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Fluorine in PDB 8dpr: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248, PDB code: 8dpr was solved by H.Bulut, H.Hayashi, K.Tsuji, N.Kuwata, D.Das, H.Tamamura, H.Mitsuya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.52 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.403, 53.926, 45.678, 90, 101.63, 90
R / Rfree (%) 19 / 24.7

Other elements in 8dpr:

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248 (pdb code 8dpr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248, PDB code: 8dpr:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8dpr

Go back to Fluorine Binding Sites List in 8dpr
Fluorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:42.7
occ:1.00
 FAJ A:T43401 0.0 42.7 1.0
CAE A:T43401 1.3 51.1 1.0
CAF A:T43401 2.3 46.1 1.0
CAD A:T43401 2.3 45.8 1.0
NAI A:T43401 2.9 40.5 1.0
CAC A:T43401 3.5 47.8 1.0
CAA A:T43401 3.6 49.8 1.0
CAB A:T43401 4.0 43.6 1.0
CAH A:T43401 4.2 38.6 1.0
CE A:MET49 4.5 68.7 1.0
SAX A:T43401 4.6 40.6 1.0
CG2 A:THR25 4.8 45.7 1.0
SAG A:T43401 4.9 41.5 1.0

Fluorine binding site 2 out of 4 in 8dpr

Go back to Fluorine Binding Sites List in 8dpr
Fluorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:53.1
occ:1.00
 FBM A:T43401 0.0 53.1 1.0
CBK A:T43401 1.4 52.1 1.0
FBL A:T43401 2.2 55.5 1.0
FBN A:T43401 2.3 55.3 1.0
CBJ A:T43401 2.4 47.2 1.0
NBI A:T43401 2.7 39.9 1.0
O A:GLU166 2.9 31.0 1.0
CD2 A:LEU167 3.1 45.4 1.0
CE A:MET165 3.2 48.4 1.0
CA A:LEU167 3.4 41.8 1.0
C A:GLU166 3.5 33.8 1.0
OBO A:T43401 3.6 44.9 1.0
N A:LEU167 3.7 39.0 1.0
CG A:LEU167 4.0 40.6 1.0
CBG A:T43401 4.1 37.7 1.0
CB A:LEU167 4.1 40.4 1.0
SD A:MET165 4.2 46.7 1.0
CG A:MET165 4.2 40.8 1.0
CB A:MET165 4.2 40.9 1.0
C A:LEU167 4.4 51.2 1.0
CD A:PRO168 4.5 66.0 1.0
N A:GLU166 4.5 30.8 1.0
CBF A:T43401 4.6 35.1 1.0
OBH A:T43401 4.6 33.6 1.0
NE2 A:GLN192 4.7 32.8 1.0
CA A:GLU166 4.7 32.4 1.0
N A:PRO168 4.7 65.0 1.0
O A:THR190 4.7 46.1 1.0

Fluorine binding site 3 out of 4 in 8dpr

Go back to Fluorine Binding Sites List in 8dpr
Fluorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:55.3
occ:1.00
 FBN A:T43401 0.0 55.3 1.0
CBK A:T43401 1.4 52.1 1.0
FBL A:T43401 2.2 55.5 1.0
FBM A:T43401 2.3 53.1 1.0
CBJ A:T43401 2.5 47.2 1.0
O A:THR190 2.8 46.1 1.0
NE2 A:GLN192 2.9 32.8 1.0
OBO A:T43401 2.9 44.9 1.0
CE A:MET165 3.1 48.4 1.0
O A:ARG188 3.5 35.0 1.0
NBI A:T43401 3.6 39.9 1.0
CD A:GLN192 3.6 37.1 1.0
CG A:GLN192 3.9 38.2 1.0
N A:THR190 4.0 42.6 1.0
C A:THR190 4.0 44.2 1.0
CB A:GLN192 4.1 39.0 1.0
CD2 A:LEU167 4.3 45.4 1.0
OE1 A:GLN192 4.6 34.8 1.0
SD A:MET165 4.6 46.7 1.0
N A:GLN192 4.6 50.7 1.0
CA A:THR190 4.6 43.0 1.0
C A:ARG188 4.7 37.7 1.0
CA A:GLN189 4.8 38.4 1.0
CBG A:T43401 4.9 37.7 1.0
C A:GLN189 4.9 39.3 1.0
CG2 A:THR190 5.0 45.6 1.0
O A:GLU166 5.0 31.0 1.0
CA A:GLN192 5.0 40.2 1.0

Fluorine binding site 4 out of 4 in 8dpr

Go back to Fluorine Binding Sites List in 8dpr
Fluorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Inhibitor Tkb-248 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:55.5
occ:1.00
 FBL A:T43401 0.0 55.5 1.0
CBK A:T43401 1.4 52.1 1.0
FBN A:T43401 2.2 55.3 1.0
FBM A:T43401 2.2 53.1 1.0
CBJ A:T43401 2.4 47.2 1.0
OBO A:T43401 3.0 44.9 1.0
O A:THR190 3.2 46.1 1.0
NBI A:T43401 3.2 39.9 1.0
CD A:PRO168 3.5 66.0 1.0
O A:GLU166 4.0 31.0 1.0
CA A:LEU167 4.0 41.8 1.0
N A:PRO168 4.1 65.0 1.0
C A:THR190 4.3 44.2 1.0
N A:GLN192 4.3 50.7 1.0
CD2 A:LEU167 4.4 45.4 1.0
C A:LEU167 4.4 51.2 1.0
CBG A:T43401 4.6 37.7 1.0
CG A:PRO168 4.6 69.3 1.0
CA A:ALA191 4.7 49.3 1.0
CB A:GLN192 4.8 39.0 1.0
N A:ALA191 4.8 49.0 1.0
CE A:MET165 4.8 48.4 1.0
C A:GLU166 4.9 33.8 1.0
O A:GLN192 4.9 45.1 1.0
CB A:LEU167 4.9 40.4 1.0
N A:THR190 4.9 42.6 1.0
C A:ALA191 4.9 55.9 1.0
CBR A:T43401 4.9 41.6 1.0
CA A:PRO168 4.9 66.3 1.0
N A:LEU167 4.9 39.0 1.0
CB A:PRO168 5.0 70.1 1.0
NE2 A:GLN192 5.0 32.8 1.0

Reference:

H.Bulut, H.Hayashi, K.Tsuji, N.Higashi-Kuwata, D.Das, H.Tamamura, H.Mitsuya. A Small Molecule Compound Inhibits the Main Protease of Sars-Cov-2 and Blocks Virus Replication. To Be Published.
Page generated: Wed Jul 16 03:28:42 2025

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