Fluorine in PDB 8hbk: The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir

All present enzymatic activity of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir:
3.4.22.69;

The structure of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir, PDB code: 8hbk was solved by M.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.26 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.093, 82.528, 51.526, 90, 115.13, 90
R / Rfree (%)	19.1 / 23.2

The structure of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

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

Fluorine binding site 1 out of 3 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:39.6 occ:1.00 F28 A:7YY401 0.0 39.6 1.0 C27 A:7YY401 1.3 38.5 1.0 C26 A:7YY401 2.3 36.2 1.0 C29 A:7YY401 2.4 40.5 1.0 C25 A:7YY401 2.7 34.2 1.0 CG A:GLN189 2.9 51.9 1.0 CB A:GLN189 3.1 40.4 1.0 CA A:GLN189 3.2 44.3 1.0 O A:HOH522 3.3 46.2 1.0 O A:HOH549 3.5 50.5 1.0 C34 A:7YY401 3.6 40.7 1.0 C30 A:7YY401 3.6 42.6 1.0 CD A:GLN189 3.7 54.6 1.0 O A:HOH543 3.8 40.5 1.0 N A:GLN189 3.8 36.9 1.0 NE2 A:GLN189 3.9 67.9 1.0 C32 A:7YY401 4.1 39.2 1.0 N24 A:7YY401 4.1 38.5 1.0 O A:ARG188 4.1 48.6 1.0 C A:ARG188 4.2 48.0 1.0 C A:GLN189 4.4 51.0 1.0 NE2 A:HIS41 4.5 30.6 1.0 CB A:MET165 4.6 39.4 1.0 O36 A:7YY401 4.6 34.1 1.0 OE1 A:GLN189 4.6 60.5 1.0 F31 A:7YY401 4.8 46.0 1.0 C35 A:7YY401 4.8 34.7 1.0 CE1 A:HIS41 4.9 41.0 1.0 SD A:MET165 4.9 40.0 1.0 N A:THR190 4.9 43.4 1.0 N12 A:7YY401 5.0 31.4 1.0

Fluorine binding site 2 out of 3 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:46.0 occ:1.00 F31 A:7YY401 0.0 46.0 1.0 C30 A:7YY401 1.4 42.6 1.0 C32 A:7YY401 2.4 39.2 1.0 C29 A:7YY401 2.4 40.5 1.0 F33 A:7YY401 2.6 33.5 1.0 CA A:ASP187 3.0 34.4 1.0 CB A:ASP187 3.0 31.4 1.0 C A:ASP187 3.2 42.2 1.0 O A:ASP187 3.5 37.8 1.0 ND1 A:HIS41 3.5 34.9 1.0 C27 A:7YY401 3.6 38.5 1.0 N A:ARG188 3.7 37.1 1.0 C34 A:7YY401 3.7 40.7 1.0 CG A:HIS41 3.8 38.5 1.0 CE1 A:HIS41 3.9 41.0 1.0 C26 A:7YY401 4.2 36.2 1.0 SD A:MET165 4.2 40.0 1.0 CB A:HIS41 4.2 36.0 1.0 O A:HOH565 4.3 32.4 1.0 CD2 A:HIS41 4.3 36.9 1.0 NE2 A:HIS41 4.3 30.6 1.0 CA A:ARG188 4.4 48.6 1.0 CG A:ASP187 4.4 33.3 1.0 N A:ASP187 4.4 28.6 1.0 OH A:TYR54 4.5 38.5 1.0 ND1 A:HIS164 4.5 32.8 1.0 C A:ARG188 4.5 48.0 1.0 O A:ARG188 4.6 48.6 1.0 CB A:HIS164 4.6 28.0 1.0 CB A:MET165 4.6 39.4 1.0 O A:VAL186 4.7 30.7 1.0 F28 A:7YY401 4.8 39.6 1.0 OD2 A:ASP187 4.9 32.0 1.0

Fluorine binding site 3 out of 3 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:33.5 occ:1.00 F33 A:7YY401 0.0 33.5 1.0 C32 A:7YY401 1.3 39.2 1.0 C30 A:7YY401 2.3 42.6 1.0 C34 A:7YY401 2.4 40.7 1.0 F31 A:7YY401 2.6 46.0 1.0 O A:HIS164 3.3 38.2 1.0 CB A:HIS41 3.3 36.0 1.0 CG A:HIS41 3.4 38.5 1.0 C29 A:7YY401 3.6 40.5 1.0 CD2 A:HIS41 3.6 36.9 1.0 SG A:CYS145 3.6 33.8 1.0 C26 A:7YY401 3.6 36.2 1.0 CB A:HIS164 3.8 28.0 1.0 C A:HIS164 3.9 31.9 1.0 ND1 A:HIS164 3.9 32.8 1.0 CA A:HIS164 4.0 30.4 1.0 C27 A:7YY401 4.0 38.5 1.0 O A:HOH565 4.0 32.4 1.0 ND1 A:HIS41 4.1 34.9 1.0 CG A:HIS164 4.3 29.7 1.0 NE2 A:HIS41 4.3 30.6 1.0 CL2 A:7YY401 4.5 36.8 1.0 CE1 A:HIS41 4.6 41.0 1.0 CB A:MET165 4.6 39.4 1.0 CB A:PRO39 4.8 25.6 1.0 CA A:HIS41 4.8 34.9 1.0 CB A:ASP187 4.8 31.4 1.0 N A:MET165 4.9 31.5 1.0 C25 A:7YY401 5.0 34.2 1.0

Y.Duan, H.Zhou, X.Liu, S.Iketani, M.Lin, X.Zhang, Q.Bian, H.Wang, H.Sun, S.J.Hong, B.Culbertson, H.Mohri, M.I.Luck, Y.Zhu, X.Liu, Y.Lu, X.Yang, K.Yang, Y.Sabo, A.Chavez, S.P.Goff, Z.Rao, D.D.Ho, H.Yang. Molecular Mechanisms of Sars-Cov-2 Resistance to Nirmatrelvir. Nature 2023.
ISSN: ESSN 1476-4687
PubMed: 37696289
DOI: 10.1038/S41586-023-06609-0