Fluorine in PDB 8uh9: Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-272

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-272

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-272:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-272, PDB code: 8uh9 was solved by H.Bulut, H.Hayashi, N.Kuwata, K.Tsuji, 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) 55.60 / 2.07
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.673, 53.09, 45.774, 90, 101.96, 90
R / Rfree (%) 19.2 / 24

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-272 (pdb code 8uh9). 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 E166V Mutant in Complex with An Inhibitor Tkb-272, PDB code: 8uh9:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8uh9

Go back to Fluorine Binding Sites List in 8uh9
Fluorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-272


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 E166V Mutant in Complex with An Inhibitor Tkb-272 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:82.2
occ:1.00
 FBS A:WOK401 0.0 82.2 1.0
CAF A:WOK401 1.2 82.2 1.0
CAA A:WOK401 2.3 83.0 1.0
CAE A:WOK401 2.3 82.7 1.0
OG1 A:THR25 2.9 66.9 1.0
CAB A:WOK401 3.5 86.9 1.0
CG2 A:THR25 3.5 64.0 1.0
CAD A:WOK401 3.5 78.3 1.0
OG A:SER46 3.6 76.1 1.0
CA A:SER46 3.7 74.7 1.0
N A:SER46 3.7 79.4 1.0
CB A:THR25 3.8 63.0 1.0
O A:CYS44 3.8 59.5 1.0
CAC A:WOK401 4.0 81.8 1.0
C A:THR45 4.1 78.2 1.0
CB A:SER46 4.2 72.8 1.0
CA A:THR25 4.4 62.6 1.0
O A:THR45 4.5 75.0 1.0
SD A:MET49 4.6 81.3 1.0
CA A:THR45 4.7 81.0 1.0
C A:CYS44 4.7 67.3 1.0
NAI A:WOK401 4.7 71.6 1.0
CE A:MET49 4.9 83.3 1.0
C A:SER46 5.0 78.4 1.0

Fluorine binding site 2 out of 4 in 8uh9

Go back to Fluorine Binding Sites List in 8uh9
Fluorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-272


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 E166V Mutant in Complex with An Inhibitor Tkb-272 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:76.6
occ:1.00
 FBL A:WOK401 0.0 76.6 1.0
CBJ A:WOK401 1.3 78.7 1.0
FBM A:WOK401 2.3 80.7 1.0
FBK A:WOK401 2.3 82.0 1.0
CBI A:WOK401 2.3 76.0 1.0
O A:THR190 2.4 63.5 1.0
OBN A:WOK401 2.7 75.0 1.0
C A:THR190 3.5 63.6 1.0
NBH A:WOK401 3.5 70.2 1.0
NE2 A:GLN192 3.9 54.0 1.0
N A:GLN192 3.9 65.6 1.0
CG A:GLN192 4.0 50.6 1.0
CB A:GLN192 4.1 50.8 1.0
N A:THR190 4.2 61.2 1.0
CA A:ALA191 4.3 71.8 1.0
N A:ALA191 4.3 67.4 1.0
C A:ALA191 4.4 71.5 1.0
CD A:GLN192 4.4 48.8 1.0
CA A:THR190 4.5 62.0 1.0
CD2 A:LEU167 4.6 64.2 1.0
CA A:GLN192 4.6 56.1 1.0
O A:ARG188 4.7 51.9 1.0
CD A:PRO168 4.7 73.1 1.0
CBF A:WOK401 4.8 61.2 1.0
O A:VAL166 4.8 54.9 1.0
CG A:PRO168 4.8 71.2 1.0

Fluorine binding site 3 out of 4 in 8uh9

Go back to Fluorine Binding Sites List in 8uh9
Fluorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-272


