Fluorine in PDB 7l8h: EV68 3C Protease (3CPRO) in Complex with Rupintrivir

The structure of EV68 3C Protease (3CPRO) in Complex with Rupintrivir, PDB code: 7l8h 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)	40.45 / 1.95
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	80.9, 80.9, 197.16, 90, 90, 120
R / Rfree (%)	15.8 / 18.6

The binding sites of Fluorine atom in the EV68 3C Protease (3CPRO) in Complex with Rupintrivir (pdb code 7l8h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the EV68 3C Protease (3CPRO) in Complex with Rupintrivir, PDB code: 7l8h:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the EV68 3C Protease (3CPRO) in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of EV68 3C Protease (3CPRO) in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:43.1 occ:1.00 F1 A:AG7201 0.0 43.1 1.0 C09 A:AG7201 1.4 29.7 1.0 HB A:THR130 2.4 36.1 1.0 HG1 A:THR130 2.4 47.5 1.0 C10 A:AG7201 2.5 29.9 1.0 C08 A:AG7201 2.5 29.7 1.0 H33 A:AG7201 2.7 35.6 1.0 H31 A:AG7201 2.7 35.4 1.0 OG1 A:THR130 2.8 39.8 1.0 CB A:THR130 3.0 30.4 1.0 O A:LEU127 3.2 31.8 1.0 O A:HOH341 3.4 35.6 1.0 O A:HOH425 3.4 42.6 1.0 HG21 A:THR130 3.5 46.0 1.0 O A:HOH304 3.8 35.3 1.0 CG2 A:THR130 3.8 38.6 1.0 H A:THR130 3.8 44.3 1.0 C11 A:AG7201 3.9 32.9 1.0 C07 A:AG7201 3.9 36.4 1.0 HG22 A:THR130 4.1 46.0 1.0 HB3 A:LEU127 4.2 35.2 1.0 CA A:THR130 4.2 32.5 1.0 N A:THR130 4.3 37.2 1.0 C A:LEU127 4.3 28.3 1.0 HA3 A:GLY128 4.3 34.6 1.0 HD2 A:HIS40 4.3 46.2 1.0 C06 A:AG7201 4.4 32.5 1.0 OE2 A:GLU71 4.6 39.6 1.0 HG A:LEU127 4.6 29.5 1.0 HG23 A:THR130 4.6 46.0 1.0 O A:GLY128 4.6 29.7 1.0 H34 A:AG7201 4.6 39.2 1.0 H30 A:AG7201 4.6 43.3 1.0 HD23 A:LEU127 4.7 37.7 1.0 C A:GLY128 4.8 30.5 1.0 CD2 A:HIS40 4.8 38.7 1.0 HA A:THR130 4.8 38.6 1.0 O A:THR130 4.9 32.3 1.0 OD1 A:ASN69 4.9 29.6 1.0 O A:HOH387 4.9 47.6 1.0 CA A:GLY128 4.9 29.1 1.0 CB A:LEU127 5.0 29.6 1.0 HB2 A:HIS40 5.0 42.2 1.0

Fluorine binding site 2 out of 2 in the EV68 3C Protease (3CPRO) in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of EV68 3C Protease (3CPRO) in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:43.8 occ:1.00 F1 B:AG7201 0.0 43.8 1.0 C09 B:AG7201 1.4 29.9 1.0 HB B:THR130 2.3 43.0 1.0 HG1 B:THR130 2.4 47.8 1.0 C10 B:AG7201 2.5 33.1 1.0 C08 B:AG7201 2.5 31.4 1.0 H33 B:AG7201 2.7 39.5 1.0 H31 B:AG7201 2.7 37.4 1.0 OG1 B:THR130 2.8 40.1 1.0 CB B:THR130 3.0 36.1 1.0 O B:LEU127 3.1 32.6 1.0 O B:HOH303 3.2 44.2 1.0 O B:HOH390 3.3 39.8 1.0 HG21 B:THR130 3.6 44.8 1.0 O B:HOH307 3.6 42.1 1.0 CG2 B:THR130 3.8 37.6 1.0 H B:THR130 3.8 49.4 1.0 O B:HOH416 3.9 49.7 1.0 C07 B:AG7201 3.9 32.1 1.0 C11 B:AG7201 3.9 34.8 1.0 HG B:LEU127 4.0 39.2 1.0 HB3 B:LEU127 4.0 37.5 1.0 HG22 B:THR130 4.1 44.8 1.0 CA B:THR130 4.2 35.3 1.0 C B:LEU127 4.2 29.7 1.0 N B:THR130 4.3 41.5 1.0 HA3 B:GLY128 4.3 37.8 1.0 HD2 B:HIS40 4.4 54.7 1.0 C06 B:AG7201 4.4 29.5 1.0 HD23 B:LEU127 4.5 34.8 1.0 OE2 B:GLU71 4.5 37.0 1.0 HD21 B:ASN69 4.6 36.5 1.0 HB2 B:HIS40 4.6 49.0 1.0 HD22 B:ASN69 4.6 36.5 1.0 H30 B:AG7201 4.6 38.2 1.0 H34 B:AG7201 4.6 41.5 1.0 HG23 B:THR130 4.6 44.8 1.0 O B:GLY128 4.7 32.6 1.0 CG B:LEU127 4.7 32.9 1.0 CB B:LEU127 4.7 31.5 1.0 ND2 B:ASN69 4.7 30.6 1.0 C B:GLY128 4.8 32.6 1.0 O B:THR130 4.8 36.9 1.0 HA B:THR130 4.9 42.1 1.0 CA B:GLY128 4.9 31.8 1.0 CD2 B:HIS40 4.9 45.9 1.0 N B:GLY128 5.0 32.0 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