Sodium in PDB 8aeb: Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide

All present enzymatic activity of Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide:
3.4.22.69;

The structure of Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide, PDB code: 8aeb was solved by X.Hanoulle, J.Charton, B.Deprez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.37 / 1.83
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.141, 53.472, 44.65, 90, 101.3, 90
R / Rfree (%)	18.4 / 23.4

The binding sites of Sodium atom in the Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide (pdb code 8aeb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide, PDB code: 8aeb:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:33.3 occ:1.00 HD1 A:HIS164 2.1 20.1 0.0 H A:HIS41 2.4 26.1 1.0 HD1 A:HIS41 2.4 34.4 0.0 HB3 A:HIS41 2.8 27.8 1.0 OD2 A:ASP187 2.8 29.8 1.0 ND1 A:HIS164 2.9 19.5 1.0 HG2 A:ARG40 3.0 26.0 1.0 H A:ARG40 3.0 26.4 1.0 ND1 A:HIS41 3.0 33.9 1.0 N A:HIS41 3.1 26.0 1.0 HB3 A:PRO39 3.1 21.7 1.0 HE1 A:HIS164 3.2 20.7 1.0 HB2 A:ASP187 3.2 27.0 1.0 HG3 A:ARG40 3.3 26.0 1.0 N A:ARG40 3.3 26.2 1.0 CE1 A:HIS164 3.4 21.5 1.0 CB A:HIS41 3.4 28.2 1.0 HB3 A:ASP187 3.4 27.0 1.0 CG A:HIS41 3.5 30.9 1.0 CG A:ARG40 3.6 25.4 1.0 HB3 A:CYS85 3.6 24.0 1.0 O A:CYS85 3.6 27.7 1.0 CB A:ASP187 3.6 25.7 1.0 CG A:ASP187 3.7 27.8 1.0 CB A:PRO39 3.8 23.1 1.0 HA A:PRO39 3.8 23.4 1.0 CA A:HIS41 3.8 24.2 1.0 HB2 A:PRO39 3.8 21.7 1.0 C A:PRO39 3.8 26.2 1.0 C A:ARG40 3.9 28.2 1.0 CA A:PRO39 4.0 23.2 1.0 CA A:ARG40 4.0 27.0 1.0 HE A:ARG40 4.1 26.2 1.0 CG A:HIS164 4.1 20.2 1.0 CE1 A:HIS41 4.1 28.6 1.0 HB3 A:HIS164 4.1 19.6 1.0 HA A:HIS41 4.3 25.7 1.0 HB2 A:HIS41 4.3 27.8 1.0 HH A:TYR54 4.3 30.7 0.0 CB A:ARG40 4.4 28.6 1.0 HE1 A:HIS41 4.4 30.2 1.0 OH A:TYR54 4.5 31.2 1.0 CB A:CYS85 4.6 22.5 1.0 NE2 A:HIS164 4.6 20.1 1.0 CB A:HIS164 4.7 18.7 1.0 C A:CYS85 4.7 27.9 1.0 O A:PRO39 4.7 23.1 1.0 CD2 A:HIS41 4.7 28.6 1.0 NE A:ARG40 4.7 27.4 1.0 HE1 A:PHE181 4.8 24.2 1.0 CD A:ARG40 4.8 24.8 1.0 HB3 A:ARG40 4.8 27.4 1.0 OD1 A:ASP187 4.9 31.8 1.0 HE1 A:TYR54 4.9 30.1 1.0 CZ A:TYR54 4.9 32.1 1.0 HA A:ARG40 5.0 27.3 1.0 H A:VAL42 5.0 26.8 1.0 HB2 A:CYS85 5.0 24.0 1.0 CD2 A:HIS164 5.0 19.5 1.0 NE2 A:HIS41 5.0 30.7 1.0

