Fluorine in PDB 7vlp: Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211, PDB code: 7vlp was solved by X.L.Zhou, F.L.Zhong, C.Lin, J.Li, J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.43 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.484, 98.695, 59.423, 90, 108.72, 90
R / Rfree (%)	19.5 / 21.9

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211 (pdb code 7vlp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211, PDB code: 7vlp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


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 PF07321332 in Spacegroup P1211 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:30.6 occ:1.00 F1 A:4WI401 0.0 30.6 1.0 C22 A:4WI401 1.2 27.1 1.0 F3 A:4WI401 2.0 29.6 1.0 F2 A:4WI401 2.1 27.6 1.0 C21 A:4WI401 2.3 24.3 1.0 N4 A:4WI401 2.9 20.8 1.0 O A:HOH564 3.1 26.6 1.0 O4 A:4WI401 3.2 26.8 1.0 O A:GLU166 3.2 19.3 1.0 CD A:PRO168 3.6 27.5 1.0 CA A:LEU167 3.9 21.3 1.0 C A:GLU166 4.2 20.1 1.0 CD2 A:LEU167 4.2 25.3 1.0 N A:PRO168 4.2 24.5 1.0 C14 A:4WI401 4.3 19.7 1.0 O A:GLN192 4.3 24.8 1.0 C A:LEU167 4.3 22.9 1.0 O A:THR190 4.4 25.5 1.0 N A:LEU167 4.4 19.2 1.0 C16 A:4WI401 4.6 22.0 1.0 CG A:PRO168 4.6 28.8 1.0 N A:GLN192 4.7 24.0 1.0 CE A:MET165 4.8 27.2 1.0 CB A:GLN192 4.8 22.3 1.0 CB A:LEU167 4.9 21.4 1.0 C15 A:4WI401 4.9 20.3 1.0 CG A:LEU167 4.9 23.6 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


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 PF07321332 in Spacegroup P1211 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:27.6 occ:1.00 F2 A:4WI401 0.0 27.6 1.0 C22 A:4WI401 1.3 27.1 1.0 F3 A:4WI401 2.1 29.6 1.0 F1 A:4WI401 2.1 30.6 1.0 C21 A:4WI401 2.3 24.3 1.0 O4 A:4WI401 2.6 26.8 1.0 O A:THR190 3.0 25.5 1.0 N4 A:4WI401 3.5 20.8 1.0 NE2 A:GLN192 3.5 22.3 1.0 CE A:MET165 3.6 27.2 1.0 CB A:GLN192 3.7 22.3 1.0 CG A:GLN192 4.0 24.4 1.0 CD A:GLN192 4.0 20.8 1.0 N A:GLN192 4.0 24.0 1.0 C A:THR190 4.2 23.9 1.0 O A:ARG188 4.3 21.4 1.0 CA A:GLN192 4.4 21.9 1.0 N A:THR190 4.4 21.6 1.0 CD2 A:LEU167 4.4 25.3 1.0 O A:GLN192 4.6 24.8 1.0 O A:GLU166 4.7 19.3 1.0 C14 A:4WI401 4.7 19.7 1.0 C A:ALA191 4.7 25.1 1.0 C A:GLN192 4.9 22.2 1.0 OE1 A:GLN192 4.9 20.9 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


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 PF07321332 in Spacegroup P1211 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:29.6 occ:1.00 F3 A:4WI401 0.0 29.6 1.0 C22 A:4WI401 1.3 27.1 1.0 F1 A:4WI401 2.0 30.6 1.0 F2 A:4WI401 2.1 27.6 1.0 C21 A:4WI401 2.3 24.3 1.0 N4 A:4WI401 2.8 20.8 1.0 O A:GLU166 2.9 19.3 1.0 CE A:MET165 3.0 27.2 1.0 O4 A:4WI401 3.4 26.8 1.0 C A:GLU166 3.5 20.1 1.0 CD2 A:LEU167 3.6 25.3 1.0 CA A:LEU167 3.8 21.3 1.0 N A:LEU167 3.9 19.2 1.0 CG A:LEU167 4.1 23.6 1.0 C14 A:4WI401 4.2 19.7 1.0 CB A:MET165 4.2 18.2 1.0 CG A:MET165 4.3 18.8 1.0 N A:GLU166 4.4 16.1 1.0 O A:HOH564 4.4 26.6 1.0 SD A:MET165 4.4 27.8 1.0 O3 A:4WI401 4.5 19.7 1.0 C13 A:4WI401 4.5 19.8 1.0 CA A:GLU166 4.6 16.3 1.0 CB A:LEU167 4.6 21.4 1.0 NE2 A:GLN192 4.7 22.3 1.0 CB A:GLN192 4.7 22.3 1.0 CD A:PRO168 4.8 27.5 1.0 C A:LEU167 4.9 22.9 1.0 C A:MET165 5.0 16.5 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


