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Fluorine in PDB 7tq3: Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C

Enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C

All present enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C:
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C, PDB code: 7tq3 was solved by S.Lovell, K.P.Battaile, H.N.Nguyen, S.D.Chamandi, H.R.Picard, T.K.Madden, H.A.Thruman, Y.Kim, W.C.Groutas, K.O.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.01 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.25, 98.851, 58.576, 90, 107.61, 90
R / Rfree (%) 18.2 / 24.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C (pdb code 7tq3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C, PDB code: 7tq3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7tq3

Go back to Fluorine Binding Sites List in 7tq3
Fluorine binding site 1 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:67.2
occ:0.50
 F28 A:IS5401 0.0 67.2 0.5
F28 A:IS5401 0.0 67.2 0.5
C27 A:IS5401 1.4 56.3 0.5
C27 A:IS5401 1.4 56.3 0.5
C26 A:IS5401 2.4 54.8 0.5
C29 A:IS5401 2.4 60.1 0.5
C26 A:IS5401 2.4 54.8 0.5
C29 A:IS5401 2.4 60.1 0.5
O A:GLN189 2.7 38.1 1.0
C A:GLN189 3.2 36.2 1.0
CA A:THR190 3.2 34.8 1.0
O A:HOH551 3.4 35.0 1.0
N A:THR190 3.4 40.4 1.0
C25 A:IS5401 3.7 57.1 0.5
C30 A:IS5401 3.7 53.3 0.5
C25 A:IS5401 3.7 57.1 0.5
C30 A:IS5401 3.7 53.3 0.5
C A:THR190 3.7 31.9 1.0
CG A:GLN189 3.8 38.9 1.0
N A:ALA191 3.9 33.1 1.0
C31 A:IS5401 4.2 55.9 0.5
C31 A:IS5401 4.2 55.9 0.5
CA A:GLN189 4.3 35.9 1.0
NE2 A:GLN189 4.4 45.5 1.0
CB A:GLN189 4.4 30.8 1.0
O A:THR190 4.5 39.1 1.0
CB A:THR190 4.5 41.2 1.0
CD A:GLN189 4.6 46.2 1.0
CD2 A:LEU50 4.8 55.9 1.0
CG2 A:THR190 4.9 44.6 1.0
C23 A:IS5401 4.9 50.4 0.5
C23 A:IS5401 4.9 50.4 0.5
CA A:ALA191 5.0 36.1 1.0

Fluorine binding site 2 out of 4 in 7tq3

Go back to Fluorine Binding Sites List in 7tq3
Fluorine binding site 2 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:67.2
occ:0.50
 F28 A:IS5401 0.0 67.2 0.5
F28 A:IS5401 0.0 67.2 0.5
C27 A:IS5401 1.4 56.3 0.5
C27 A:IS5401 1.4 56.3 0.5
C26 A:IS5401 2.4 54.8 0.5
C26 A:IS5401 2.4 54.8 0.5
C29 A:IS5401 2.4 60.1 0.5
C29 A:IS5401 2.4 60.1 0.5
O A:GLN189 2.7 38.1 1.0
C A:GLN189 3.2 36.2 1.0
CA A:THR190 3.2 34.8 1.0
O A:HOH551 3.4 35.0 1.0
N A:THR190 3.4 40.4 1.0
C25 A:IS5401 3.6 57.1 0.5
C30 A:IS5401 3.7 53.3 0.5
C25 A:IS5401 3.7 57.1 0.5
C30 A:IS5401 3.7 53.3 0.5
C A:THR190 3.7 31.9 1.0
CG A:GLN189 3.8 38.9 1.0
N A:ALA191 3.9 33.1 1.0
C31 A:IS5401 4.2 55.9 0.5
C31 A:IS5401 4.2 55.9 0.5
CA A:GLN189 4.3 35.9 1.0
NE2 A:GLN189 4.4 45.5 1.0
CB A:GLN189 4.4 30.8 1.0
O A:THR190 4.5 39.1 1.0
CB A:THR190 4.5 41.2 1.0
CD A:GLN189 4.6 46.2 1.0
CD2 A:LEU50 4.8 55.9 1.0
C23 A:IS5401 4.9 50.4 0.5
C23 A:IS5401 4.9 50.4 0.5
CG2 A:THR190 4.9 44.6 1.0
CA A:ALA191 5.0 36.1 1.0

