Chlorine in PDB 7avd: Structure of Sars-Cov-2 Main Protease Bound to SEN1269 Ligand

All present enzymatic activity of Structure of Sars-Cov-2 Main Protease Bound to SEN1269 Ligand:
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 SEN1269 Ligand, PDB code: 7avd was solved by F.Koua, G.Sebastian, P.Reinke, D.Oberthuer, O.Yefanov, L.Gelisio, H.Ginn, J.Lieske, W.Ewert, M.Domaracky, W.Brehm, A.Rahmani Mashour, T.A.White, J.Knoska, G.Pena Esperanza, 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, I.Dunkel, T.J.Lane, 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)	48.60 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.552, 53.857, 114.731, 90.00, 100.61, 90.00
R / Rfree (%)	19.4 / 23.9

The binding sites of Chlorine atom in the Structure of Sars-Cov-2 Main Protease Bound to SEN1269 Ligand (pdb code 7avd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Structure of Sars-Cov-2 Main Protease Bound to SEN1269 Ligand, PDB code: 7avd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Structure of Sars-Cov-2 Main Protease Bound to SEN1269 Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Sars-Cov-2 Main Protease Bound to SEN1269 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:30.0 occ:1.00 HE21 A:GLN127 2.1 32.6 1.0 HG1 A:THR111 2.4 23.5 1.0 OD1 A:ASN151 2.6 23.7 1.0 HE2 A:PHE8 2.7 35.1 1.0 OG1 A:THR111 2.8 19.5 1.0 NE2 A:GLN127 2.9 27.1 1.0 HH21 A:ARG298 3.0 43.7 1.0 HH22 A:ARG298 3.2 43.7 1.0 HE22 A:GLN127 3.3 32.6 1.0 O A:THR111 3.3 18.6 1.0 HA A:PHE112 3.3 21.9 1.0 NH2 A:ARG298 3.4 36.4 1.0 CE2 A:PHE8 3.4 29.2 1.0 OD1 A:ASP295 3.4 25.9 1.0 HZ A:PHE8 3.5 33.4 1.0 C A:THR111 3.5 18.2 1.0 HB A:THR111 3.6 24.0 1.0 CB A:THR111 3.7 20.0 1.0 CG A:ASN151 3.8 20.5 1.0 CZ A:PHE8 3.8 27.8 1.0 N A:PHE112 3.9 15.2 1.0 CD A:GLN127 4.0 22.6 1.0 O A:HOH591 4.0 29.7 1.0 O A:HOH620 4.0 22.1 1.0 CA A:PHE112 4.1 18.2 1.0 HD21 A:ASN151 4.1 26.6 1.0 OE1 A:GLN127 4.2 27.2 1.0 CA A:THR111 4.2 15.9 1.0 CG A:ASP295 4.2 24.5 1.0 OD2 A:ASP295 4.2 18.4 1.0 H A:THR111 4.3 25.2 0.5 H A:THR111 4.3 25.2 0.5 ND2 A:ASN151 4.4 22.1 1.0 H A:PHE112 4.4 18.3 1.0 CD2 A:PHE8 4.5 24.2 1.0 CZ A:ARG298 4.7 50.4 1.0 HD2 A:PHE8 4.7 29.1 1.0 N A:THR111 4.8 21.0 1.0 C A:PHE112 4.8 16.5 1.0 HB3 A:ASN151 4.9 22.9 1.0 HA A:ASN151 4.9 25.7 1.0 CB A:ASN151 5.0 19.1 1.0

Chlorine binding site 2 out of 2 in the Structure of Sars-Cov-2 Main Protease Bound to SEN1269 Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Sars-Cov-2 Main Protease Bound to SEN1269 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:30.0 occ:1.00 HE22 B:GLN127 2.2 29.5 1.0 OD1 B:ASN151 2.8 23.9 1.0 OG1 B:THR111 2.8 15.5 1.0 NE2 B:GLN127 3.0 24.6 1.0 HE2 B:PHE8 3.0 22.9 1.0 HA B:PHE112 3.2 21.3 1.0 HG1 B:THR111 3.2 18.6 1.0 HE21 B:GLN127 3.2 29.5 1.0 O B:THR111 3.5 16.2 1.0 HB B:THR111 3.5 22.1 1.0 OD1 B:ASP295 3.5 23.4 1.0 C B:THR111 3.5 14.2 1.0 CB B:THR111 3.7 18.4 1.0 N B:PHE112 3.7 15.9 1.0 CE2 B:PHE8 3.8 19.1 1.0 O B:HOH525 3.8 23.5 1.0 CA B:PHE112 3.9 17.7 1.0 CG B:ASN151 3.9 16.6 1.0 HH21 B:ARG298 4.0 49.0 1.0 CD B:GLN127 4.1 26.2 1.0 HD21 B:ASN151 4.1 23.2 1.0 CG B:ASP295 4.2 20.7 1.0 OD2 B:ASP295 4.2 15.5 1.0 H B:PHE112 4.2 19.1 1.0 CA B:THR111 4.2 17.0 1.0 O B:HOH607 4.3 22.0 1.0 OE1 B:GLN127 4.3 22.9 1.0 HD2 B:PHE8 4.4 27.1 1.0 HZ B:PHE8 4.4 21.3 1.0 ND2 B:ASN151 4.5 19.3 1.0 C B:PHE112 4.5 16.6 1.0 HG B:SER113 4.5 22.6 1.0 NH2 B:ARG298 4.5 40.8 1.0 CZ B:PHE8 4.5 17.7 1.0 CD2 B:PHE8 4.5 22.6 1.0 H B:THR111 4.6 23.0 0.5 H B:THR111 4.6 23.0 0.5 HH22 B:ARG298 4.6 49.0 1.0 H B:SER113 4.8 18.4 1.0 N B:SER113 4.9 15.3 1.0 N B:THR111 4.9 19.1 1.0 O B:HOH708 4.9 22.6 1.0 HA B:THR111 5.0 20.5 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