Chlorine in PDB 6dmi: A Multiconformer Ligand Model of 5T5 Bound to Bace-1

All present enzymatic activity of A Multiconformer Ligand Model of 5T5 Bound to Bace-1:
3.4.23.46;

The structure of A Multiconformer Ligand Model of 5T5 Bound to Bace-1, PDB code: 6dmi was solved by B.M.Hudson, G.Van Zundert, D.Keedy, R.Fonseca, A.Heliou, P.Suresh, K.Borrelli, T.Day, J.S.Fraser, H.Van Den Bedem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.70 / 1.90
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.320, 102.320, 169.820, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.6

The structure of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Sodium	(Na)	2 atoms

The binding sites of Chlorine atom in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1 (pdb code 6dmi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1, PDB code: 6dmi:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:25.0 occ:0.32 CL A:5T5504 0.0 25.0 0.3 CL A:5T5504 0.4 25.3 0.3 CL A:5T5504 0.8 26.6 0.3 C22 A:5T5504 1.3 26.0 0.3 C22 A:5T5504 1.4 25.6 0.3 C22 A:5T5504 1.8 25.4 0.3 C14 A:5T5504 2.1 25.2 0.3 C14 A:5T5504 2.4 25.4 0.3 C28 A:5T5504 2.5 27.1 0.3 C28 A:5T5504 2.5 27.1 0.3 C28 A:5T5504 2.7 26.7 0.3 C14 A:5T5504 2.8 26.0 0.3 C A:GLY291 3.3 24.1 1.0 O A:HOH687 3.3 25.8 0.6 O A:GLY291 3.3 22.2 1.0 C8 A:5T5504 3.4 28.2 0.3 CA A:GLY74 3.5 28.3 1.0 CA A:GLY291 3.6 20.5 1.0 C8 A:5T5504 3.6 28.1 0.3 O A:HOH670 3.7 31.8 1.0 N13 A:5T5504 3.7 27.9 0.3 N A:THR292 3.7 21.3 1.0 N13 A:5T5504 3.7 27.4 0.3 N A:GLY74 3.7 24.5 1.0 O A:SER290 3.8 15.5 1.0 N13 A:5T5504 3.9 26.1 0.3 C A:THR292 4.0 26.6 1.0 C20 A:5T5504 4.0 25.2 0.3 CA A:THR292 4.0 27.4 1.0 OG1 A:THR293 4.0 26.7 1.0 N A:THR293 4.1 22.4 1.0 C8 A:5T5504 4.1 27.5 0.3 C20 A:5T5504 4.2 25.2 0.3 O A:HOH657 4.4 23.0 1.0 O A:THR292 4.4 24.0 1.0 C A:GLN73 4.4 31.5 1.0 O A:HOH731 4.5 28.8 1.0 C20 A:5T5504 4.5 25.9 0.3 O A:HOH819 4.5 26.3 1.0 N A:GLY291 4.6 18.2 1.0 C A:SER290 4.6 16.4 1.0 C6 A:5T5504 4.6 26.8 0.3 CA A:THR293 4.7 20.8 1.0 CD1 A:LEU91 4.7 27.7 1.0 C2 A:5T5504 4.8 25.6 0.3 O A:GLN73 4.9 27.0 1.0 C6 A:5T5504 4.9 26.8 0.3 C A:GLY74 4.9 24.2 1.0 CB A:THR293 5.0 29.7 1.0

