Fluorine in PDB 7abu: Structure of Sars-Cov-2 Main Protease Bound to RS102895

All present enzymatic activity of Structure of Sars-Cov-2 Main Protease Bound to RS102895:
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 RS102895, PDB code: 7abu 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)	43.63 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.915, 52.973, 44.763, 90.00, 102.94, 90.00
R / Rfree (%)	17.7 / 21.5

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 Main Protease Bound to RS102895 (pdb code 7abu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Sars-Cov-2 Main Protease Bound to RS102895, PDB code: 7abu:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of Sars-Cov-2 Main Protease Bound to RS102895


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 RS102895 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:54.8 occ:0.48 F25 A:R6Q401 0.0 54.8 0.5 C24 A:R6Q401 1.3 61.1 0.5 F27 A:R6Q401 2.1 62.8 0.5 F26 A:R6Q401 2.1 61.0 0.5 C21 A:R6Q401 2.4 63.8 0.5 HD23 A:LEU253 2.7 41.3 1.0 HA A:LEU253 2.9 28.3 1.0 H221 A:R6Q401 2.9 75.2 0.5 C22 A:R6Q401 3.0 62.6 0.5 HB3 A:GLN256 3.1 48.4 1.0 HB2 A:GLN256 3.2 48.4 1.0 C20 A:R6Q401 3.4 62.5 0.5 HG22 A:VAL297 3.4 37.1 1.0 O A:PRO252 3.4 30.1 1.0 H201 A:R6Q401 3.5 75.1 0.5 O A:HOH666 3.5 41.0 1.0 CB A:GLN256 3.6 40.3 1.0 CD2 A:LEU253 3.6 34.4 1.0 HG2 A:GLN256 3.6 73.3 1.0 CA A:LEU253 3.8 23.5 1.0 HD21 A:LEU253 3.8 41.3 1.0 C A:PRO252 3.9 28.3 1.0 HG A:LEU253 4.0 33.8 1.0 N A:LEU253 4.1 26.9 1.0 CG A:GLN256 4.1 61.0 1.0 HD22 A:LEU253 4.2 41.3 1.0 CG A:LEU253 4.2 28.1 1.0 C23 A:R6Q401 4.3 59.3 0.5 HB2 A:PRO252 4.3 34.9 1.0 CG2 A:VAL297 4.3 30.9 1.0 H A:GLN256 4.4 43.7 1.0 HA A:VAL297 4.5 29.8 1.0 HD11 A:ILE213 4.5 27.4 1.0 C19 A:R6Q401 4.5 64.0 0.5 CB A:LEU253 4.6 27.4 1.0 HG21 A:VAL297 4.6 37.1 1.0 HG13 A:VAL297 4.6 41.1 1.0 HD13 A:ILE213 4.6 27.4 1.0 HB3 A:PRO252 4.6 34.9 1.0 H A:LEU253 4.7 32.3 1.0 HG23 A:VAL297 4.8 37.1 1.0 HG3 A:GLN256 4.8 73.3 1.0 CB A:PRO252 4.8 29.0 1.0 C A:LEU253 4.8 29.2 1.0 C18 A:R6Q401 4.9 63.5 0.5 CA A:GLN256 4.9 34.2 1.0 H231 A:R6Q401 4.9 71.2 0.5 O A:LEU253 4.9 27.4 1.0 CA A:PRO252 4.9 32.4 1.0 HB3 A:LEU253 5.0 33.0 1.0

Fluorine binding site 2 out of 3 in the Structure of Sars-Cov-2 Main Protease Bound to RS102895