Sodium binding site 2 out of 4 in the Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:36.4 occ:1.00 H A:GLY174 2.0 22.2 1.0 HA A:ALA173 2.5 23.7 1.0 HB2 A:TYR182 2.7 23.6 1.0 O A:PHE134 2.8 28.5 1.0 N A:GLY174 2.9 22.2 1.0 O A:TYR182 2.9 29.7 1.0 O A:GLY174 3.1 19.1 1.0 HD2 A:PHE185 3.2 24.5 1.0 CA A:ALA173 3.2 22.9 1.0 HB1 A:ALA173 3.3 25.0 1.0 HB2 A:ALA173 3.3 25.0 1.0 CB A:ALA173 3.5 26.0 1.0 HD2 A:PHE181 3.5 22.7 1.0 C A:ALA173 3.5 24.9 1.0 H A:TYR182 3.6 23.7 1.0 CB A:TYR182 3.6 24.1 1.0 C A:TYR182 3.7 25.2 1.0 HE1 A:TYR161 3.8 21.4 1.0 HA A:THR135 3.8 24.4 1.0 CD2 A:PHE185 3.9 23.0 1.0 HB3 A:TYR182 3.9 23.6 1.0 C A:GLY174 3.9 19.3 1.0 HE2 A:PHE185 4.0 25.6 1.0 CA A:TYR182 4.0 21.8 1.0 CA A:GLY174 4.0 19.4 1.0 HB3 A:PHE134 4.0 24.1 1.0 N A:TYR182 4.0 23.1 1.0 C A:PHE134 4.1 24.6 1.0 HD2 A:TYR182 4.2 21.6 1.0 CE2 A:PHE185 4.3 25.8 1.0 HH A:TYR161 4.4 20.0 0.0 CD2 A:PHE181 4.4 22.1 1.0 HE3 A:MET130 4.4 33.5 1.0 HB3 A:ALA173 4.4 25.0 1.0 O A:HIS172 4.5 22.4 1.0 HA3 A:GLY174 4.5 20.0 1.0 N A:ALA173 4.5 22.2 1.0 HB2 A:PHE185 4.6 27.8 1.0 HA2 A:GLY174 4.7 20.0 1.0 CG A:TYR182 4.7 24.1 1.0 HE2 A:PHE181 4.7 22.4 1.0 CA A:THR135 4.7 23.9 1.0 CE1 A:TYR161 4.7 21.9 1.0 HB3 A:PHE181 4.7 24.3 1.0 O A:ALA173 4.8 22.8 1.0 CD2 A:TYR182 4.8 20.9 1.0 HA3 A:GLY183 4.8 23.4 1.0 N A:THR135 4.8 26.1 1.0 CB A:PHE134 4.9 23.8 1.0 N A:GLY183 4.9 23.2 1.0 HG21 A:ILE136 4.9 29.2 1.0 CG A:PHE185 4.9 25.6 1.0 HA A:TYR182 4.9 23.1 1.0 C A:HIS172 4.9 22.9 1.0 HG23 A:THR135 5.0 22.0 1.0 CE2 A:PHE181 5.0 22.5 1.0

Sodium binding site 3 out of 4 in the Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:33.0 occ:1.00 H A:LYS137 2.1 26.0 1.0 O A:ALA129 2.6 26.1 1.0 H A:ALA129 2.8 27.2 1.0 OE2 A:GLU290 2.8 35.1 1.0 HB2 A:CYS128 2.9 40.8 1.0 N A:LYS137 3.0 25.9 1.0 HA A:ILE136 3.0 26.0 1.0 HD3 A:ARG131 3.0 30.0 1.0 HB2 A:LYS137 3.1 32.0 1.0 HB A:ILE136 3.3 29.4 1.0 OE1 A:GLU290 3.4 31.3 1.0 CD A:GLU290 3.5 40.0 1.0 HD2 A:ARG131 3.5 29.9 1.0 HG3 A:LYS137 3.5 39.5 1.0 N A:ALA129 3.5 26.3 1.0 CA A:ILE136 3.7 24.9 1.0 CD A:ARG131 3.7 30.1 1.0 C A:ALA129 3.7 23.7 1.0 HG2 A:ARG131 3.7 28.2 1.0 CB A:LYS137 3.7 30.4 1.0 C A:ILE136 3.8 23.4 1.0 CA A:LYS137 3.9 29.1 1.0 CB A:CYS128 3.9 43.6 1.0 HB3 A:ALA129 3.9 25.4 1.0 CB A:ILE136 4.0 32.9 1.0 HH11 A:ARG131 4.1 21.9 0.0 CG A:LYS137 4.1 39.5 1.0 CA A:ALA129 4.1 24.7 1.0 O A:LYS137 4.1 31.6 1.0 HD2 A:LYS137 4.1 49.2 1.0 HG A:CYS128 4.2 42.9 0.0 CG A:ARG131 4.2 27.3 1.0 C A:LYS137 4.3 29.2 1.0 SG A:CYS128 4.4 43.0 1.0 HB3 A:CYS128 4.4 40.8 1.0 C A:CYS128 4.5 31.6 1.0 CB A:ALA129 4.5 25.6 1.0 H A:ARG131 4.6 27.8 1.0 HB3 A:LYS137 4.6 32.0 1.0 CA A:CYS128 4.6 33.5 1.0 HG22 A:ILE136 4.6 29.1 1.0 HG3 A:ARG131 4.7 28.2 1.0 HA A:CYS128 4.7 34.0 1.0 CD A:LYS137 4.7 51.5 1.0 O A:THR135 4.7 24.0 1.0 HA A:LYS137 4.7 28.7 1.0 HG13 A:ILE136 4.9 30.5 1.0 CG2 A:ILE136 4.9 27.7 1.0 N A:MET130 4.9 26.3 1.0 CG A:GLU290 4.9 34.1 1.0 NH1 A:ARG131 4.9 22.1 1.0 N A:ILE136 4.9 25.2 1.0 HG2 A:LYS137 4.9 39.6 1.0 NE A:ARG131 4.9 32.6 1.0 HA A:MET130 5.0 27.4 1.0 HG2 A:GLU290 5.0 35.0 1.0 O A:ILE136 5.0 19.8 1.0 N A:ARG131 5.0 28.4 1.0

