Fluorine in PDB 7tiz: Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63

All present enzymatic activity of Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63, PDB code: 7tiz was solved by F.Forouhar, H.Liu, S.Iketani, A.Zack, N.Khanizeman, E.Bednarova, B.Fowler, S.J.Hong, H.Mohri, M.S.Nair, Y.Huang, N.E.S.Tay, S.Lee, C.Karan, S.J.Resnick, C.Quinn, W.Li, H.Shion, C.Jurtschenko, M.A.Lauber, T.Mcdonald, M.E.Stokes, B.Hurst, T.Rovis, A.Chavez, D.D.Ho, B.R.Stockwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.17 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.433, 81.64, 51.831, 90, 114.5, 90
R / Rfree (%)	17 / 19.1

The structure of Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63 (pdb code 7tiz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63, PDB code: 7tiz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63


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 3CL in Complex with Inhibitor NK01-63 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:82.1 occ:1.00 F1 A:N63401 0.0 82.1 1.0 C19 A:N63401 1.4 75.0 1.0 F3 A:N63401 2.2 78.4 1.0 F2 A:N63401 2.2 82.7 1.0 C18 A:N63401 2.4 56.6 1.0 C20 A:N63401 3.0 54.3 1.0 C17 A:N63401 3.4 47.4 1.0 ND2 A:ASN142 4.1 61.8 1.0 C21 A:N63401 4.3 50.6 1.0 C16 A:N63401 4.6 40.4 1.0 O A:HOH520 4.8 45.0 1.0 CG A:ASN142 4.9 51.8 1.0 C22 A:N63401 4.9 43.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63


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 3CL in Complex with Inhibitor NK01-63 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:82.7 occ:1.00 F2 A:N63401 0.0 82.7 1.0 C19 A:N63401 1.4 75.0 1.0 F3 A:N63401 2.2 78.4 1.0 F1 A:N63401 2.2 82.1 1.0 C18 A:N63401 2.4 56.6 1.0 C20 A:N63401 2.9 54.3 1.0 C2 A:N63401 3.3 32.1 1.0 ND2 A:ASN142 3.3 61.8 1.0 C3 A:N63401 3.4 32.7 1.0 C17 A:N63401 3.5 47.4 1.0 CG A:ASN142 3.5 51.8 1.0 CB A:ASN142 3.6 43.5 1.0 O A:HOH652 3.8 43.1 1.0 C21 A:N63401 4.2 50.6 1.0 CA A:ASN142 4.2 38.1 1.0 N A:ASN142 4.3 38.7 1.0 OD1 A:ASN142 4.3 46.9 1.0 C16 A:N63401 4.6 40.4 1.0 N1 A:N63401 4.7 28.4 1.0 C4 A:N63401 4.9 27.3 1.0 C22 A:N63401 4.9 43.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Sars-Cov-2 3CL in Complex with Inhibitor NK01-63 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:78.4 occ:1.00 F3 A:N63401 0.0 78.4 1.0 C19 A:N63401 1.4 75.0 1.0 F2 A:N63401 2.2 82.7 1.0 F1 A:N63401 2.2 82.1 1.0 C18 A:N63401 2.4 56.6 1.0 C17 A:N63401 2.7 47.4 1.0 O A:HOH520 3.0 45.0 1.0 ND2 A:ASN142 3.3 61.8 1.0 O5 A:N63401 3.6 34.6 1.0 C20 A:N63401 3.7 54.3 1.0 CG A:ASN142 3.8 51.8 1.0 C3 A:N63401 3.9 32.7 1.0 C16 A:N63401 4.1 40.4 1.0 OD1 A:ASN142 4.2 46.9 1.0 C2 A:N63401 4.4 32.1 1.0 O3 A:N63401 4.6 33.1 1.0 CB A:ASN142 4.7 43.5 1.0 C8 A:N63401 4.8 32.7 1.0 C21 A:N63401 4.8 50.6 1.0 C14 A:N63401 4.8 34.8 1.0 C22 A:N63401 4.9 43.1 1.0

H.Liu, S.Iketani, A.Zask, N.Khanizeman, E.Bednarova, F.Forouhar, B.Fowler, S.J.Hong, H.Mohri, M.S.Nair, Y.Huang, N.E.S.Tay, S.Lee, C.Karan, S.J.Resnick, C.Quinn, W.Li, H.Shion, X.Xia, J.D.Daniels, M.Bartolo-Cruz, M.Farina, P.Rajbhandari, C.Jurtschenko, M.A.Lauber, T.Mcdonald, M.E.Stokes, B.L.Hurst, T.Rovis, A.Chavez, D.D.Ho, B.R.Stockwell. Development of Optimized Drug-Like Small Molecule Inhibitors of the Sars-Cov-2 3CL Protease For Treatment of Covid-19. Nat Commun V. 13 1891 2022.
ISSN: ESSN 2041-1723
PubMed: 35393402
DOI: 10.1038/S41467-022-29413-2