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Chlorine in PDB 5dg6: 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor

Enzymatic activity of 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor

All present enzymatic activity of 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor:
3.4.22.66;

Protein crystallography data

The structure of 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor, PDB code: 5dg6 was solved by S.Lovell, K.P.Battaile, N.Mehzabeen, V.C.Damalanka, Y.Kim, K.R.Alliston, P.M.Weerawarna, A.C.G.Kankanamalage, G.H.Lushington, 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) 35.90 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.686, 67.113, 127.471, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 27.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor (pdb code 5dg6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor, PDB code: 5dg6:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5dg6

Go back to Chlorine Binding Sites List in 5dg6
Chlorine binding site 1 out of 3 in the 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:28.9
occ:1.00
 NE A:ARG8 3.2 26.3 1.0
NH2 A:ARG8 3.3 29.9 1.0
O A:HOH309 3.4 34.0 1.0
CZ A:ARG8 3.7 27.1 1.0
N A:LEU5 3.8 22.1 1.0
CG2 A:THR4 3.8 26.4 1.0
CB A:THR4 3.9 23.4 1.0
CA A:LEU5 3.9 23.9 1.0
C A:THR4 3.9 23.6 1.0
CB A:LEU5 4.2 26.1 1.0
O A:THR4 4.2 21.3 1.0
CD A:ARG8 4.3 24.3 1.0
CD1 A:LEU5 4.5 24.5 1.0
CA A:THR4 4.6 22.4 1.0
OG1 A:THR69 4.8 51.8 1.0
CG A:LEU5 4.9 28.8 1.0

Chlorine binding site 2 out of 3 in 5dg6

Go back to Chlorine Binding Sites List in 5dg6
Chlorine binding site 2 out of 3 in the 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:18.3
occ:1.00
 CL B:CL201 2.9 18.0 1.0
O B:HOH319 3.0 26.2 1.0
NZ A:LYS88 3.2 15.8 1.0
CA A:SER7 3.5 15.5 1.0
N A:SER7 3.6 21.7 1.0
C A:TRP6 3.8 15.5 1.0
CE A:LYS88 3.8 20.8 1.0
O A:TRP6 3.9 14.3 1.0
CB A:SER7 3.9 25.0 1.0
CD2 B:LEU94 4.0 21.6 1.0
CB A:TRP6 4.1 21.5 1.0
NZ B:LYS88 4.2 21.9 1.0
CE B:LYS88 4.3 15.1 1.0
CD1 B:LEU94 4.5 21.8 1.0
O A:PRO3 4.5 23.8 1.0
CG B:LEU94 4.6 22.5 1.0
CA A:TRP6 4.6 18.3 1.0
C A:SER7 4.8 15.5 1.0
O B:HOH323 4.9 30.5 1.0
O A:HOH320 4.9 23.4 1.0
O A:HOH321 4.9 26.7 1.0

Chlorine binding site 3 out of 3 in 5dg6

Go back to Chlorine Binding Sites List in 5dg6
Chlorine binding site 3 out of 3 in the 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 2.35A Resolution Structure of Norovirus 3CL Protease in Complex An Oxadiazole-Based, Cell Permeable Macrocyclic (21-Mer) Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:18.0
occ:1.00
 O A:HOH320 2.9 23.4 1.0
CL A:CL202 2.9 18.3 1.0
NZ B:LYS88 2.9 21.9 1.0
CA B:SER7 3.4 17.9 1.0
N B:SER7 3.5 18.3 1.0
CE B:LYS88 3.7 15.1 1.0
C B:TRP6 3.7 15.1 1.0
O B:TRP6 3.7 14.7 1.0
CB B:SER7 3.9 18.9 1.0
CD2 A:LEU94 4.1 21.6 1.0
CB B:TRP6 4.1 16.9 1.0
CE A:LYS88 4.2 20.8 1.0
NZ A:LYS88 4.4 15.8 1.0
CA B:TRP6 4.6 19.6 1.0
O B:PRO3 4.6 19.7 1.0
C B:SER7 4.6 21.6 1.0
CD1 A:LEU94 4.7 20.8 1.0
O A:HOH331 4.7 28.0 1.0
CG A:LEU94 4.7 25.2 1.0
O B:HOH319 4.8 26.2 1.0
O A:GLY92 4.9 26.8 1.0

Reference:

V.C.Damalanka, Y.Kim, K.R.Alliston, P.M.Weerawarna, A.C.Galasiti Kankanamalage, G.H.Lushington, N.Mehzabeen, K.P.Battaile, S.Lovell, K.O.Chang, W.C.Groutas. Oxadiazole-Based Cell Permeable Macrocyclic Transition State Inhibitors of Norovirus 3CL Protease. J.Med.Chem. V. 59 1899 2016.
ISSN: ISSN 0022-2623
PubMed: 26823007
DOI: 10.1021/ACS.JMEDCHEM.5B01464
Page generated: Fri Jul 26 06:42:23 2024

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