Sodium binding site 4 out of 4 in the Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Sars-Cov-2 Main Protease Complexed with N-(Pyridin-3-Ylmethyl) Thioformamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:69.0 occ:1.00 HE1 A:MET49 2.4 63.8 1.0 HE3 A:MET49 2.5 63.8 1.0 SD A:MET165 2.5 20.4 0.2 HG3 A:MET165 2.8 23.2 0.2 CE A:MET49 2.9 61.9 1.0 CG A:MET165 3.1 24.5 0.2 HE2 A:MET165 3.3 53.4 0.8 HG2 A:MET165 3.4 23.2 0.2 CE A:MET165 3.4 21.6 0.2 HE2 A:MET165 3.4 21.3 0.2 HE3 A:MET165 3.5 21.4 0.2 HE2 A:MET49 3.5 63.7 1.0 HB3 A:MET165 3.5 34.0 0.8 HD1 A:HIS41 3.6 34.4 0.0 ND1 A:HIS41 3.6 33.9 1.0 CE1 A:HIS41 3.9 28.6 1.0 HB2 A:ASP187 4.1 27.0 1.0 HA A:ASP187 4.1 27.3 1.0 O A:HIS164 4.1 27.0 1.0 CG A:HIS41 4.1 30.9 1.0 HE1 A:HIS41 4.1 30.2 1.0 SD A:MET49 4.1 68.2 1.0 HB2 A:MET165 4.2 34.0 0.8 CE A:MET165 4.2 52.4 0.8 O A:HOH597 4.3 26.0 1.0 HE1 A:MET165 4.3 21.3 0.2 CB A:MET165 4.3 34.4 0.8 HB2 A:HIS41 4.4 27.8 1.0 CB A:MET165 4.4 23.2 0.2 HB3 A:HIS41 4.5 27.8 1.0 NE2 A:HIS41 4.5 30.7 1.0 HA A:MET165 4.5 23.6 0.2 C A:ASP187 4.6 25.1 1.0 CD2 A:HIS41 4.6 28.6 1.0 HA A:MET165 4.6 27.2 0.8 HB2 A:MET165 4.6 23.5 0.2 HE3 A:MET165 4.6 53.4 0.8 CB A:HIS41 4.6 28.2 1.0 CA A:ASP187 4.6 29.2 1.0 HA A:ARG188 4.6 40.0 1.0 H3 A:35J402 4.7 32.1 1.0 N A:ARG188 4.7 32.2 1.0 HB3 A:HIS164 4.7 19.6 1.0 HE1 A:MET165 4.7 53.4 0.8 CB A:ASP187 4.7 25.7 1.0 O A:ASP187 4.8 29.6 1.0 H4 A:35J402 4.9 32.1 1.0 HB3 A:ASP187 4.9 27.0 1.0 HH A:TYR54 4.9 30.7 0.0 H A:ARG188 5.0 32.1 1.0 C A:ARG188 5.0 41.2 1.0 C A:HIS164 5.0 23.6 1.0 HB2 A:GLN189 5.0 45.4 1.0 CA A:MET165 5.0 27.4 0.8

L.Brier, H.Hassan, X.Hanoulle, V.Landry, D.Moschidi, L.Desmarets, Y.Rouille, J.Dumont, A.Herledan, S.Warenghem, C.Piveteau, P.Carre, S.Ikherbane, F.X.Cantrelle, E.Dupre, J.Dubuisson, S.Belouzard, F.Leroux, B.Deprez, J.Charton. Novel Dithiocarbamates Selectively Inhibit 3CL Protease of Sars-Cov-2 and Other Coronaviruses. Eur.J.Med.Chem. V. 250 15186 2023.
ISSN: ISSN 0223-5234
PubMed: 36796300
DOI: 10.1016/J.EJMECH.2023.115186