Fluorine in PDB 7uup: Sars-Cov-2 Main Protease S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332)

Enzymatic activity of Sars-Cov-2 Main Protease S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332)

All present enzymatic activity of Sars-Cov-2 Main Protease S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332):
3.4.22.69;

Protein crystallography data

The structure of Sars-Cov-2 Main Protease S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332), PDB code: 7uup 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) 35.08 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.451, 63.962, 105.16, 90, 90, 90
R / Rfree (%) 19.1 / 23.7

Other elements in 7uup:

The structure of Sars-Cov-2 Main Protease S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332) 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 S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332) (pdb code 7uup). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Sars-Cov-2 Main Protease S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332), PDB code: 7uup:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7uup

Go back to Fluorine Binding Sites List in 7uup
Fluorine binding site 1 out of 3 in the Sars-Cov-2 Main Protease S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332)


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 S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:67.7
occ:1.00
 F1 A:4WI401 0.0 67.7 1.0
C22 A:4WI401 1.3 64.1 1.0
F3 A:4WI401 2.1 76.3 1.0
F2 A:4WI401 2.1 73.2 1.0
C21 A:4WI401 2.3 55.5 1.0
N4 A:4WI401 2.6 42.4 1.0
O A:GLU166 2.6 32.8 1.0
CD2 A:LEU167 3.3 45.6 1.0
C A:GLU166 3.4 33.3 1.0
O4 A:4WI401 3.4 49.0 1.0
CA A:LEU167 3.6 40.4 1.0
O A:HOH560 3.6 46.7 1.0
N A:LEU167 3.8 36.0 1.0
CG A:LEU167 3.8 47.1 1.0
C14 A:4WI401 4.0 41.9 1.0
CB A:LEU167 4.2 42.5 1.0
O A:HOH513 4.3 50.5 1.0
SD A:MET165 4.3 56.6 1.0
N A:GLU166 4.5 28.7 1.0
O3 A:4WI401 4.5 39.5 1.0
C13 A:4WI401 4.6 40.3 1.0
CA A:GLU166 4.6 30.9 1.0
CG A:MET165 4.6 46.3 1.0
CB A:MET165 4.6 40.6 1.0
CD A:PRO168 4.7 50.7 1.0
C A:LEU167 4.7 45.0 1.0
CB A:GLN192 4.8 43.9 1.0
O A:THR190 4.8 56.6 1.0
O A:GLN192 4.9 52.1 1.0
NE2 A:GLN192 4.9 45.9 1.0
CE A:MET165 4.9 55.8 1.0
C15 A:4WI401 4.9 39.2 1.0
C16 A:4WI401 4.9 40.4 1.0

Fluorine binding site 2 out of 3 in 7uup

Go back to Fluorine Binding Sites List in 7uup
Fluorine binding site 2 out of 3 in the Sars-Cov-2 Main Protease S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332)


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 S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:73.2
occ:1.00
 F2 A:4WI401 0.0 73.2 1.0
C22 A:4WI401 1.3 64.1 1.0
F1 A:4WI401 2.1 67.7 1.0
F3 A:4WI401 2.2 76.3 1.0
C21 A:4WI401 2.3 55.5 1.0
O A:HOH513 2.6 50.5 1.0
O4 A:4WI401 3.0 49.0 1.0
O A:HOH560 3.1 46.7 1.0
N4 A:4WI401 3.1 42.4 1.0
O A:THR190 3.5 56.6 1.0
O A:GLU166 3.8 32.8 1.0
O A:GLN192 4.1 52.1 1.0
CD A:PRO168 4.1 50.7 1.0
C14 A:4WI401 4.4 41.9 1.0
CA A:LEU167 4.4 40.4 1.0
CD2 A:LEU167 4.5 45.6 1.0
N A:GLN192 4.5 44.3 1.0
C17 A:4WI401 4.5 44.5 1.0
C A:THR190 4.6 52.3 1.0
CB A:GLN192 4.7 43.9 1.0
C A:GLU166 4.8 33.3 1.0
N A:PRO168 4.9 49.5 1.0
C15 A:4WI401 5.0 39.2 1.0
CA A:GLN192 5.0 44.8 1.0
C A:GLN192 5.0 48.2 1.0

Fluorine binding site 3 out of 3 in 7uup

Go back to Fluorine Binding Sites List in 7uup
Fluorine binding site 3 out of 3 in the Sars-Cov-2 Main Protease S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332)


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 S144A (Mpro S144A) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:76.3
occ:1.00
 F3 A:4WI401 0.0 76.3 1.0
C22 A:4WI401 1.3 64.1 1.0
F1 A:4WI401 2.1 67.7 1.0
F2 A:4WI401 2.2 73.2 1.0
C21 A:4WI401 2.3 55.5 1.0
O4 A:4WI401 2.7 49.0 1.0
O A:THR190 3.0 56.6 1.0
NE2 A:GLN192 3.2 45.9 1.0
N4 A:4WI401 3.4 42.4 1.0
O A:HOH513 3.7 50.5 1.0
CD A:GLN192 3.7 43.9 1.0
CB A:GLN192 3.7 43.9 1.0
CG A:GLN192 3.9 45.0 1.0
O A:ARG188 4.1 46.0 1.0
CD2 A:LEU167 4.1 45.6 1.0
C A:THR190 4.2 52.3 1.0
N A:THR190 4.3 50.3 1.0
N A:GLN192 4.4 44.3 1.0
SD A:MET165 4.5 56.6 1.0
OE1 A:GLN192 4.6 41.7 1.0
CA A:GLN192 4.6 44.8 1.0
O A:GLU166 4.6 32.8 1.0
C14 A:4WI401 4.7 41.9 1.0
O A:GLN192 4.7 52.1 1.0
CA A:THR190 4.9 55.4 1.0
CA A:GLN189 5.0 42.5 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: Fri Aug 2 14:16:35 2024

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