Chlorine in PDB 6w5h: 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D

All present enzymatic activity of 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D:
3.4.22.66;

The structure of 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D, PDB code: 6w5h was solved by S.Lovell, M.M.Kashipathy, K.P.Battaile, A.D.Rathnayake, Y.Kim, K.O.Chang, W.C.Groutas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.43 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.943, 38.028, 115.241, 92.31, 98.31, 96.64
R / Rfree (%)	18.3 / 22.4

The binding sites of Chlorine atom in the 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D (pdb code 6w5h). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D, PDB code: 6w5h:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:63.8 occ:1.00 CL3 A:TKP201 0.0 63.8 1.0 C32 A:TKP201 1.8 35.2 1.0 C31 A:TKP201 2.7 39.2 1.0 C34 A:TKP201 2.8 38.9 1.0 CG2 A:VAL168 3.4 36.1 1.0 C A:ALA160 3.9 33.7 1.0 N A:THR161 4.0 33.5 1.0 C30 A:TKP201 4.0 37.3 1.0 C35 A:TKP201 4.1 42.8 1.0 CG2 A:THR161 4.1 43.4 1.0 O A:ALA160 4.1 33.0 1.0 CB A:ALA159 4.2 29.1 1.0 CD1 A:ILE109 4.3 36.3 1.0 N A:ALA160 4.4 27.5 1.0 CA A:THR161 4.4 37.0 1.0 CA A:ALA160 4.4 29.9 1.0 CB A:VAL168 4.5 29.4 1.0 C36 A:TKP201 4.5 40.3 1.0 C A:ALA159 4.7 29.6 1.0 CB A:THR161 4.9 44.1 1.0

Chlorine binding site 2 out of 4 in the 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:70.6 occ:1.00 CL3 B:TKP201 0.0 70.6 1.0 C32 B:TKP201 1.8 56.3 1.0 C31 B:TKP201 2.7 52.8 1.0 C34 B:TKP201 2.8 55.3 1.0 CG2 B:VAL168 3.4 45.3 1.0 CG2 B:THR161 3.8 57.5 1.0 N B:THR161 3.8 47.4 1.0 C B:ALA160 3.9 48.0 1.0 C30 B:TKP201 4.0 52.7 1.0 C35 B:TKP201 4.1 50.3 1.0 O B:ALA160 4.2 46.7 1.0 CA B:ALA160 4.3 41.6 1.0 CA B:THR161 4.3 56.5 1.0 N B:ALA160 4.3 37.6 1.0 CB B:ALA159 4.4 36.0 1.0 C36 B:TKP201 4.5 52.8 1.0 CD1 B:ILE109 4.6 41.7 1.0 CB B:VAL168 4.6 36.4 1.0 C B:ALA159 4.7 35.4 1.0 CB B:THR161 4.7 53.0 1.0 O B:THR166 5.0 46.9 1.0

Chlorine binding site 3 out of 4 in the 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:67.7 occ:1.00 CL3 C:TKP201 0.0 67.7 1.0 C32 C:TKP201 1.8 50.3 1.0 C31 C:TKP201 2.7 48.0 1.0 C34 C:TKP201 2.8 52.7 1.0 CG2 C:VAL168 3.6 35.8 1.0 CG2 C:THR161 3.7 53.4 1.0 N C:THR161 3.8 44.8 1.0 C C:ALA160 3.9 44.3 1.0 C30 C:TKP201 4.0 51.5 1.0 C35 C:TKP201 4.0 55.5 1.0 CA C:THR161 4.2 51.0 1.0 O C:ALA160 4.2 40.4 1.0 CB C:ALA159 4.3 37.2 1.0 N C:ALA160 4.3 35.8 1.0 CA C:ALA160 4.4 35.4 1.0 C36 C:TKP201 4.5 51.5 1.0 CD1 C:ILE109 4.6 42.9 1.0 CB C:THR161 4.6 50.1 1.0 CB C:VAL168 4.6 36.8 1.0 C C:ALA159 4.7 33.0 1.0

Chlorine binding site 4 out of 4 in the 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 1.85 A Resolution Structure of Norovirus 3CL Protease in Complex with Inhibitor 5D within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl201 b:71.6 occ:1.00 CL3 D:TKP201 0.0 71.6 1.0 C32 D:TKP201 1.8 42.7 1.0 C31 D:TKP201 2.7 41.0 1.0 C34 D:TKP201 2.8 39.9 1.0 CG2 D:VAL168 3.4 41.9 1.0 CG2 D:THR161 3.9 42.0 1.0 C30 D:TKP201 4.0 36.6 1.0 C35 D:TKP201 4.1 37.4 1.0 N D:THR161 4.1 35.2 1.0 C D:ALA160 4.1 37.6 1.0 O D:ALA160 4.3 33.3 1.0 CA D:THR161 4.4 38.8 1.0 CB D:ALA159 4.5 32.7 1.0 CB D:VAL168 4.5 32.3 1.0 C36 D:TKP201 4.5 39.6 1.0 CD1 D:ILE109 4.6 38.3 1.0 N D:ALA160 4.6 31.6 1.0 CA D:ALA160 4.6 34.2 1.0 CB D:THR161 4.8 43.1 1.0 C D:ALA159 4.9 34.7 1.0

A.D.Rathnayake, Y.Kim, C.S.Dampalla, H.N.Nguyen, A.M.Jesri, M.M.Kashipathy, G.H.Lushington, K.P.Battaile, S.Lovell, K.O.Chang, W.C.Groutas. Structure-Guided Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease. J.Med.Chem. V. 63 11945 2020.
ISSN: ISSN 0022-2623
PubMed: 32945669
DOI: 10.1021/ACS.JMEDCHEM.0C01252