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Sars-Cov-2 Main Protease Bound to RS102895 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:61.0 occ:0.48 F26 A:R6Q401 0.0 61.0 0.5 C24 A:R6Q401 1.3 61.1 0.5 F25 A:R6Q401 2.1 54.8 0.5 F27 A:R6Q401 2.1 62.8 0.5 C21 A:R6Q401 2.3 63.8 0.5 HG22 A:VAL297 2.4 37.1 1.0 HA A:VAL297 2.5 29.8 1.0 H221 A:R6Q401 2.7 75.2 0.5 C22 A:R6Q401 2.9 62.6 0.5 HG13 A:VAL297 2.9 41.1 1.0 CG2 A:VAL297 3.2 30.9 1.0 HD23 A:LEU253 3.2 41.3 1.0 CA A:VAL297 3.3 24.8 1.0 C20 A:R6Q401 3.5 62.5 0.5 HD21 A:LEU253 3.5 41.3 1.0 CB A:VAL297 3.5 30.4 1.0 CG1 A:VAL297 3.6 34.2 1.0 H201 A:R6Q401 3.7 75.1 0.5 HG23 A:VAL297 3.8 37.1 1.0 HG21 A:VAL297 3.8 37.1 1.0 HB2 A:CYS300 3.8 33.1 1.0 CD2 A:LEU253 3.8 34.4 1.0 HG11 A:VAL297 3.9 41.1 1.0 HG A:SER301 4.1 66.2 1.0 O A:VAL297 4.1 26.1 1.0 C23 A:R6Q401 4.2 59.3 0.5 C A:VAL297 4.2 27.8 1.0 OG A:SER301 4.2 55.1 1.0 N A:VAL297 4.3 21.1 1.0 HG A:LEU253 4.3 33.8 1.0 HG12 A:VAL297 4.4 41.1 1.0 HB A:VAL297 4.5 36.5 1.0 HA A:LEU253 4.6 28.3 1.0 HD22 A:LEU253 4.6 41.3 1.0 HB3 A:CYS300 4.6 33.1 1.0 C19 A:R6Q401 4.6 64.0 0.5 HG12 A:VAL296 4.6 28.7 1.0 CB A:CYS300 4.6 27.6 1.0 CG A:LEU253 4.7 28.1 1.0 HD13 A:ILE213 4.7 27.4 1.0 H A:VAL297 4.7 25.4 1.0 O A:VAL296 4.8 24.8 1.0 H231 A:R6Q401 4.8 71.2 0.5 HG2 A:GLN256 4.9 73.3 1.0 C18 A:R6Q401 4.9 63.5 0.5 C A:VAL296 4.9 18.3 1.0

Fluorine binding site 3 out of 3 in the Structure of Sars-Cov-2 Main Protease Bound to RS102895


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Sars-Cov-2 Main Protease Bound to RS102895 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:62.8 occ:0.48 F27 A:R6Q401 0.0 62.8 0.5 C24 A:R6Q401 1.4 61.1 0.5 F25 A:R6Q401 2.1 54.8 0.5 F26 A:R6Q401 2.1 61.0 0.5 C21 A:R6Q401 2.4 63.8 0.5 H201 A:R6Q401 2.4 75.1 0.5 C20 A:R6Q401 2.7 62.5 0.5 HG22 A:VAL297 3.1 37.1 1.0 O A:HOH666 3.2 41.0 1.0 HG13 A:VAL297 3.2 41.1 1.0 C22 A:R6Q401 3.6 62.6 0.5 HG11 A:VAL297 3.7 41.1 1.0 CG1 A:VAL297 3.8 34.2 1.0 CG2 A:VAL297 3.9 30.9 1.0 H221 A:R6Q401 3.9 75.2 0.5 HG21 A:VAL297 4.0 37.1 1.0 HB3 A:PRO252 4.1 34.9 1.0 C19 A:R6Q401 4.1 64.0 0.5 HB2 A:PRO252 4.1 34.9 1.0 HA A:VAL297 4.2 29.8 1.0 HG A:SER301 4.3 66.2 1.0 HB2 A:GLN256 4.3 48.4 1.0 CB A:VAL297 4.4 30.4 1.0 HD23 A:LEU253 4.4 41.3 1.0 O A:PRO252 4.5 30.1 1.0 CB A:PRO252 4.5 29.0 1.0 H191 A:R6Q401 4.6 76.9 0.5 HG12 A:VAL297 4.7 41.1 1.0 OG A:SER301 4.7 55.1 1.0 HG23 A:VAL297 4.7 37.1 1.0 HA A:LEU253 4.7 28.3 1.0 C23 A:R6Q401 4.8 59.3 0.5 HG2 A:GLN256 4.8 73.3 1.0 C A:PRO252 4.8 28.3 1.0 CA A:VAL297 4.8 24.8 1.0 HB3 A:GLN256 4.9 48.4 1.0 C18 A:R6Q401 4.9 63.5 0.5 CB A:GLN256 5.0 40.3 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