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Fluorine in PDB 8czx: Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 17D

Enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 17D

All present enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 17D:
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 17D, PDB code: 8czx was solved by A.J.Machen, 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) 33.46 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.857, 98.497, 58.682, 90, 107.65, 90
R / Rfree (%) 17.8 / 22

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 17D (pdb code 8czx). 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 17D, PDB code: 8czx:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8czx

Go back to Fluorine Binding Sites List in 8czx
Fluorine binding site 1 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 17D


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 17D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:59.1
occ:0.50
 F32 A:PJR401 0.0 59.1 0.5
F32 A:P8C402 0.1 59.1 0.5
C29 A:PJR401 1.4 58.6 0.5
C29 A:P8C402 1.4 58.6 0.5
F33 A:PJR401 2.1 61.0 0.5
F33 A:P8C402 2.2 61.0 0.5
C30 A:PJR401 2.4 55.2 0.5
C30 A:P8C402 2.4 55.2 0.5
C28 A:PJR401 2.4 51.1 0.5
C28 A:P8C402 2.5 51.1 0.5
O A:HOH582 2.9 31.7 1.0
O A:HOH603 3.0 46.5 1.0
C31 A:PJR401 3.0 51.5 0.5
C31 A:P8C402 3.0 51.6 0.5
C27 A:PJR401 3.1 50.7 0.5
C27 A:P8C402 3.1 50.7 0.5
N A:ALA191 3.3 31.9 1.0
CA A:THR190 3.5 31.0 1.0
C A:THR190 3.6 29.5 1.0
C26 A:PJR401 3.7 50.5 0.5
C26 A:P8C402 3.7 50.5 0.5
O A:GLN189 3.8 34.9 1.0
O A:HOH671 3.8 42.1 1.0
N A:THR190 4.1 28.2 1.0
C A:GLN189 4.2 34.8 1.0
CA A:ALA191 4.2 29.1 1.0
CB A:ALA191 4.2 30.7 1.0
O A:THR190 4.5 30.3 1.0
CB A:THR190 4.8 32.3 1.0

Fluorine binding site 2 out of 4 in 8czx

Go back to Fluorine Binding Sites List in 8czx
Fluorine binding site 2 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 17D


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 17D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:61.0
occ:0.50
 F33 A:PJR401 0.0 61.0 0.5
F33 A:P8C402 0.1 61.0 0.5
C29 A:P8C402 1.3 58.6 0.5
C29 A:PJR401 1.4 58.6 0.5
F32 A:P8C402 2.1 59.1 0.5
F32 A:PJR401 2.1 59.1 0.5
C30 A:P8C402 2.4 55.2 0.5
C30 A:PJR401 2.4 55.2 0.5
C28 A:PJR401 2.4 51.1 0.5
C28 A:P8C402 2.4 51.1 0.5
O A:HOH603 3.6 46.5 1.0
C31 A:P8C402 3.7 51.6 0.5
C31 A:PJR401 3.7 51.5 0.5
C27 A:PJR401 3.7 50.7 0.5
C27 A:P8C402 3.7 50.7 0.5
O A:HOH671 4.1 42.1 1.0
O A:HOH582 4.2 31.7 1.0
C26 A:P8C402 4.2 50.5 0.5
C26 A:PJR401 4.2 50.5 0.5
O A:GLN189 5.0 34.9 1.0

Fluorine binding site 3 out of 4 in 8czx

Go back to Fluorine Binding Sites List in 8czx
Fluorine binding site 3 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 17D


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 17D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:59.1
occ:0.50
 F32 A:P8C402 0.0 59.1 0.5
F32 A:PJR401 0.1 59.1 0.5
C29 A:PJR401 1.3 58.6 0.5
C29 A:P8C402 1.4 58.6 0.5
F33 A:PJR401 2.1 61.0 0.5
F33 A:P8C402 2.1 61.0 0.5
C28 A:PJR401 2.4 51.1 0.5
C30 A:PJR401 2.4 55.2 0.5
C30 A:P8C402 2.4 55.2 0.5
C28 A:P8C402 2.4 51.1 0.5
O A:HOH582 2.9 31.7 1.0
O A:HOH603 3.0 46.5 1.0
C31 A:PJR401 3.0 51.5 0.5
C31 A:P8C402 3.0 51.6 0.5
C27 A:PJR401 3.1 50.7 0.5
C27 A:P8C402 3.1 50.7 0.5
N A:ALA191 3.3 31.9 1.0
CA A:THR190 3.6 31.0 1.0
C A:THR190 3.7 29.5 1.0
C26 A:PJR401 3.7 50.5 0.5
C26 A:P8C402 3.7 50.5 0.5
O A:HOH671 3.8 42.1 1.0
O A:GLN189 3.8 34.9 1.0
N A:THR190 4.2 28.2 1.0
CA A:ALA191 4.2 29.1 1.0
CB A:ALA191 4.2 30.7 1.0
C A:GLN189 4.2 34.8 1.0
O A:THR190 4.5 30.3 1.0
CB A:THR190 4.8 32.3 1.0

Fluorine binding site 4 out of 4 in 8czx

Go back to Fluorine Binding Sites List in 8czx
Fluorine binding site 4 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with the Cyclopropane Based Inhibitor 17D


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 17D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:61.0
occ:0.50
 F33 A:P8C402 0.0 61.0 0.5
F33 A:PJR401 0.1 61.0 0.5
C29 A:P8C402 1.4 58.6 0.5
C29 A:PJR401 1.4 58.6 0.5
F32 A:P8C402 2.1 59.1 0.5
F32 A:PJR401 2.2 59.1 0.5
C28 A:PJR401 2.4 51.1 0.5
C30 A:P8C402 2.4 55.2 0.5
C28 A:P8C402 2.4 51.1 0.5
C30 A:PJR401 2.4 55.2 0.5
O A:HOH603 3.7 46.5 1.0
C31 A:P8C402 3.7 51.6 0.5
C27 A:PJR401 3.7 50.7 0.5
C27 A:P8C402 3.7 50.7 0.5
C31 A:PJR401 3.7 51.5 0.5
O A:HOH671 4.1 42.1 1.0
O A:HOH582 4.2 31.7 1.0
C26 A:P8C402 4.2 50.5 0.5
C26 A:PJR401 4.2 50.5 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, A.J.Machen, 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 17D To Be Published.
Page generated: Wed Jul 16 03:15:48 2025

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