Chlorine in PDB 6fcj: Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations

The structure of Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations, PDB code: 6fcj was solved by D.Musil, M.Lehmann, H.-M.Eggenweiler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.15 / 2.49
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	66.015, 89.814, 98.470, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.4

The binding sites of Chlorine atom in the Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations (pdb code 6fcj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations, PDB code: 6fcj:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:91.7 occ:0.50 CL1 A:D4W301 0.0 91.7 0.5 C10 A:D4W301 0.5 52.9 0.5 C14 A:D4W301 1.4 51.7 0.5 C11 A:D4W301 1.7 92.7 0.5 C5 A:D4W301 1.9 54.1 0.5 C17 A:D4W301 2.6 53.2 0.5 C15 A:D4W301 2.7 93.2 0.5 C5 A:D4W301 2.7 93.1 0.5 N2 A:D4W301 2.8 52.4 0.5 O A:ASN51 2.8 58.8 1.0 C11 A:D4W301 2.9 55.3 0.5 N2 A:D4W301 3.0 93.8 0.5 C15 A:D4W301 3.2 55.1 0.5 CB A:ASP54 3.5 65.7 1.0 C1 A:D4W301 3.6 93.4 0.5 N A:ALA55 3.6 63.7 1.0 C1 A:D4W301 3.7 47.8 0.5 C A:ASN51 3.7 56.0 1.0 N6 A:D4W301 3.7 94.1 0.5 N6 A:D4W301 3.8 52.4 0.5 CA A:ASN51 3.8 52.1 1.0 C3 A:D4W301 3.9 42.1 0.5 C3 A:D4W301 4.0 91.9 0.5 C17 A:D4W301 4.0 93.5 0.5 CB A:ASN51 4.0 48.8 1.0 C10 A:D4W301 4.0 93.0 0.5 CB A:ALA55 4.1 59.5 1.0 C A:ASP54 4.1 70.2 1.0 CA A:ALA55 4.2 62.4 1.0 C8 A:D4W301 4.2 91.0 0.5 O19 A:D4W301 4.3 90.1 0.5 C7 A:D4W301 4.3 41.5 0.5 CA A:ASP54 4.3 65.2 1.0 C8 A:D4W301 4.4 38.6 0.5 C4 A:D4W301 4.4 93.8 0.5 C9 A:D4W301 4.4 94.1 0.5 CG A:ASN51 4.5 64.2 1.0 C14 A:D4W301 4.5 93.1 0.5 CL1 A:D4W301 4.6 56.3 0.5 CG A:ASP54 4.6 80.7 1.0 OD2 A:ASP54 4.6 88.1 1.0 C7 A:D4W301 4.7 91.6 0.5 O19 A:D4W301 4.7 35.5 0.5 C4 A:D4W301 4.7 47.2 0.5 C9 A:D4W301 4.8 49.7 0.5 OD1 A:ASN51 4.8 53.3 1.0 N A:ASP54 4.8 63.6 1.0 NZ A:LYS58 4.9 0.7 1.0 N A:SER52 4.9 49.8 1.0 O A:ASP54 4.9 73.3 1.0

Chlorine binding site 2 out of 2 in the Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:56.3 occ:0.50 CL1 A:D4W301 0.0 56.3 0.5 C10 A:D4W301 1.5 93.0 0.5 C11 A:D4W301 1.7 55.3 0.5 C5 A:D4W301 2.0 93.1 0.5 N2 A:D4W301 2.3 93.8 0.5 C14 A:D4W301 2.6 93.1 0.5 N6 A:D4W301 2.6 94.1 0.5 C15 A:D4W301 2.7 55.1 0.5 C5 A:D4W301 2.7 54.1 0.5 O A:LEU107 2.9 0.3 1.0 N2 A:D4W301 3.0 52.4 0.5 C11 A:D4W301 3.2 92.7 0.5 C1 A:D4W301 3.4 93.4 0.5 N6 A:D4W301 3.4 52.4 0.5 C17 A:D4W301 3.6 93.5 0.5 C A:LEU107 3.6 0.4 1.0 C1 A:D4W301 3.7 47.8 0.5 C9 A:D4W301 3.7 94.1 0.5 SD A:MET98 3.8 68.7 1.0 C7 A:D4W301 3.9 41.5 0.5 C15 A:D4W301 3.9 93.2 0.5 CA A:GLY108 3.9 0.5 1.0 C17 A:D4W301 4.0 53.2 0.5 C10 A:D4W301 4.0 52.9 0.5 O A:GLY108 4.0 0.2 1.0 N A:GLY108 4.1 0.5 1.0 C A:GLY108 4.1 0.1 1.0 C4 A:D4W301 4.1 93.8 0.5 C7 A:D4W301 4.1 91.6 0.5 C9 A:D4W301 4.2 49.7 0.5 C3 A:D4W301 4.3 42.1 0.5 C3 A:D4W301 4.3 91.9 0.5 C4 A:D4W301 4.3 47.2 0.5 CG A:MET98 4.5 67.8 1.0 C14 A:D4W301 4.5 51.7 0.5 CL1 A:D4W301 4.6 91.7 0.5 CE A:MET98 4.7 62.7 1.0 CA A:LEU107 4.8 91.7 1.0 CG2 A:THR109 4.8 0.8 1.0 CB A:LEU107 4.9 88.3 1.0 N A:THR109 4.9 0.2 1.0

S.Wolf, M.Amaral, M.Lowinski, F.Vallee, D.Musil, J.Guldenhaupt, M.K.Dreyer, J.Bomke, M.Frech, J.Schlitter, K.Gerwert. Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations Arxiv 2019.
ISSN: ISSN 2331-8422