Fluorine in PDB 8dox: Crystal Structure of Sars-Cov-2 Main Protease in Complex with An Inhibitor Tkb-245

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with An Inhibitor Tkb-245:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with An Inhibitor Tkb-245, PDB code: 8dox 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)	56.02 / 1.46
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.333, 52.913, 45.604, 90, 103.74, 90
R / Rfree (%)	19.9 / 22.9

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with An Inhibitor Tkb-245 (pdb code 8dox). 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-245, PDB code: 8dox:
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-245


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-245 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:33.4 occ:1.00 FBS A:T2L401 0.0 33.4 1.0 CBN A:T2L401 1.4 35.5 1.0 CBO A:T2L401 2.4 35.0 1.0 CBK A:T2L401 2.4 31.3 1.0 NBJ A:T2L401 2.9 29.2 1.0 O A:HOH575 3.1 31.2 1.0 CBL A:T2L401 3.6 35.7 1.0 CBP A:T2L401 3.6 34.8 1.0 O A:HOH531 4.1 33.4 1.0 CBQ A:T2L401 4.1 33.1 1.0 CBI A:T2L401 4.2 29.4 1.0 SBM A:T2L401 5.0 32.1 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-245


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-245 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:36.7 occ:1.00 FAX A:T2L401 0.0 36.7 1.0 CAV A:T2L401 1.3 31.8 1.0 FAW A:T2L401 2.0 32.2 1.0 FAY A:T2L401 2.2 34.0 1.0 CAU A:T2L401 2.4 28.1 1.0 OAZ A:T2L401 2.7 31.3 1.0 O A:THR190 2.9 31.7 1.0 CE A:MET165 3.3 34.2 1.0 NE2 A:GLN192 3.3 23.2 1.0 NAT A:T2L401 3.5 20.7 1.0 CB A:GLN192 3.7 26.7 1.0 CG A:GLN192 3.7 26.8 1.0 CD A:GLN192 3.8 23.7 1.0 N A:GLN192 4.0 27.8 1.0 O A:ARG188 4.1 20.8 1.0 C A:THR190 4.2 33.8 1.0 CD2 A:LEU167 4.3 28.1 1.0 N A:THR190 4.3 30.4 1.0 CA A:GLN192 4.4 27.1 1.0 O A:GLN192 4.6 33.3 1.0 O A:GLU166 4.7 20.5 1.0 CAS A:T2L401 4.7 18.8 1.0 OE1 A:GLN192 4.7 23.5 1.0 C A:ALA191 4.9 30.3 1.0 C A:GLN192 4.9 31.2 1.0 CA A:THR190 4.9 33.3 1.0 CA A:GLN189 5.0 26.7 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-245


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-245 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:34.0 occ:1.00 FAY A:T2L401 0.0 34.0 1.0 CAV A:T2L401 1.3 31.8 1.0 FAW A:T2L401 2.0 32.2 1.0 FAX A:T2L401 2.2 36.7 1.0 CAU A:T2L401 2.4 28.1 1.0 NAT A:T2L401 3.0 20.7 1.0 OAZ A:T2L401 3.2 31.3 1.0 O A:HOH591 3.2 34.8 1.0 O A:GLU166 3.3 20.5 1.0 CD A:PRO168 3.9 27.4 1.0 CA A:LEU167 3.9 24.8 1.0 O A:GLN192 4.2 33.3 1.0 O A:THR190 4.2 31.7 1.0 CG A:PRO168 4.2 27.6 1.0 CAS A:T2L401 4.3 18.8 1.0 CD2 A:LEU167 4.3 28.1 1.0 C A:GLU166 4.3 23.2 1.0 N A:PRO168 4.4 25.3 1.0 C A:LEU167 4.5 26.1 1.0 CBD A:T2L401 4.5 22.5 1.0 N A:LEU167 4.6 24.9 1.0 N A:GLN192 4.7 27.8 1.0 CE A:MET165 4.7 34.2 1.0 CB A:LEU167 4.8 24.3 1.0 CB A:GLN192 4.9 26.7 1.0 CBA A:T2L401 4.9 20.2 1.0 CG A:LEU167 5.0 26.2 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-245


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-245 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.2 occ:1.00 FAW A:T2L401 0.0 32.2 1.0 CAV A:T2L401 1.2 31.8 1.0 FAX A:T2L401 2.0 36.7 1.0 FAY A:T2L401 2.0 34.0 1.0 CAU A:T2L401 2.3 28.1 1.0 NAT A:T2L401 2.7 20.7 1.0 CE A:MET165 2.8 34.2 1.0 O A:GLU166 2.9 20.5 1.0 OAZ A:T2L401 3.3 31.3 1.0 CD2 A:LEU167 3.5 28.1 1.0 C A:GLU166 3.7 23.2 1.0 CA A:LEU167 3.9 24.8 1.0 CAS A:T2L401 4.1 18.8 1.0 N A:LEU167 4.1 24.9 1.0 CG A:LEU167 4.1 26.2 1.0 CB A:MET165 4.3 21.9 1.0 SD A:MET165 4.4 34.3 1.0 CG A:MET165 4.4 25.7 1.0 O A:HOH591 4.4 34.8 1.0 CAR A:T2L401 4.5 19.6 1.0 N A:GLU166 4.5 20.1 1.0 NE2 A:GLN192 4.5 23.2 1.0 CB A:LEU167 4.5 24.3 1.0 OBE A:T2L401 4.6 20.3 1.0 CB A:GLN192 4.7 26.7 1.0 CA A:GLU166 4.8 20.7 1.0 O A:THR190 4.9 31.7 1.0 CD A:GLN192 4.9 23.7 1.0 CD A:PRO168 5.0 27.4 1.0

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.