6 47.5 1.0
F2 B:99W401 4.7 72.6 1.0
CA B:MET165 4.7 21.9 1.0
F3 B:99W401 4.7 57.6 1.0
C B:ARG188 4.8 22.0 1.0
C3 B:99W401 4.9 27.5 1.0
CB B:GLN189 4.9 29.4 1.0
NE2 B:GLN192 5.0 27.5 1.0

Fluorine binding site 5 out of 12 in 7sgh

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Fluorine binding site 5 out of 12 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:72.6
occ:1.00
 F2 B:99W401 0.0 72.6 1.0
C12 B:99W401 1.4 65.3 1.0
C11 B:99W401 2.3 61.6 1.0
C13 B:99W401 2.3 62.7 1.0
O B:THR190 2.6 24.6 1.0
N B:GLN192 2.7 27.4 1.0
CA B:ALA191 3.3 31.3 1.0
C B:ALA191 3.4 29.0 1.0
C B:THR190 3.4 27.4 1.0
C10 B:99W401 3.6 60.5 1.0
C14 B:99W401 3.6 58.8 1.0
O B:GLN192 3.6 32.4 1.0
N B:ALA191 3.7 29.9 1.0
CA B:GLN192 3.7 28.5 1.0
CB B:GLN192 3.7 27.3 1.0
C9 B:99W401 4.1 56.2 1.0
C B:GLN192 4.2 30.7 1.0
CG B:GLN192 4.2 27.4 1.0
CD B:PRO168 4.3 42.6 1.0
O B:ALA191 4.5 32.1 1.0
NE2 B:GLN192 4.5 27.5 1.0
C B:GLN189 4.6 27.9 1.0
CB B:ALA191 4.6 34.4 1.0
O B:HOH540 4.6 47.5 1.0
O B:GLN189 4.6 28.5 1.0
CG B:PRO168 4.6 42.1 1.0
N B:THR190 4.7 28.9 1.0
F1 B:99W401 4.7 61.2 1.0
CA B:THR190 4.7 28.4 1.0
F3 B:99W401 4.7 57.6 1.0
CD B:GLN192 4.9 27.6 1.0
CD2 B:LEU167 4.9 32.5 1.0
CA B:GLN189 5.0 27.5 1.0

Fluorine binding site 6 out of 12 in 7sgh

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Fluorine binding site 6 out of 12 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:57.6
occ:1.00
 F3 B:99W401 0.0 57.6 1.0
C14 B:99W401 1.3 58.8 1.0
C9 B:99W401 2.3 56.2 1.0
C13 B:99W401 2.4 62.7 1.0
N2 B:99W401 2.7 46.0 1.0
C12 B:99W401 3.6 65.3 1.0
C10 B:99W401 3.6 60.5 1.0
C8 B:99W401 3.7 34.9 1.0
O B:HOH540 3.8 47.5 1.0
C11 B:99W401 4.1 61.6 1.0
CB B:GLN189 4.2 29.4 1.0
O B:GLN189 4.4 28.5 1.0
CD B:GLN189 4.5 29.7 1.0
NE2 B:GLN189 4.5 31.5 1.0
CG B:GLN189 4.6 29.3 1.0
CA B:GLN189 4.7 27.5 1.0
F2 B:99W401 4.7 72.6 1.0
F1 B:99W401 4.7 61.2 1.0
C B:GLN189 4.9 27.9 1.0
OE1 B:GLN189 5.0 27.9 1.0

Fluorine binding site 7 out of 12 in 7sgh

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Fluorine binding site 7 out of 12 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:86.8
occ:1.00
 F1 C:99W401 0.0 86.8 1.0
C10 C:99W401 1.3 82.0 1.0
C11 C:99W401 2.3 81.0 1.0
C9 C:99W401 2.4 78.1 1.0
NE2 C:GLN189 2.6 62.8 1.0
N2 C:99W401 2.8 67.0 1.0
C8 C:99W401 2.9 58.2 1.0
C12 C:99W401 3.6 79.9 1.0
C14 C:99W401 3.6 79.5 1.0
CD C:GLN189 3.8 58.5 1.0
O C:HOH552 3.9 46.7 1.0
O C:THR190 3.9 45.6 1.0
N C:THR190 4.0 55.2 1.0
CA C:GLN189 4.1 51.1 1.0
C13 C:99W401 4.1 77.0 1.0
C C:THR190 4.2 48.8 1.0
C C:GLN189 4.2 56.6 1.0
C7 C:99W401 4.3 50.8 1.0
OE1 C:GLN189 4.4 55.8 1.0
CB C:GLN189 4.6 53.9 1.0
CA C:THR190 4.6 49.6 1.0
N C:ALA191 4.6 45.7 1.0
F2 C:99W401 4.7 76.6 1.0
O C:HOH548 4.7 49.1 1.0
F3 C:99W401 4.7 77.6 1.0
N1 C:99W401 4.7 47.1 1.0
CG C:GLN189 4.7 56.6 1.0

