Fluorine in PDB 8uh5: Crystal Structure of Sars-Cov-2 Main Protease in Complex with An Inhibitor Tkb-272

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

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with An Inhibitor Tkb-272, PDB code: 8uh5 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)	55.72 / 1.74
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.003, 53.078, 45.783, 90, 102.17, 90
R / Rfree (%)	19.4 / 23.3

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with An Inhibitor Tkb-272 (pdb code 8uh5). 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 An Inhibitor Tkb-272, PDB code: 8uh5:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease 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 in Complex with An Inhibitor Tkb-272 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:49.6 occ:1.00 FBS A:WOK401 0.0 49.6 1.0 CAF A:WOK401 1.2 59.6 1.0 CAA A:WOK401 2.2 50.2 1.0 CAE A:WOK401 2.3 44.4 1.0 OG1 A:THR25 3.3 43.0 1.0 CA A:SER46 3.4 71.2 1.0 N A:SER46 3.4 66.8 1.0 CAB A:WOK401 3.5 47.2 1.0 CAD A:WOK401 3.5 42.0 1.0 CB A:SER46 3.6 66.5 1.0 CG2 A:THR25 3.8 42.6 1.0 C A:THR45 3.9 55.5 1.0 CAC A:WOK401 3.9 45.7 1.0 O A:CYS44 4.0 40.8 1.0 CE A:MET49 4.1 47.9 1.0 CB A:THR25 4.1 43.2 1.0 CA A:THR45 4.4 53.2 1.0 O A:THR45 4.5 62.3 1.0 OG A:SER46 4.6 65.5 1.0 SD A:MET49 4.7 62.8 1.0 NAI A:WOK401 4.7 35.5 1.0 CA A:THR25 4.8 42.9 1.0 C A:SER46 4.8 60.8 1.0 C A:CYS44 4.8 47.8 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease 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 in Complex with An Inhibitor Tkb-272 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:59.8 occ:1.00 FBL A:WOK401 0.0 59.8 1.0 CBJ A:WOK401 1.3 55.0 1.0 FBM A:WOK401 2.1 50.9 1.0 FBK A:WOK401 2.2 68.5 1.0 CBI A:WOK401 2.4 45.1 1.0 NBH A:WOK401 3.1 36.2 1.0 OBN A:WOK401 3.1 51.8 1.0 CD A:PRO168 3.3 44.5 1.0 O A:THR190 3.6 53.7 1.0 O A:GLU166 3.6 37.2 1.0 CG A:PRO168 3.7 51.9 1.0 CA A:LEU167 4.0 40.8 1.0 N A:PRO168 4.0 47.0 1.0 C A:LEU167 4.3 47.9 1.0 CBF A:WOK401 4.4 35.4 1.0 N A:GLN192 4.5 47.2 1.0 CD2 A:LEU167 4.5 50.6 1.0 C A:THR190 4.5 47.3 1.0 C A:GLU166 4.5 39.1 1.0 CBR A:WOK401 4.6 40.9 1.0 N A:LEU167 4.8 38.6 1.0 CA A:ALA191 4.8 50.2 1.0 CA A:PRO168 4.8 51.5 1.0 CB A:LEU167 4.9 40.9 1.0 O A:GLN192 4.9 56.7 1.0 CB A:PRO168 4.9 53.0 1.0 CE A:MET165 4.9 46.6 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease 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 in Complex with An Inhibitor Tkb-272 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:50.9 occ:1.00 FBM A:WOK401 0.0 50.9 1.0 CBJ A:WOK401 1.2 55.0 1.0 FBK A:WOK401 2.1 68.5 1.0 FBL A:WOK401 2.1 59.8 1.0 CBI A:WOK401 2.3 45.1 1.0 NBH A:WOK401 2.7 36.2 1.0 O A:GLU166 2.8 37.2 1.0 CE A:MET165 3.1 46.6 1.0 CD2 A:LEU167 3.3 50.6 1.0 OBN A:WOK401 3.4 51.8 1.0 C A:GLU166 3.6 39.1 1.0 CA A:LEU167 3.6 40.8 1.0 N A:LEU167 4.0 38.6 1.0 CBF A:WOK401 4.1 35.4 1.0 CG A:LEU167 4.2 38.8 1.0 CB A:LEU167 4.3 40.9 1.0 CD A:PRO168 4.3 44.5 1.0 CB A:MET165 4.4 37.8 1.0 O A:THR190 4.4 53.7 1.0 CG A:MET165 4.4 39.1 1.0 CBE A:WOK401 4.5 38.1 1.0 SD A:MET165 4.5 48.7 1.0 N A:GLU166 4.5 30.7 1.0 C A:LEU167 4.6 47.9 1.0 OBG A:WOK401 4.7 38.2 1.0 NE2 A:GLN192 4.7 42.9 1.0 CA A:GLU166 4.7 31.6 1.0 N A:PRO168 4.8 47.0 1.0 CB A:GLN192 5.0 40.9 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease 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 in Complex with An Inhibitor Tkb-272 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:68.5 occ:1.00 FBK A:WOK401 0.0 68.5 1.0 CBJ A:WOK401 1.4 55.0 1.0 FBM A:WOK401 2.1 50.9 1.0 FBL A:WOK401 2.2 59.8 1.0 O A:THR190 2.4 53.7 1.0 CBI A:WOK401 2.4 45.1 1.0 OBN A:WOK401 2.8 51.8 1.0 NE2 A:GLN192 3.4 42.9 1.0 CE A:MET165 3.5 46.6 1.0 C A:THR190 3.6 47.3 1.0 NBH A:WOK401 3.6 36.2 1.0 CG A:GLN192 3.7 38.9 1.0 CD A:GLN192 3.9 40.1 1.0 N A:THR190 3.9 41.2 1.0 CB A:GLN192 4.0 40.9 1.0 O A:ARG188 4.0 39.5 1.0 N A:GLN192 4.2 47.2 1.0 CD2 A:LEU167 4.4 50.6 1.0 CA A:THR190 4.4 42.7 1.0 N A:ALA191 4.6 46.8 1.0 CA A:GLN192 4.6 36.0 1.0 C A:ALA191 4.6 49.8 1.0 CA A:ALA191 4.7 50.2 1.0 O A:GLU166 4.8 37.2 1.0 CBF A:WOK401 4.8 35.4 1.0 C A:GLN189 4.8 43.0 1.0 CD A:PRO168 4.9 44.5 1.0 CA A:GLN189 4.9 41.4 1.0 OE1 A:GLN192 4.9 34.1 1.0

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.