Fluorine in PDB 8hhu: Crystal Structure of the Sars-Cov-2 Main Protease in Complex with SY110

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with SY110:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with SY110, PDB code: 8hhu was solved by R.Zeng, L.W.Xie, C.Huang, K.Wang, Y.Z.Liu, S.Y.Yang, J.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.84 / 2.26
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.704, 82.411, 51.946, 90, 114.69, 90
R / Rfree (%)	18.5 / 22.7

The binding sites of Fluorine atom in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with SY110 (pdb code 8hhu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with SY110, PDB code: 8hhu:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with SY110


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 the Sars-Cov-2 Main Protease in Complex with SY110 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:88.1 occ:1.00 F01 A:LVX401 0.0 88.1 1.0 C02 A:LVX401 1.4 87.5 1.0 F03 A:LVX401 2.2 87.8 1.0 C37 A:LVX401 2.3 87.2 1.0 C04 A:LVX401 2.4 86.9 1.0 CE A:MET49 2.9 98.0 1.0 C36 A:LVX401 3.0 87.0 1.0 C05 A:LVX401 3.2 86.3 1.0 C35 A:LVX401 3.6 86.7 1.0 C A:ASP187 3.8 56.9 1.0 O A:ASP187 4.0 56.1 1.0 N A:ARG188 4.1 58.7 1.0 CA A:ASP187 4.1 54.1 1.0 CG A:HIS41 4.2 58.9 1.0 SD A:MET49 4.3 100.1 1.0 CB A:ASP187 4.3 53.8 1.0 ND1 A:HIS41 4.3 60.5 1.0 CB A:HIS41 4.4 56.2 1.0 CD2 A:HIS41 4.5 60.2 1.0 CA A:ARG188 4.6 61.5 1.0 C06 A:LVX401 4.6 85.5 1.0 CE1 A:HIS41 4.6 61.2 1.0 NE2 A:HIS41 4.8 61.0 1.0 OH A:TYR54 4.8 56.6 1.0 C A:ARG188 4.9 64.9 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with SY110


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 the Sars-Cov-2 Main Protease in Complex with SY110 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:87.8 occ:1.00 F03 A:LVX401 0.0 87.8 1.0 C02 A:LVX401 1.4 87.5 1.0 F01 A:LVX401 2.2 88.1 1.0 C37 A:LVX401 2.4 87.2 1.0 C04 A:LVX401 2.4 86.9 1.0 CB A:MET165 3.6 54.6 1.0 C36 A:LVX401 3.7 87.0 1.0 SD A:MET165 3.7 66.8 1.0 C05 A:LVX401 3.8 86.3 1.0 O A:HIS164 3.9 51.9 1.0 CB A:ASP187 3.9 53.8 1.0 CA A:ASP187 3.9 54.1 1.0 ND1 A:HIS41 4.1 60.5 1.0 CE1 A:HIS41 4.1 61.2 1.0 C35 A:LVX401 4.2 86.7 1.0 CG A:MET165 4.2 58.2 1.0 C A:HIS164 4.4 50.8 1.0 C A:ASP187 4.4 56.9 1.0 CB A:HIS164 4.5 48.2 1.0 CG A:HIS41 4.6 58.9 1.0 NE2 A:HIS41 4.7 61.0 1.0 CA A:MET165 4.7 52.4 1.0 O A:VAL186 4.8 51.6 1.0 N A:ARG188 4.8 58.7 1.0 N A:MET165 4.8 50.9 1.0 C06 A:LVX401 4.8 85.5 1.0 O34 A:LVX401 4.8 85.8 1.0 O A:HOH536 4.9 53.5 1.0 O A:ASP187 5.0 56.1 1.0 CD2 A:HIS41 5.0 60.2 1.0 CE A:MET49 5.0 98.0 1.0

C.Huang, H.Shuai, J.Qiao, Y.Hou, R.Zeng, A.Xia, L.Xie, Z.Fang, Y.Li, C.Yoon, Q.Huang, B.Hu, J.You, B.Quan, X.Zhao, N.Guo, S.Zhang, R.Ma, J.Zhang, Y.Wang, R.Yang, S.Zhang, J.Nan, H.Xu, F.Wang, J.Lei, H.Chu, S.Yang. A New Generation M Pro Inhibitor with Potent Activity Against Sars-Cov-2 Omicron Variants. Signal Transduct Target Ther V. 8 128 2023.
ISSN: ESSN 2059-3635
PubMed: 36928316
DOI: 10.1038/S41392-023-01392-W