Fluorine in PDB 7l8j: Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21212)

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21212):
3.4.22.69;

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21212), PDB code: 7l8j was solved by G.J.Lockbaum, M.Henes, J.M.Lee, J.Timm, E.A.Nalivaika, N.K.Yilmaz, P.R.Thompson, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.40 / 2.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	44.88, 62.09, 107.18, 90, 90, 90
R / Rfree (%)	22.3 / 28.1

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21212) (pdb code 7l8j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21212), PDB code: 7l8j:

Fluorine binding site 1 out of 1 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21212)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21212) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:87.9 occ:1.00 F1 A:AG7401 0.0 87.9 1.0 C09 A:AG7401 1.4 79.9 1.0 HD22 A:LEU27 2.4 79.3 1.0 HB2 A:PRO39 2.5 79.9 1.0 C10 A:AG7401 2.5 66.7 1.0 C08 A:AG7401 2.5 77.8 1.0 H33 A:AG7401 2.7 80.3 1.0 H31 A:AG7401 2.7 93.7 1.0 HG2 A:PRO39 2.8 81.9 1.0 HD23 A:LEU27 2.9 79.3 1.0 HB3 A:HIS41 2.9 98.7 1.0 CD2 A:LEU27 2.9 65.8 1.0 HB2 A:CYS145 3.1 66.9 1.0 HD21 A:LEU27 3.1 79.3 1.0 CB A:PRO39 3.3 66.3 1.0 HB3 A:CYS145 3.3 66.9 1.0 H41 A:AG7401 3.3 75.1 1.0 CG A:PRO39 3.5 68.0 1.0 CB A:CYS145 3.6 55.5 1.0 HB3 A:PRO39 3.6 79.9 1.0 CB A:HIS41 3.8 82.0 1.0 H A:HIS41 3.8 107.9 1.0 C11 A:AG7401 3.9 75.2 1.0 C07 A:AG7401 3.9 81.5 1.0 HB2 A:HIS41 4.0 98.7 1.0 HG3 A:PRO39 4.1 81.9 1.0 SG A:CYS145 4.1 58.2 1.0 C A:HIS41 4.2 80.3 1.0 C20 A:AG7401 4.2 62.3 1.0 HB3 A:LEU27 4.3 79.8 1.0 N A:VAL42 4.3 78.5 1.0 CA A:HIS41 4.3 89.9 1.0 CG A:LEU27 4.4 70.4 1.0 HD2 A:PRO39 4.4 73.4 1.0 H A:VAL42 4.4 94.5 1.0 N A:HIS41 4.4 89.7 1.0 C06 A:AG7401 4.4 64.4 1.0 O A:HIS41 4.4 86.4 1.0 CA A:PRO39 4.5 68.5 1.0 CD A:PRO39 4.5 60.9 1.0 HB2 A:LEU27 4.5 79.8 1.0 O A:PRO39 4.6 62.8 1.0 C A:PRO39 4.6 68.0 1.0 H34 A:AG7401 4.6 90.5 1.0 HB A:VAL42 4.7 97.3 1.0 CB A:LEU27 4.7 66.2 1.0 H30 A:AG7401 4.7 98.1 1.0 C21 A:AG7401 4.7 68.7 1.0 HA A:VAL42 4.7 105.5 1.0 H42 A:AG7401 4.7 75.1 1.0 HA A:HIS164 4.7 60.8 1.0 CG A:HIS41 4.9 90.6 1.0 HG A:LEU27 4.9 84.8 1.0 O23 A:AG7401 4.9 71.4 1.0 HD13 A:LEU27 4.9 80.9 1.0 CA A:CYS145 5.0 55.1 1.0

G.J.Lockbaum, M.Henes, J.M.Lee, J.Timm, E.A.Nalivaika, P.R.Thompson, N.Kurt Yilmaz, C.A.Schiffer. Pan-3C Protease Inhibitor Rupintrivir Binds Sars-Cov-2 Main Protease in A Unique Binding Mode. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 34506130
DOI: 10.1021/ACS.BIOCHEM.1C00414