Fluorine binding site 8 out of 12 in 7sgh

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Fluorine binding site 8 out of 12 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:76.6
occ:1.00
 F2 C:99W401 0.0 76.6 1.0
C12 C:99W401 1.4 79.9 1.0
C13 C:99W401 2.3 77.0 1.0
C11 C:99W401 2.3 81.0 1.0
CG C:PRO168 3.4 37.4 1.0
CB C:PRO168 3.5 37.9 1.0
C14 C:99W401 3.6 79.5 1.0
C10 C:99W401 3.6 82.0 1.0
CB C:ALA191 3.8 43.7 1.0
CA C:PRO168 3.9 36.6 1.0
C9 C:99W401 4.1 78.1 1.0
CA C:ALA191 4.1 43.9 1.0
CD C:PRO168 4.2 38.3 1.0
N C:PRO168 4.3 35.9 1.0
F3 C:99W401 4.7 77.6 1.0
F1 C:99W401 4.7 86.8 1.0
N C:ALA191 4.8 45.7 1.0
O C:HOH552 4.9 46.7 1.0

Fluorine binding site 9 out of 12 in 7sgh

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Fluorine binding site 9 out of 12 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:77.6
occ:1.00
 F3 C:99W401 0.0 77.6 1.0
C14 C:99W401 1.3 79.5 1.0
O C:HOH581 2.2 44.1 1.0
C13 C:99W401 2.3 77.0 1.0
C9 C:99W401 2.4 78.1 1.0
O C:GLU166 2.5 28.6 1.0
N2 C:99W401 2.8 67.0 1.0
C C:GLU166 3.1 26.8 1.0
CB C:GLU166 3.5 32.1 1.0
C12 C:99W401 3.6 79.9 1.0
O C:LEU167 3.6 31.0 1.0
C10 C:99W401 3.6 82.0 1.0
CG C:GLU166 3.6 36.2 1.0
C C:LEU167 3.8 31.5 1.0
CA C:GLU166 3.9 28.9 1.0
N C:LEU167 3.9 25.3 1.0
C8 C:99W401 4.0 58.2 1.0
OE1 C:GLU166 4.1 44.1 1.0
C11 C:99W401 4.1 81.0 1.0
CA C:LEU167 4.2 28.6 1.0
N C:PRO168 4.3 35.9 1.0
CD C:GLU166 4.3 41.7 1.0
N C:GLU166 4.5 26.7 1.0
CA C:PRO168 4.6 36.6 1.0
O C:HOH552 4.6 46.7 1.0
O2 C:99W401 4.6 41.5 1.0
F2 C:99W401 4.7 76.6 1.0
F1 C:99W401 4.7 86.8 1.0
C7 C:99W401 4.8 50.8 1.0

Fluorine binding site 10 out of 12 in 7sgh

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Fluorine binding site 10 out of 12 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML124N within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:81.7
occ:1.00
 F1 D:99W401 0.0 81.7 1.0
C10 D:99W401 1.3 64.3 1.0
C11 D:99W401 2.3 64.9 1.0
C9 D:99W401 2.4 65.1 1.0
O D:GLU166 2.7 22.5 1.0
N2 D:99W401 2.8 53.7 1.0
O D:HOH594 3.2 49.0 1.0
C D:GLU166 3.3 22.2 1.0
O D:LEU167 3.5 31.1 1.0
C D:LEU167 3.5 29.8 1.0
C12 D:99W401 3.6 65.6 1.0
C14 D:99W401 3.6 67.6 1.0
C8 D:99W401 3.7 47.4 1.0
N D:PRO168 3.9 32.4 1.0
CA D:LEU167 3.9 25.0 1.0
N D:LEU167 3.9 22.4 1.0
CB D:GLU166 3.9 22.9 1.0
CG D:GLU166 4.0 28.5 1.0
C13 D:99W401 4.1 66.4 1.0
CA D:GLU166 4.2 22.6 1.0
O D:HOH543 4.3 39.6 1.0
CA D:PRO168 4.3 33.9 1.0
OE1 D:GLU166 4.6 32.6 1.0
CD D:PRO168 4.7 37.1 1.0
F2 D:99W401 4.7 58.6 1.0
F3 D:99W401 4.7 71.7 1.0
O2 D:99W401 4.7 30.3 1.0
C7 D:99W401 4.8 41.5 1.0
N D:GLU166 4.9 20.9 1.0
CD D:GLU166 4.9 30.9 1.0

Reference:

M.Westberg, Y.Su, X.Zou, A.Rustagi, A.Beck, L.Ning, D.Fernandez, C.Blish, M.Z.Lin. Rational Design of A New Class of Protease Inhibitors For the Potential Treatment of Coronavirus Diseases To Be Published.
Page generated: Wed Apr 5 01:02:33 2023

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