Fluorine in PDB 7rfs: Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor

All present enzymatic activity of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor:
3.4.22.69;

The structure of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor, PDB code: 7rfs was solved by S.E.Greasley, R.A.Ferre, W.Liu, A.E.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.74 / 1.91
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.2, 53.03, 45.68, 90, 102.52, 90
R / Rfree (%)	21.5 / 26

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor (pdb code 7rfs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor, PDB code: 7rfs:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:54.6 occ:1.00 F1 A:4WI401 0.0 54.6 1.0 C22 A:4WI401 1.4 54.3 1.0 F2 A:4WI401 2.1 54.4 1.0 F3 A:4WI401 2.2 54.1 1.0 H16 A:4WI401 2.2 53.3 0.0 C21 A:4WI401 2.4 54.1 1.0 N4 A:4WI401 2.6 53.3 1.0 O A:GLU166 2.8 46.6 1.0 CE A:MET165 2.8 53.5 1.0 C A:GLU166 3.5 46.5 1.0 O4 A:4WI401 3.5 54.3 1.0 CA A:LEU167 3.8 51.6 1.0 CD2 A:LEU167 3.9 54.3 1.0 N A:LEU167 3.9 49.3 1.0 C14 A:4WI401 4.0 52.1 1.0 CG A:MET165 4.1 44.4 1.0 SD A:MET165 4.1 55.1 1.0 CB A:MET165 4.2 40.5 1.0 CG A:LEU167 4.2 53.1 1.0 O3 A:4WI401 4.3 51.7 1.0 N A:GLU166 4.3 41.2 1.0 C13 A:4WI401 4.3 51.9 1.0 H30 A:4WI401 4.4 50.4 0.0 H15 A:4WI401 4.5 52.1 0.0 H25 A:4WI401 4.5 51.2 0.0 CA A:GLU166 4.5 42.7 1.0 CB A:LEU167 4.6 51.8 1.0 CD A:PRO168 4.8 54.6 1.0 H17 A:4WI401 4.8 50.6 0.0 NE2 A:GLN192 4.8 49.7 1.0 C A:LEU167 4.9 54.3 1.0 O A:THR190 4.9 46.6 1.0 C A:MET165 4.9 40.4 1.0 H29 A:4WI401 4.9 50.4 0.0 C23 A:4WI401 5.0 50.4 1.0

Fluorine binding site 2 out of 3 in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:54.4 occ:1.00 F2 A:4WI401 0.0 54.4 1.0 C22 A:4WI401 1.4 54.3 1.0 F1 A:4WI401 2.1 54.6 1.0 F3 A:4WI401 2.2 54.1 1.0 C21 A:4WI401 2.4 54.1 1.0 O A:THR190 2.7 46.6 1.0 O4 A:4WI401 2.8 54.3 1.0 CE A:MET165 3.4 53.5 1.0 NE2 A:GLN192 3.4 49.7 1.0 N4 A:4WI401 3.5 53.3 1.0 H16 A:4WI401 3.7 53.3 0.0 C A:THR190 3.9 46.3 1.0 O A:ARG188 3.9 41.4 1.0 CD A:GLN192 3.9 50.9 1.0 CB A:GLN192 4.0 50.1 1.0 CG A:GLN192 4.1 50.6 1.0 N A:THR190 4.2 43.3 1.0 N A:GLN192 4.2 49.1 1.0 O A:HOH555 4.5 52.5 1.0 CD2 A:LEU167 4.6 54.3 1.0 O A:GLU166 4.7 46.6 1.0 CA A:THR190 4.7 44.7 1.0 C A:ALA191 4.8 49.1 1.0 CA A:GLN192 4.8 49.7 1.0 N A:ALA191 4.8 47.2 1.0 H15 A:4WI401 4.8 52.1 0.0 C14 A:4WI401 4.8 52.1 1.0 OE1 A:GLN192 4.8 51.3 1.0 CA A:ALA191 4.8 48.4 1.0 CA A:GLN189 4.9 41.8 1.0 SD A:MET165 4.9 55.1 1.0

Fluorine binding site 3 out of 3 in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:54.1 occ:1.00 F3 A:4WI401 0.0 54.1 1.0 C22 A:4WI401 1.4 54.3 1.0 F2 A:4WI401 2.2 54.4 1.0 F1 A:4WI401 2.2 54.6 1.0 C21 A:4WI401 2.4 54.1 1.0 O4 A:4WI401 3.1 54.3 1.0 H16 A:4WI401 3.1 53.3 0.0 N4 A:4WI401 3.1 53.3 1.0 CD A:PRO168 3.3 54.6 1.0 O A:GLU166 3.4 46.6 1.0 CA A:LEU167 3.8 51.6 1.0 CG A:PRO168 3.9 56.5 1.0 H17 A:4WI401 3.9 50.6 0.0 N A:PRO168 4.0 54.9 1.0 O A:HOH555 4.1 52.5 1.0 O A:THR190 4.1 46.6 1.0 C A:LEU167 4.2 54.3 1.0 H30 A:4WI401 4.2 50.4 0.0 CD2 A:LEU167 4.3 54.3 1.0 C A:GLU166 4.3 46.5 1.0 N A:LEU167 4.5 49.3 1.0 N A:GLN192 4.5 49.1 1.0 C14 A:4WI401 4.5 52.1 1.0 CE A:MET165 4.7 53.5 1.0 CB A:LEU167 4.7 51.8 1.0 H15 A:4WI401 4.8 52.1 0.0 O A:GLN192 4.8 51.6 1.0 CG A:LEU167 4.9 53.1 1.0 C16 A:4WI401 4.9 50.6 1.0 CA A:PRO168 4.9 55.3 1.0 CB A:GLN192 4.9 50.1 1.0 C A:THR190 5.0 46.3 1.0

D.R.Owen, C.M.N.Allerton, A.S.Anderson, L.Aschenbrenner, M.Avery, S.Berritt, B.Boras, R.D.Cardin, A.Carlo, K.J.Coffman, A.Dantonio, L.Di, H.Eng, R.A.Ferre, K.S.Gajiwala, S.A.Gibson, S.E.Greasley, B.L.Hurst, E.P.Kadar, A.S.Kalgutkar, J.C.Lee, J.Lee, W.Liu, S.W.Mason, S.Noell, J.J.Novak, R.S.Obach, K.Ogilvie, N.C.Patel, M.Pettersson, D.K.Rai, M.R.Reese, M.F.Sammons, J.G.Sathish, R.S.P.Singh, C.M.Steppan, A.E.Stewart, J.B.Tuttle, L.Updyke, P.R.Verhoest, L.Wei, Q.Yang, Y.Zhu. An Oral Sars-Cov-2 Mpro Inhibitor Clinical Candidate For the Treatment of Covid-19 Science 2021.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ABL4784