Fluorine in PDB 7tzj: Sars Cov-2 Plpro in Complex with Inhibitor 3K

Enzymatic activity of Sars Cov-2 Plpro in Complex with Inhibitor 3K

All present enzymatic activity of Sars Cov-2 Plpro in Complex with Inhibitor 3K:
3.4.19.12;

Protein crystallography data

The structure of Sars Cov-2 Plpro in Complex with Inhibitor 3K, PDB code: 7tzj was solved by D.J.Calleja, T.Klemm, B.C.Lechtenberg, N.W.Kuchel, G.Lessene, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.49 / 2.66
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.951, 90.632, 99.766, 90, 90, 90
R / Rfree (%) 20.1 / 25.7

Other elements in 7tzj:

The structure of Sars Cov-2 Plpro in Complex with Inhibitor 3K also contains other interesting chemical elements:

Zinc (Zn) 9 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sars Cov-2 Plpro in Complex with Inhibitor 3K (pdb code 7tzj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Sars Cov-2 Plpro in Complex with Inhibitor 3K, PDB code: 7tzj:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7tzj

Go back to Fluorine Binding Sites List in 7tzj
Fluorine binding site 1 out of 2 in the Sars Cov-2 Plpro in Complex with Inhibitor 3K


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 Plpro in Complex with Inhibitor 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:73.0
occ:1.00
F29 A:S88401 0.0 73.0 1.0
C27 A:S88401 1.4 77.1 1.0
C26 A:S88401 2.3 76.8 1.0
C28 A:S88401 2.3 87.4 1.0
H4 A:S88401 2.6 104.9 1.0
H1 A:S88401 2.6 92.1 1.0
CE1 A:TYR268 3.2 65.3 1.0
CD1 A:TYR268 3.3 68.2 1.0
C25 A:S88401 3.6 77.0 1.0
C23 A:S88401 3.6 83.2 1.0
C24 A:S88401 4.1 80.1 1.0
CG A:GLN269 4.4 80.6 1.0
H2 A:S88401 4.5 92.5 1.0
CZ A:TYR268 4.5 73.7 1.0
CG A:TYR268 4.7 65.2 1.0
O A:TYR268 4.7 77.1 1.0
H7 A:S88401 4.8 84.8 1.0
C22 A:S88401 4.9 70.1 1.0
CA A:GLN269 4.9 76.4 1.0
NE2 A:GLN269 5.0 93.5 1.0

Fluorine binding site 2 out of 2 in 7tzj

Go back to Fluorine Binding Sites List in 7tzj
Fluorine binding site 2 out of 2 in the Sars Cov-2 Plpro in Complex with Inhibitor 3K


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 Plpro in Complex with Inhibitor 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:72.0
occ:1.00
F29 B:S88401 0.0 72.0 1.0
C27 B:S88401 1.4 63.2 1.0
C28 B:S88401 2.3 70.1 1.0
C26 B:S88401 2.3 66.4 1.0
H4 B:S88401 2.6 84.2 1.0
H1 B:S88401 2.6 79.7 1.0
C25 B:S88401 3.6 71.7 1.0
C23 B:S88401 3.6 70.7 1.0
CD1 B:TYR268 3.7 73.0 1.0
CG B:GLN269 3.9 66.5 1.0
CE1 B:TYR268 3.9 69.6 1.0
C24 B:S88401 4.1 72.2 1.0
NE2 B:GLN269 4.3 82.2 1.0
H2 B:S88401 4.5 86.0 1.0
CD B:GLN269 4.5 73.6 1.0
CA B:GLN269 4.5 57.5 1.0
CB B:GLN269 4.7 64.8 1.0
O B:TYR268 4.8 70.2 1.0
C22 B:S88401 4.9 65.7 1.0
CG B:TYR268 5.0 70.6 1.0
N B:GLN269 5.0 60.5 1.0

Reference:

D.J.Calleja, N.Kuchel, B.G.C.Lu, R.W.Birkinshaw, T.Klemm, M.Doerflinger, J.P.Cooney, L.Mackiewicz, A.E.Au, Y.Q.Yap, T.R.Blackmore, K.Katneni, E.Crighton, J.Newman, K.E.Jarman, M.J.Call, B.C.Lechtenberg, P.E.Czabotar, M.Pellegrini, S.A.Charman, K.N.Lowes, J.P.Mitchell, U.Nachbur, G.Lessene, D.Komander. Insights Into Drug Repurposing, As Well As Specificity and Compound Properties of Piperidine-Based Sars-Cov-2 Plpro Inhibitors. Front Chem V. 10 61209 2022.
ISSN: ESSN 2296-2646
PubMed: 35494659
DOI: 10.3389/FCHEM.2022.861209
Page generated: Wed Apr 5 01:24:12 2023

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