Fluorine in PDB 7l8i: Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21)

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21):
3.4.22.69;

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21), PDB code: 7l8i 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)	23.74 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.78, 106.378, 54.105, 90, 103.06, 90
R / Rfree (%)	20.6 / 26.3

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21) (pdb code 7l8i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21), PDB code: 7l8i:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21)


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 (P21) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:55.7 occ:1.00 F1 A:AG7401 0.0 55.7 1.0 C09 A:AG7401 1.4 37.0 1.0 HD22 A:LEU27 2.4 38.2 1.0 HB2 A:PRO39 2.4 33.0 1.0 C10 A:AG7401 2.5 35.2 1.0 C08 A:AG7401 2.5 41.9 1.0 H31 A:AG7401 2.7 50.2 1.0 H33 A:AG7401 2.7 42.2 1.0 HB3 A:HIS41 2.8 41.9 1.0 HB3 A:CYS145 2.9 29.9 1.0 HG2 A:PRO39 3.0 37.2 1.0 CD2 A:LEU27 3.1 31.9 1.0 HD21 A:LEU27 3.2 38.2 1.0 CB A:PRO39 3.2 27.6 1.0 HB2 A:CYS145 3.3 29.9 1.0 HD23 A:LEU27 3.4 38.2 1.0 CB A:CYS145 3.5 25.0 1.0 HB3 A:PRO39 3.5 33.0 1.0 CG A:PRO39 3.6 31.1 1.0 CB A:HIS41 3.6 35.0 1.0 HB2 A:HIS41 3.7 41.9 1.0 C11 A:AG7401 3.9 39.9 1.0 C07 A:AG7401 3.9 38.7 1.0 H41 A:AG7401 4.0 49.7 1.0 HD2 A:PRO39 4.0 36.3 1.0 SG A:CYS145 4.1 26.9 1.0 H A:HIS41 4.3 36.8 1.0 H A:VAL42 4.3 38.1 1.0 HG3 A:PRO39 4.4 37.2 1.0 CD A:PRO39 4.4 30.3 1.0 O A:PRO39 4.4 28.3 1.0 CG A:LEU27 4.4 38.5 1.0 C06 A:AG7401 4.4 43.4 1.0 N A:VAL42 4.4 31.8 1.0 O22 A:AG7401 4.4 39.0 1.0 HB3 A:LEU27 4.5 39.2 1.0 CA A:PRO39 4.5 29.4 1.0 CA A:HIS41 4.5 31.6 1.0 C21 A:AG7401 4.5 40.2 1.0 C A:HIS41 4.5 31.7 1.0 CG A:HIS41 4.6 39.8 1.0 C20 A:AG7401 4.6 41.5 1.0 HB2 A:LEU27 4.6 39.2 1.0 HD13 A:LEU27 4.6 35.5 1.0 H34 A:AG7401 4.6 47.7 1.0 H30 A:AG7401 4.6 46.4 1.0 C A:PRO39 4.7 31.1 1.0 HB A:VAL42 4.7 37.3 1.0 N A:HIS41 4.7 30.7 1.0 HA A:VAL42 4.7 39.2 1.0 HA A:HIS164 4.8 42.3 1.0 CB A:LEU27 4.8 32.7 1.0 CA A:CYS145 4.9 20.3 1.0 ND1 A:HIS41 4.9 42.3 1.0 HD11 A:LEU27 4.9 35.5 1.0 CD1 A:LEU27 4.9 29.7 1.0 N A:PRO39 5.0 31.5 1.0

Fluorine binding site 2 out of 2 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sars-Cov-2 Main Protease (Mpro) in Complex with Rupintrivir (P21) within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:52.1 occ:1.00 F1 B:AG7401 0.0 52.1 1.0 C09 B:AG7401 1.4 30.3 1.0 HB2 B:PRO39 2.3 35.8 1.0 HD22 B:LEU27 2.4 36.2 1.0 C10 B:AG7401 2.5 33.9 1.0 C08 B:AG7401 2.5 37.9 1.0 H33 B:AG7401 2.7 40.6 1.0 H31 B:AG7401 2.7 45.4 1.0 HB3 B:HIS41 2.9 36.7 1.0 HD21 B:LEU27 2.9 36.2 1.0 HG2 B:PRO39 3.0 32.1 1.0 CD2 B:LEU27 3.0 30.2 1.0 CB B:PRO39 3.1 29.9 1.0 HB3 B:CYS145 3.1 32.1 1.0 HD23 B:LEU27 3.3 36.2 1.0 HB3 B:PRO39 3.4 35.8 1.0 CG B:PRO39 3.5 26.8 1.0 HB2 B:CYS145 3.6 32.1 1.0 CB B:CYS145 3.7 26.8 1.0 CB B:HIS41 3.8 30.6 1.0 H41 B:AG7401 3.9 40.7 1.0 C11 B:AG7401 3.9 35.7 1.0 C07 B:AG7401 3.9 39.9 1.0 H B:VAL42 4.0 40.3 1.0 H B:HIS41 4.1 33.6 1.0 HD2 B:PRO39 4.1 31.9 1.0 N B:VAL42 4.2 33.7 1.0 HB2 B:HIS41 4.2 36.7 1.0 C B:HIS41 4.2 31.1 1.0 HG3 B:PRO39 4.3 32.1 1.0 SG B:CYS145 4.3 30.1 1.0 CG B:LEU27 4.3 34.3 1.0 CD B:PRO39 4.4 26.7 1.0 O B:PRO39 4.4 22.9 1.0 CA B:PRO39 4.4 32.5 1.0 CA B:HIS41 4.4 31.6 1.0 HB B:VAL42 4.4 35.8 1.0 C06 B:AG7401 4.4 35.1 1.0 N B:HIS41 4.5 28.1 1.0 C B:PRO39 4.5 29.2 1.0 HB3 B:LEU27 4.5 27.6 1.0 HA B:VAL42 4.6 42.9 1.0 H34 B:AG7401 4.6 42.8 1.0 HD13 B:LEU27 4.6 40.4 1.0 H30 B:AG7401 4.6 47.8 1.0 HB2 B:LEU27 4.6 27.6 1.0 HD11 B:LEU27 4.7 40.4 1.0 CG B:HIS41 4.7 41.6 1.0 HD1 B:HIS41 4.7 60.4 1.0 O B:HOH577 4.7 32.2 1.0 C20 B:AG7401 4.7 34.0 1.0 O B:HIS41 4.8 42.4 1.0 CB B:LEU27 4.8 23.0 1.0 CD1 B:LEU27 4.8 33.7 1.0 H52 B:AG7401 4.8 46.5 1.0 CA B:VAL42 4.9 35.8 1.0 HA B:HIS164 4.9 30.8 1.0 ND1 B:HIS41 4.9 50.4 1.0 N B:PRO39 5.0 24.6 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