Fluorine in PDB 8ezz: Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2

Enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2:
3.4.22.69;

Protein crystallography data

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2, PDB code: 8ezz 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) 40.10 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.494, 63.18, 103.655, 90, 90, 90
R / Rfree (%) 19 / 25.4

Other elements in 8ezz:

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2 (pdb code 8ezz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2, PDB code: 8ezz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 8ezz

Go back to Fluorine Binding Sites List in 8ezz
Fluorine binding site 1 out of 5 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2


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 ML2006A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:55.4
occ:1.00
 F1 A:X70401 0.0 55.4 1.0
C16 A:X70401 1.3 52.0 1.0
F3 A:X70401 2.0 58.9 1.0
F2 A:X70401 2.1 67.0 1.0
C15 A:X70401 2.4 43.5 1.0
N2 A:X70401 2.7 33.0 1.0
O A:GLU166 2.7 33.5 1.0
CD2 A:LEU167 3.2 34.2 1.0
CE A:MET165 3.3 49.4 1.0
O2 A:X70401 3.4 38.7 1.0
CA A:LEU167 3.5 34.4 1.0
C A:GLU166 3.5 30.8 1.0
N A:LEU167 3.9 33.6 1.0
CG A:LEU167 3.9 37.4 1.0
C10 A:X70401 4.1 32.5 1.0
CB A:LEU167 4.1 34.0 1.0
N A:GLU166 4.6 29.4 1.0
CD A:PRO168 4.6 43.3 1.0
SD A:MET165 4.6 47.7 1.0
C A:LEU167 4.7 39.6 1.0
CA A:GLU166 4.7 28.4 1.0
C9 A:X70401 4.7 27.9 1.0
O A:GLN192 4.7 46.7 1.0
NE2 A:GLN192 4.7 33.3 1.0
CB A:MET165 4.7 34.5 1.0
O3 A:X70401 4.8 31.6 1.0
CG A:MET165 4.8 37.6 1.0
CB A:GLN192 4.8 41.7 1.0
O A:THR190 4.9 45.1 1.0

Fluorine binding site 2 out of 5 in 8ezz

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Fluorine binding site 2 out of 5 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2


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 ML2006A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:67.0
occ:1.00
 F2 A:X70401 0.0 67.0 1.0
C16 A:X70401 1.3 52.0 1.0
F1 A:X70401 2.1 55.4 1.0
F3 A:X70401 2.2 58.9 1.0
C15 A:X70401 2.4 43.5 1.0
O2 A:X70401 3.1 38.7 1.0
N2 A:X70401 3.1 33.0 1.0
O A:GLU166 3.7 33.5 1.0
CD A:PRO168 3.9 43.3 1.0
O A:GLN192 4.1 46.7 1.0
O A:THR190 4.1 45.1 1.0
O A:HOH601 4.1 38.4 1.0
CA A:LEU167 4.1 34.4 1.0
C12 A:X70401 4.4 35.2 1.0
N A:GLN192 4.4 42.8 1.0
C10 A:X70401 4.4 32.5 1.0
CG A:PRO168 4.4 45.0 1.0
CD2 A:LEU167 4.5 34.2 1.0
N A:PRO168 4.6 41.8 1.0
C A:GLU166 4.6 30.8 1.0
C A:LEU167 4.7 39.6 1.0
N A:LEU167 4.9 33.6 1.0
C11 A:X70401 4.9 30.7 1.0
C A:GLN192 4.9 40.8 1.0
C A:THR190 5.0 52.2 1.0
CB A:LEU167 5.0 34.0 1.0
CB A:GLN192 5.0 41.7 1.0

Fluorine binding site 3 out of 5 in 8ezz

Go back to Fluorine Binding Sites List in 8ezz
Fluorine binding site 3 out of 5 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2