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 E166V Mutant in Complex with An Inhibitor Tkb-272 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:80.7
occ:1.00
 FBM A:WOK401 0.0 80.7 1.0
CBJ A:WOK401 1.5 78.7 1.0
FBL A:WOK401 2.3 76.6 1.0
FBK A:WOK401 2.4 82.0 1.0
CBI A:WOK401 2.5 76.0 1.0
NBH A:WOK401 2.9 70.2 1.0
O A:VAL166 3.0 54.9 1.0
CD A:PRO168 3.5 73.1 1.0
OBN A:WOK401 3.5 75.0 1.0
CA A:LEU167 3.6 63.4 1.0
N A:PRO168 3.7 73.2 1.0
CG A:PRO168 3.7 71.2 1.0
C A:LEU167 3.8 69.0 1.0
C A:VAL166 4.0 52.5 1.0
N A:LEU167 4.3 61.8 1.0
CBF A:WOK401 4.3 61.2 1.0
O A:THR190 4.4 63.5 1.0
CD2 A:LEU167 4.4 64.2 1.0
CA A:PRO168 4.5 72.5 1.0
CBR A:WOK401 4.7 57.1 1.0
CB A:LEU167 4.7 62.4 1.0
CB A:PRO168 4.7 71.2 1.0
O A:LEU167 4.7 67.8 1.0
CBQ A:WOK401 4.8 48.3 1.0
CBO A:WOK401 4.9 54.2 1.0

Fluorine binding site 4 out of 4 in 8uh9

Go back to Fluorine Binding Sites List in 8uh9
Fluorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-272


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 E166V Mutant in Complex with An Inhibitor Tkb-272 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:82.0
occ:1.00
 FBK A:WOK401 0.0 82.0 1.0
CBJ A:WOK401 1.5 78.7 1.0
FBL A:WOK401 2.3 76.6 1.0
FBM A:WOK401 2.4 80.7 1.0
CBI A:WOK401 2.4 76.0 1.0
NBH A:WOK401 3.0 70.2 1.0
CD2 A:LEU167 3.1 64.2 1.0
O A:VAL166 3.3 54.9 1.0
OBN A:WOK401 3.3 75.0 1.0
SD A:MET165 3.5 66.5 1.0
C A:VAL166 3.8 52.5 1.0
CA A:LEU167 3.9 63.4 1.0
NE2 A:GLN192 4.1 54.0 1.0
N A:LEU167 4.1 61.8 1.0
CB A:MET165 4.2 52.7 1.0
CBF A:WOK401 4.3 61.2 1.0
CG A:LEU167 4.3 59.7 1.0
CG A:MET165 4.4 54.5 1.0
O A:THR190 4.5 63.5 1.0
CB A:LEU167 4.6 62.4 1.0
N A:VAL166 4.6 50.3 1.0
CBE A:WOK401 4.7 52.7 1.0
CD A:GLN192 4.7 48.8 1.0
CB A:GLN192 4.7 50.8 1.0
OBG A:WOK401 4.7 51.4 1.0
CD A:PRO168 4.8 73.1 1.0
C A:LEU167 4.9 69.0 1.0
CG A:GLN192 4.9 50.6 1.0
CA A:VAL166 4.9 52.0 1.0
CE A:MET165 4.9 68.2 1.0

Reference:

N.Higashi-Kuwata, H.Bulut, H.Hayashi, K.Tsuji, H.Ogata-Aoki, M.Kiso, N.Takamune, N.Kishimoto, S.Hattori, T.Ishii, T.Kobayakawa, K.Nakano, D.Das, J.Saruwatari, K.Hasegawa, K.Murayama, Y.Sukenaga, Y.Takamatsu, K.Yoshimura, M.Aoki, T.Okamura, S.Yamayoshi, Y.Kawaoka, S.Misumi, H.Tamamura, H.Mitsuya. TKB272, An Orally Available Sars-Cov-2-Mpro Inhibitor Containing 5-Fluorobenzothiazole, Potently Blocks Sars-Cov-2 Replication Without Ritonavir To Be Published.
Page generated: Sat Aug 3 00:54:13 2024

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