Fluorine in PDB 7b2u: Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1, PDB code: 7b2u was solved by V.O.Talibov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.45 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.517, 53.682, 114.508, 90, 100.59, 90
R / Rfree (%)	20.8 / 24.6

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1 (pdb code 7b2u). 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 Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1, PDB code: 7b2u:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1


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 (NSP5) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:35.6 occ:1.00 F1 A:SQ5401 0.0 35.6 1.0 C14 A:SQ5401 1.4 36.3 1.0 C15 A:SQ5401 2.4 29.1 1.0 C13 A:SQ5401 2.4 29.8 1.0 O A:HOH676 3.3 41.0 1.0 O A:PHE140 3.3 26.8 1.0 OE2 A:GLU166 3.4 29.3 1.0 N B:SER1 3.5 31.0 1.0 O B:HOH599 3.5 40.0 1.0 N A:ASN142 3.5 32.2 1.0 C A:LEU141 3.6 29.6 1.0 N3 A:SQ5401 3.6 28.1 1.0 C11 A:SQ5401 3.6 31.2 1.0 CA A:LEU141 3.6 29.6 1.0 CD A:GLU166 4.0 35.4 1.0 C12 A:SQ5401 4.0 25.2 1.0 C A:PHE140 4.1 23.8 1.0 O A:LEU141 4.2 25.6 1.0 N A:LEU141 4.3 28.4 1.0 OE1 A:GLU166 4.4 45.4 1.0 CA A:ASN142 4.4 23.6 1.0 CB A:GLU166 4.5 22.3 1.0 N2 A:SQ5401 4.8 29.5 1.0 CG A:GLU166 4.8 27.0 1.0 CB A:LEU141 4.8 30.8 1.0 CA B:SER1 4.9 33.5 1.0 CB A:ASN142 5.0 33.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1


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 (NSP5) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:36.8 occ:1.00 F1 B:SQ5401 0.0 36.8 1.0 C14 B:SQ5401 1.4 33.1 1.0 C15 B:SQ5401 2.4 27.2 1.0 C13 B:SQ5401 2.4 29.2 1.0 O B:HOH697 3.3 44.9 1.0 N A:SER1 3.3 30.2 1.0 O B:HOH644 3.3 40.5 1.0 O B:PHE140 3.3 27.6 1.0 OE2 B:GLU166 3.5 27.0 1.0 O A:HOH528 3.5 39.4 1.0 N B:ASN142 3.6 31.2 1.0 C B:LEU141 3.6 25.4 1.0 N3 B:SQ5401 3.6 26.2 1.0 C11 B:SQ5401 3.6 26.3 1.0 CA B:LEU141 3.7 27.8 1.0 C12 B:SQ5401 4.1 21.1 1.0 CD B:GLU166 4.1 33.0 1.0 C B:PHE140 4.1 26.1 1.0 O B:LEU141 4.2 26.0 1.0 N B:LEU141 4.3 27.5 1.0 CA B:ASN142 4.3 25.2 1.0 CB B:GLU166 4.5 20.8 1.0 OE1 B:GLU166 4.6 39.6 1.0 CA A:SER1 4.7 31.3 1.0 N2 B:SQ5401 4.8 28.6 1.0 CG B:GLU166 4.9 25.2 1.0 CB B:LEU141 4.9 24.1 1.0 CB B:ASN142 4.9 33.9 1.0

A.Luttens, H.Gullberg, E.Abdurakhmanov, D.D.Vo, D.Akaberi, V.O.Talibov, N.Nekhotiaeva, L.Vangeel, S.De Jonghe, D.Jochmans, J.Krambrich, A.Tas, B.Lundgren, Y.Gravenfors, A.J.Craig, Y.Atilaw, A.Sandstrom, L.W.K.Moodie, A.Lundkvist, M.J.Van Hemert, J.Neyts, J.Lennerstrand, J.Kihlberg, K.Sandberg, U.H.Danielson, J.Carlsson. Ultralarge Virtual Screening Identifies Sars-Cov-2 Main Protease Inhibitors with Broad-Spectrum Activity Against Coronaviruses. J.Am.Chem.Soc. V. 144 2905 2022.
ISSN: ESSN 1520-5126
PubMed: 35142215
DOI: 10.1021/JACS.1C08402