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 ML2006A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:58.9
occ:1.00
 F3 A:X70401 0.0 58.9 1.0
C16 A:X70401 1.3 52.0 1.0
F1 A:X70401 2.0 55.4 1.0
F2 A:X70401 2.2 67.0 1.0
C15 A:X70401 2.3 43.5 1.0
O2 A:X70401 2.7 38.7 1.0
O A:THR190 2.9 45.1 1.0
NE2 A:GLN192 3.3 33.3 1.0
N2 A:X70401 3.4 33.0 1.0
CE A:MET165 3.4 49.4 1.0
CD A:GLN192 3.7 38.1 1.0
CB A:GLN192 3.8 41.7 1.0
CG A:GLN192 3.8 39.7 1.0
N A:GLN192 4.0 42.8 1.0
C A:THR190 4.1 52.2 1.0
CD2 A:LEU167 4.2 34.2 1.0
O A:ARG188 4.2 35.7 1.0
CA A:GLN192 4.4 42.9 1.0
N A:THR190 4.4 41.8 1.0
O A:GLN192 4.5 46.7 1.0
OE1 A:GLN192 4.6 37.6 1.0
O A:GLU166 4.6 33.5 1.0
O A:HOH601 4.6 38.4 1.0
C10 A:X70401 4.7 32.5 1.0
C A:ALA191 4.7 46.4 1.0
C A:GLN192 4.8 40.8 1.0
CA A:THR190 5.0 49.7 1.0
N A:ALA191 5.0 49.4 1.0

Fluorine binding site 4 out of 5 in 8ezz

Go back to Fluorine Binding Sites List in 8ezz
Fluorine binding site 4 out of 5 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2


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 ML2006A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:86.2
occ:1.00
 F4 A:X70401 0.0 86.2 1.0
C21 A:X70401 1.4 79.6 1.0
F5 A:X70401 2.2 86.1 1.0
C22 A:X70401 2.4 71.9 1.0
C20 A:X70401 2.5 71.9 1.0
O A:HOH583 2.9 43.6 1.0
CG2 A:THR25 3.1 33.1 1.0
N4 A:X70401 3.2 71.4 1.0
O A:THR26 3.3 35.7 1.0
N A:THR26 3.7 38.4 1.0
C A:THR26 4.1 37.0 1.0
CA A:THR25 4.1 35.0 1.0
CB A:THR25 4.2 33.2 1.0
C A:THR25 4.3 37.6 1.0
C19 A:X70401 4.5 48.9 1.0
CA A:THR26 4.6 36.2 1.0
OD1 A:ASN142 4.7 31.5 0.5
OG1 A:THR25 4.8 35.4 1.0

Fluorine binding site 5 out of 5 in 8ezz

Go back to Fluorine Binding Sites List in 8ezz
Fluorine binding site 5 out of 5 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A2


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 ML2006A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:86.1
occ:1.00
 F5 A:X70401 0.0 86.1 1.0
C21 A:X70401 1.4 79.6 1.0
F4 A:X70401 2.2 86.2 1.0
C22 A:X70401 2.5 71.9 1.0
C20 A:X70401 2.5 71.9 1.0
OD1 A:ASN142 2.9 31.5 0.5
N4 A:X70401 2.9 71.4 1.0
ND2 A:ASN142 3.0 37.1 0.5
CG A:ASN142 3.2 35.6 0.5
C19 A:X70401 4.0 48.9 1.0
O A:HOH583 4.2 43.6 1.0
CB A:ASN142 4.6 33.3 0.5
O4 A:X70401 4.6 44.3 1.0
O5 A:X70401 4.6 49.7 1.0
N A:GLY143 4.8 29.4 1.0
OD1 A:ASN142 4.9 35.0 0.5
CG2 A:THR25 4.9 33.1 1.0
C18 A:X70401 4.9 42.8 1.0

Reference:

M.Westberg, D.Fernandez, M.Z.Lin. Rational Design of A New Class of Protease Inhibitors For the Potential Treatment of Coronavirus Diseases To Be Published.
Page generated: Fri Aug 2 18:26:47 2024

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