Fluorine in PDB 7axm: Structure of Sars-Cov-2 Main Protease Bound to Pelitinib

All present enzymatic activity of Structure of Sars-Cov-2 Main Protease Bound to Pelitinib:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

The structure of Structure of Sars-Cov-2 Main Protease Bound to Pelitinib, PDB code: 7axm was solved by S.Guenther, P.Y.A.Reinke, D.Oberthuer, O.Yefanov, L.Gelisio, H.Ginn, J.Lieske, M.Domaracky, W.Brehm, A.Rahmani Mashour, T.A.White, J.Knoska, G.Pena Esperanza, F.Koua, A.Tolstikova, M.Groessler, P.Fischer, V.Hennicke, H.Fleckenstein, F.Trost, M.Galchenkova, Y.Gevorkov, C.Li, S.Awel, L.X.Paulraj, N.Ullah, S.Falke, B.Alves Franca, M.Schwinzer, H.Brognaro, N.Werner, M.Perbandt, H.Tidow, B.Seychell, T.Beck, S.Meier, J.J.Doyle, H.Giseler, D.Melo, T.J.Lane, I.Dunkel, A.Peck, S.Saouane, J.Hakanpaeae, J.Meyer, H.Noei, P.Gribbon, B.Ellinger, M.Kuzikov, M.Wolf, L.Zhang, C.Ehrt, J.Pletzer-Zelgert, J.Wollenhaupt, C.Feiler, M.Weiss, E.C.Schulz, P.Mehrabi, B.Norton-Baker, C.Schmidt, K.Lorenzen, R.Schubert, H.Han, A.Chari, Y.Fernandez Garcia, D.Turk, R.Hilgenfeld, M.Rarey, A.Zaliani, H.N.Chapman, A.Pearson, C.Betzel, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.60 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.400, 53.200, 44.776, 90.00, 103.05, 90.00
R / Rfree (%)	14.3 / 21

The structure of Structure of Sars-Cov-2 Main Protease Bound to Pelitinib also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 Main Protease Bound to Pelitinib (pdb code 7axm). 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 Structure of Sars-Cov-2 Main Protease Bound to Pelitinib, PDB code: 7axm:

Fluorine binding site 1 out of 1 in the Structure of Sars-Cov-2 Main Protease Bound to Pelitinib


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 Bound to Pelitinib within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:52.5 occ:0.61 F01 A:93J502 0.0 52.5 0.6 C22 A:93J502 1.3 50.6 0.6 C23 A:93J502 2.3 48.7 0.6 C21 A:93J502 2.4 47.8 0.6 H24 A:93J502 2.5 58.4 0.6 HD23 A:LEU253 2.7 30.7 1.0 HB2 A:GLN256 3.0 44.4 1.0 HG22 A:VAL297 3.0 38.0 1.0 CL1 A:93J502 3.0 49.4 0.6 HG2 A:GLN256 3.0 51.4 1.0 HA A:LEU253 3.3 28.4 1.0 HB3 A:GLN256 3.4 44.4 1.0 CB A:GLN256 3.5 37.0 1.0 C24 A:93J502 3.6 48.1 0.6 CD2 A:LEU253 3.6 25.6 1.0 C20 A:93J502 3.6 48.1 0.6 HD21 A:LEU253 3.7 30.7 1.0 CG A:GLN256 3.7 42.8 1.0 CG2 A:VAL297 3.9 31.6 1.0 O A:PRO252 3.9 28.0 1.0 O A:HOH703 4.0 34.1 1.0 HG13 A:VAL297 4.0 41.7 1.0 HG A:LEU253 4.0 28.8 1.0 C19 A:93J502 4.1 46.1 0.6 HA A:VAL297 4.2 34.0 1.0 CA A:LEU253 4.2 23.6 1.0 HG21 A:VAL297 4.2 38.0 1.0 HD12 A:ILE213 4.2 37.3 1.0 HD22 A:LEU253 4.2 30.7 1.0 H5 A:93J502 4.3 57.8 0.6 C A:PRO252 4.3 25.1 1.0 CG A:LEU253 4.3 23.9 1.0 H4 A:93J502 4.4 57.8 0.6 HG23 A:VAL297 4.4 38.0 1.0 HG3 A:GLN256 4.4 51.4 1.0 N A:LEU253 4.5 23.6 1.0 OE1 A:GLN256 4.6 54.4 1.0 CD A:GLN256 4.6 49.3 1.0 HD11 A:ILE213 4.6 37.3 1.0 CG1 A:VAL297 4.6 34.7 1.0 HB2 A:PRO252 4.6 34.5 1.0 HG11 A:VAL297 4.7 41.7 1.0 H A:GLN256 4.7 37.5 1.0 CB A:VAL297 4.7 30.9 1.0 CD1 A:ILE213 4.8 31.0 1.0 CB A:LEU253 4.9 21.9 1.0 HB3 A:PRO252 4.9 34.5 1.0 CA A:VAL297 4.9 28.3 1.0 CA A:GLN256 4.9 33.9 1.0

S.Guenther, P.Y.A., Reinke, Y., Fernandez-Garcia, J., Lieske, T.J., Lane, H.M., Ginn, F.H.M., Koua, C., Ehrt, W., Ewert, D., Oberthuer, O., Yefanov, S., Meier, K., Lorenzen, B., Krichel, J.D., Kopicki, L., Gelisio, W., Brehm, I., Dunkel, B., Seychell, H., Gieseler, B., Norton-Baker, B., Escudero-Perez, M., Domaracky, S., Saouane, A., Tolstikova, T.A., White, A., Hanle, M., Groessler, H., Fleckenstein, F., Trost, M., Galchenkova, Y., Gevorkov, C., Li, S., Awel, A.Peck, M., Barthelmess, F., Schluenzen, L.X., Paulraj, N., Werner, H., Andaleeb, N., Ullah, S., Falke, V., Srinivasan, B., Franca, M., Schwinzer, H., Brognaro, C., Rogers, D., Melo, J.J., Doyle, J., Knoska, G.E., Pena Murillo, A., Rahmani Mashhour, F., Guicking, V., Hennicke, P., Fischer, J., Hakanpaeae, J., Meyer, P., Gribbon, B., Ellinger, M., Kuzikov, M., Wolf, G., Burenkov, D., Von Stetten, G., Pompidor, I., Bento, S., Panneerselvam, I., Karpics, T.R., Schneider, M., Garcia Alai, S., Niebling, C., Guenther, C., Schmidt, R., Schubert, H., Han, J., Boger, D., Monteiro, L., Zhang, X., Sun, J., Pletzer-Zelgert, J., Wollenhaupt, C., Feiler, M., Weiss, E.C., Schulz, P., Mehrabi, K., Karnicar, A., Usenik, J., Loboda, H., Tidow, A., Chari, R., Hilgenfeld, C., Uetrecht, R., Cox, A., Zaliani, T., Beck, M., Rarey, S., Guenther, D., Turk, W., Hinrichs, H.N., Chapman, A., Pearson, C., Betzel, A.Meents. Inhibition of Sars-Cov-2 Main Protease By Allosteric Drug-Binding Biorxiv 2020.
DOI: 10.1101/2020.11.12.378422