Fluorine in PDB 8doy: Crystal Structure of Sars-Cov-2 Main Protease in Complex with An Inhibitor Tkb-198

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with An Inhibitor Tkb-198:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with An Inhibitor Tkb-198, PDB code: 8doy 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)	55.47 / 1.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.046, 98.942, 57.724, 90, 106.28, 90
R / Rfree (%)	19.7 / 24.6

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with An Inhibitor Tkb-198 (pdb code 8doy). 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-198, PDB code: 8doy:
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-198


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-198 within 5.0Å range: probe atom residue distance (Å) B Occ A:F405 b:36.9 occ:1.00 FAJ A:T1X405 0.0 36.9 1.0 CAF A:T1X405 1.4 37.6 1.0 CAA A:T1X405 2.4 34.3 1.0 CAG A:T1X405 2.4 36.4 1.0 NAE A:T1X405 2.9 31.3 1.0 CAB A:T1X405 3.7 38.3 1.0 CAH A:T1X405 3.7 37.7 1.0 CAI A:T1X405 4.2 34.6 1.0 CAD A:T1X405 4.3 33.7 1.0 CE A:MET49 4.7 67.0 1.0 OAX A:T1X405 4.8 25.6 1.0 CG2 A:THR25 5.0 41.7 1.0 SAC A:T1X405 5.0 33.5 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-198


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-198 within 5.0Å range: probe atom residue distance (Å) B Occ A:F405 b:26.7 occ:1.00 FBK A:T1X405 0.0 26.7 1.0 CBJ A:T1X405 1.4 26.1 1.0 CBE A:T1X405 2.4 23.9 1.0 CBI A:T1X405 2.4 23.2 1.0 NBF A:T1X405 3.0 23.0 1.0 C23 A:1PE401 3.0 38.4 1.0 N A:PRO168 3.1 30.6 1.0 O A:GLU166 3.2 27.7 1.0 CD A:PRO168 3.3 30.1 1.0 C A:LEU167 3.4 27.7 1.0 CA A:PRO168 3.5 29.5 1.0 CBD A:T1X405 3.6 24.7 1.0 CBH A:T1X405 3.7 25.9 1.0 CG A:PRO168 3.7 30.6 1.0 O A:LEU167 3.8 25.8 1.0 OH3 A:1PE401 3.9 41.3 1.0 O A:HOH536 3.9 23.8 1.0 CA A:LEU167 4.0 25.1 1.0 OH4 A:1PE401 4.1 33.9 1.0 CBG A:T1X405 4.1 24.8 1.0 OH2 A:1PE401 4.1 44.8 1.0 CB A:PRO168 4.1 30.7 1.0 C A:GLU166 4.1 23.1 1.0 C13 A:1PE401 4.2 35.0 1.0 C12 A:1PE401 4.2 47.2 1.0 CBB A:T1X405 4.2 24.1 1.0 C22 A:1PE401 4.4 49.7 1.0 N A:LEU167 4.5 22.4 1.0 CBC A:T1X405 4.6 25.7 1.0 C A:PRO168 4.8 29.8 1.0 CA A:ALA191 4.9 28.4 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-198


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-198 within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:33.4 occ:1.00 FAJ B:T1X402 0.0 33.4 1.0 CAF B:T1X402 1.4 29.3 1.0 CAA B:T1X402 2.4 26.6 1.0 CAG B:T1X402 2.4 28.6 1.0 NAE B:T1X402 2.9 26.1 1.0 O B:HOH543 3.2 28.5 1.0 CAB B:T1X402 3.6 27.8 1.0 CAH B:T1X402 3.7 29.8 1.0 CAI B:T1X402 4.2 27.0 1.0 CAD B:T1X402 4.2 27.8 1.0 O B:HOH501 4.8 35.9 1.0 SAC B:T1X402 4.9 27.2 1.0 CG2 B:THR25 5.0 31.0 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-198


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-198 within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:36.0 occ:1.00 FBK B:T1X402 0.0 36.0 1.0 CBJ B:T1X402 1.6 40.9 1.0 CBI B:T1X402 2.5 38.9 1.0 CBE B:T1X402 2.6 37.2 1.0 N B:PRO168 2.9 35.9 1.0 NBF B:T1X402 3.1 31.1 1.0 C B:LEU167 3.1 29.8 1.0 CD B:PRO168 3.2 35.9 1.0 O B:GLU166 3.2 32.7 1.0 CA B:PRO168 3.3 35.2 1.0 CG B:PRO168 3.5 34.5 1.0 O B:LEU167 3.5 27.5 1.0 CA B:LEU167 3.7 30.3 1.0 CBD B:T1X402 3.8 37.3 1.0 CBH B:T1X402 3.8 38.5 1.0 O B:HOH530 3.8 27.4 1.0 CB B:PRO168 3.9 34.9 1.0 C B:GLU166 4.0 30.5 1.0 N B:LEU167 4.2 28.4 1.0 CBG B:T1X402 4.3 39.4 1.0 CBB B:T1X402 4.4 31.5 1.0 C B:PRO168 4.7 34.4 1.0 CBC B:T1X402 4.7 33.3 1.0 CA B:ALA191 5.0 35.1 1.0

K.Tsuji, T.Ishii, T.Kobayakawa, N.Higashi-Kuwata, C.Azuma, M.Nakayama, T.Onishi, H.Nakano, N.Wada, M.Hori, K.Shinohara, Y.Miura, T.Kawada, H.Hayashi, S.I.Hattori, H.Bulut, D.Das, N.Takamune, N.Kishimoto, J.Saruwatari, T.Okamura, K.Nakano, S.Misumi, H.Mitsuya, H.Tamamura. Potent and Biostable Inhibitors of the Main Protease of Sars-Cov-2. Iscience V. 25 05365 2022.
ISSN: ESSN 2589-0042
PubMed: 36338434
DOI: 10.1016/J.ISCI.2022.105365