Fluorine binding site 3 out of 4 in 7tq3

Go back to Fluorine Binding Sites List in 7tq3
Fluorine binding site 3 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:82.5
occ:0.50
 F28 B:IS5401 0.0 82.5 0.5
F28 B:IS5401 0.0 82.5 0.5
C27 B:IS5401 1.4 77.7 0.5
C27 B:IS5401 1.4 77.7 0.5
C26 B:IS5401 2.4 75.2 0.5
C26 B:IS5401 2.4 75.2 0.5
C29 B:IS5401 2.4 82.2 0.5
C29 B:IS5401 2.4 82.2 0.5
O B:GLN189 2.6 53.5 1.0
C B:GLN189 3.2 56.6 1.0
CA B:THR190 3.5 67.7 1.0
C B:THR190 3.6 64.6 1.0
N B:THR190 3.6 65.7 1.0
C25 B:IS5401 3.6 75.1 0.5
C25 B:IS5401 3.6 75.1 0.5
C30 B:IS5401 3.7 80.9 0.5
C30 B:IS5401 3.7 80.8 0.5
N B:ALA191 3.7 68.4 1.0
CG B:GLN189 3.9 53.3 1.0
O B:THR190 4.1 62.8 1.0
C31 B:IS5401 4.1 79.3 0.5
C31 B:IS5401 4.2 79.3 0.5
CA B:GLN189 4.2 45.8 1.0
NE2 B:GLN189 4.3 59.0 1.0
CB B:GLN189 4.5 45.5 1.0
CA B:ALA191 4.6 63.9 1.0
CD B:GLN189 4.6 57.0 1.0
C23 B:IS5401 4.9 66.9 0.5
C23 B:IS5401 4.9 66.9 0.5

Fluorine binding site 4 out of 4 in 7tq3

Go back to Fluorine Binding Sites List in 7tq3
Fluorine binding site 4 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:82.5
occ:0.50
 F28 B:IS5401 0.0 82.5 0.5
F28 B:IS5401 0.0 82.5 0.5
C27 B:IS5401 1.4 77.7 0.5
C27 B:IS5401 1.4 77.7 0.5
C26 B:IS5401 2.4 75.2 0.5
C26 B:IS5401 2.4 75.2 0.5
C29 B:IS5401 2.4 82.2 0.5
C29 B:IS5401 2.4 82.2 0.5
O B:GLN189 2.6 53.5 1.0
C B:GLN189 3.2 56.6 1.0
CA B:THR190 3.5 67.7 1.0
C B:THR190 3.6 64.6 1.0
N B:THR190 3.6 65.7 1.0
C25 B:IS5401 3.6 75.1 0.5
C25 B:IS5401 3.7 75.1 0.5
C30 B:IS5401 3.7 80.9 0.5
C30 B:IS5401 3.7 80.8 0.5
N B:ALA191 3.7 68.4 1.0
CG B:GLN189 3.9 53.3 1.0
O B:THR190 4.1 62.8 1.0
C31 B:IS5401 4.2 79.3 0.5
C31 B:IS5401 4.2 79.3 0.5
CA B:GLN189 4.2 45.8 1.0
NE2 B:GLN189 4.3 59.0 1.0
CB B:GLN189 4.5 45.5 1.0
CA B:ALA191 4.6 63.9 1.0
CD B:GLN189 4.6 57.0 1.0
C23 B:IS5401 4.9 66.9 0.5
C23 B:IS5401 4.9 66.9 0.5

Reference:

S.D.Chamandi, H.N.Nguyen, A.D.Rathnayake, Y.Kim, K.D.Perera, H.R.Picard, T.Madden, H.A.Thurman, M.M.Kashipathy, L.Liu, K.P.Battaile, S.Lovell, K.O.Chang, W.C.Groutas. Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 5C To Be Published.
Page generated: Wed Jul 16 00:34:00 2025

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