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 PF07321332 in Spacegroup P1211 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:26.3 occ:1.00 F1 B:4WI401 0.0 26.3 1.0 C22 B:4WI401 1.3 27.1 1.0 F3 B:4WI401 2.1 30.2 1.0 F2 B:4WI401 2.2 28.7 1.0 C21 B:4WI401 2.4 21.0 1.0 O B:THR190 2.8 23.8 1.0 O4 B:4WI401 2.8 23.8 1.0 NE2 B:GLN192 3.0 17.8 1.0 CE B:MET165 3.2 27.1 1.0 N4 B:4WI401 3.5 19.7 1.0 CD B:GLN192 3.6 18.9 1.0 CG B:GLN192 3.7 18.4 1.0 O B:ARG188 3.8 18.6 1.0 CB B:GLN192 3.8 17.7 1.0 C B:THR190 3.9 22.5 1.0 N B:GLN192 4.1 20.4 1.0 N B:THR190 4.1 20.6 1.0 CD2 B:LEU167 4.4 22.2 1.0 SD B:MET165 4.6 31.3 1.0 CA B:GLN192 4.6 18.6 1.0 C B:ALA191 4.6 20.5 1.0 OE1 B:GLN192 4.6 17.1 1.0 CA B:THR190 4.7 21.4 1.0 O B:GLU166 4.7 18.0 1.0 C14 B:4WI401 4.7 18.4 1.0 CA B:ALA191 4.8 22.8 1.0 N B:ALA191 4.8 22.5 1.0 C B:ARG188 5.0 18.7 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:28.7 occ:1.00 F2 B:4WI401 0.0 28.7 1.0 C22 B:4WI401 1.4 27.1 1.0 F3 B:4WI401 2.1 30.2 1.0 F1 B:4WI401 2.2 26.3 1.0 C21 B:4WI401 2.4 21.0 1.0 N4 B:4WI401 2.6 19.7 1.0 O B:GLU166 2.8 18.0 1.0 CE B:MET165 3.1 27.1 1.0 CD2 B:LEU167 3.4 22.2 1.0 C B:GLU166 3.4 15.9 1.0 O4 B:4WI401 3.5 23.8 1.0 CA B:LEU167 3.7 20.5 1.0 N B:LEU167 3.8 15.6 1.0 CB B:MET165 3.9 19.4 1.0 CG B:MET165 3.9 19.4 1.0 C14 B:4WI401 4.0 18.4 1.0 SD B:MET165 4.1 31.3 1.0 N B:GLU166 4.1 15.3 1.0 O3 B:4WI401 4.3 19.5 1.0 CA B:GLU166 4.4 16.1 1.0 C13 B:4WI401 4.4 18.0 1.0 O B:HOH571 4.4 24.3 1.0 CG B:LEU167 4.5 20.4 1.0 CB B:LEU167 4.6 19.5 1.0 C B:MET165 4.7 14.9 1.0 NE2 B:GLN192 4.7 17.8 1.0 CD B:PRO168 4.7 22.2 1.0 C B:LEU167 4.8 21.4 1.0 O B:THR190 4.8 23.8 1.0 C15 B:4WI401 4.8 22.0 1.0 CA B:MET165 4.9 15.6 1.0 CB B:GLN192 5.0 17.7 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:30.2 occ:1.00 F3 B:4WI401 0.0 30.2 1.0 C22 B:4WI401 1.2 27.1 1.0 F2 B:4WI401 2.1 28.7 1.0 F1 B:4WI401 2.1 26.3 1.0 C21 B:4WI401 2.3 21.0 1.0 N4 B:4WI401 3.0 19.7 1.0 O4 B:4WI401 3.1 23.8 1.0 O B:HOH571 3.4 24.3 1.0 O B:GLU166 3.4 18.0 1.0 CD B:PRO168 3.4 22.2 1.0 O B:THR190 3.7 23.8 1.0 CA B:LEU167 3.9 20.5 1.0 N B:GLN192 4.0 20.4 1.0 CD2 B:LEU167 4.2 22.2 1.0 N B:PRO168 4.2 21.2 1.0 C B:GLU166 4.3 15.9 1.0 C14 B:4WI401 4.3 18.4 1.0 C B:LEU167 4.4 21.4 1.0 CA B:ALA191 4.5 22.8 1.0 C B:THR190 4.5 22.5 1.0 N B:LEU167 4.6 15.6 1.0 CG B:PRO168 4.6 27.8 1.0 O B:GLN192 4.6 22.5 1.0 CB B:GLN192 4.6 17.7 1.0 C B:ALA191 4.7 20.5 1.0 CE B:MET165 4.7 27.1 1.0 C15 B:4WI401 4.8 22.0 1.0 CB B:LEU167 4.8 19.5 1.0 CA B:GLN192 4.8 18.6 1.0 N B:ALA191 4.9 22.5 1.0 C23 B:4WI401 5.0 21.9 1.0

J.Li, C.Lin, X.Zhou, F.Zhong, P.Zeng, Y.Yang, Y.Zhang, B.Yu, X.Fan, P.J.Mccormick, R.Fu, Y.Fu, H.Jiang, J.Zhang. Structural Basis of the Main Proteases of Coronavirus Bound to Drug Candidate Pf-07321332. J.Virol. V. 96 01321 2022.
ISSN: ESSN 1098-5514
PubMed: 35389231
DOI: 10.1128/JVI.02013-21