Chlorine binding site 2 out of 3 in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:25.3 occ:0.34 CL A:5T5504 0.0 25.3 0.3 CL A:5T5504 0.4 25.0 0.3 CL A:5T5504 0.5 26.6 0.3 C22 A:5T5504 1.6 26.0 0.3 C22 A:5T5504 1.8 25.6 0.3 C22 A:5T5504 2.2 25.4 0.3 C14 A:5T5504 2.5 25.2 0.3 C28 A:5T5504 2.6 27.1 0.3 C28 A:5T5504 2.7 27.1 0.3 C14 A:5T5504 2.8 25.4 0.3 O A:HOH687 2.9 25.8 0.6 C28 A:5T5504 2.9 26.7 0.3 C14 A:5T5504 3.2 26.0 0.3 CA A:GLY74 3.2 28.3 1.0 O A:HOH670 3.3 31.8 1.0 C A:GLY291 3.5 24.1 1.0 N A:GLY74 3.5 24.5 1.0 O A:GLY291 3.7 22.2 1.0 O A:SER290 3.7 15.5 1.0 N A:THR292 3.8 21.3 1.0 CA A:GLY291 3.8 20.5 1.0 C8 A:5T5504 3.8 28.2 0.3 N13 A:5T5504 3.9 27.9 0.3 OG1 A:THR293 3.9 26.7 1.0 C A:THR292 3.9 26.6 1.0 N13 A:5T5504 3.9 27.4 0.3 N A:THR293 4.0 22.4 1.0 C8 A:5T5504 4.0 28.1 0.3 CA A:THR292 4.1 27.4 1.0 O A:HOH657 4.2 23.0 1.0 O A:THR292 4.2 24.0 1.0 N13 A:5T5504 4.2 26.1 0.3 C A:GLN73 4.3 31.5 1.0 C20 A:5T5504 4.3 25.2 0.3 C8 A:5T5504 4.5 27.5 0.3 C20 A:5T5504 4.5 25.2 0.3 CA A:THR293 4.5 20.8 1.0 C A:SER290 4.5 16.4 1.0 N A:GLY291 4.6 18.2 1.0 C A:GLY74 4.7 24.2 1.0 CD1 A:LEU91 4.7 27.7 1.0 O A:HOH819 4.8 26.3 1.0 O A:HOH731 4.8 28.8 1.0 O A:GLN73 4.8 27.0 1.0 CB A:THR293 4.9 29.7 1.0 C20 A:5T5504 4.9 25.9 0.3

Chlorine binding site 3 out of 3 in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:26.6 occ:0.34 CL A:5T5504 0.0 26.6 0.3 CL A:5T5504 0.5 25.3 0.3 CL A:5T5504 0.8 25.0 0.3 C22 A:5T5504 1.8 26.0 0.3 C22 A:5T5504 2.0 25.6 0.3 C22 A:5T5504 2.4 25.4 0.3 C28 A:5T5504 2.6 27.1 0.3 C28 A:5T5504 2.7 27.1 0.3 O A:HOH687 2.8 25.8 0.6 C14 A:5T5504 2.8 25.2 0.3 C28 A:5T5504 2.9 26.7 0.3 O A:HOH670 3.0 31.8 1.0 C14 A:5T5504 3.1 25.4 0.3 OG1 A:THR293 3.5 26.7 1.0 C A:GLY291 3.5 24.1 1.0 C14 A:5T5504 3.5 26.0 0.3 C A:THR292 3.5 26.6 1.0 N A:THR293 3.5 22.4 1.0 CA A:GLY74 3.6 28.3 1.0 N A:THR292 3.6 21.3 1.0 O A:GLY291 3.7 22.2 1.0 N A:GLY74 3.7 24.5 1.0 O A:SER290 3.8 15.5 1.0 O A:THR292 3.8 24.0 1.0 CA A:THR292 3.8 27.4 1.0 N13 A:5T5504 3.9 27.9 0.3 CA A:GLY291 4.0 20.5 1.0 N13 A:5T5504 4.0 27.4 0.3 CA A:THR293 4.0 20.8 1.0 C8 A:5T5504 4.0 28.2 0.3 C8 A:5T5504 4.3 28.1 0.3 N13 A:5T5504 4.3 26.1 0.3 CB A:THR293 4.4 29.7 1.0 O A:HOH819 4.4 26.3 1.0 C20 A:5T5504 4.5 25.2 0.3 C A:GLN73 4.5 31.5 1.0 O A:HOH657 4.6 23.0 1.0 C A:SER290 4.6 16.4 1.0 C20 A:5T5504 4.6 25.2 0.3 C8 A:5T5504 4.7 27.5 0.3 O A:HOH731 4.7 28.8 1.0 N A:GLY291 4.7 18.2 1.0

G.C.P.Van Zundert, B.M.Hudson, S.H.P.De Oliveira, D.A.Keedy, R.Fonseca, A.Heliou, P.Suresh, K.Borrelli, T.Day, J.S.Fraser, H.Van Den Bedem. Qfit-Ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J. Med. Chem. V. 61 11183 2018.
ISSN: ISSN 1520-4804
PubMed: 30457858
DOI: 10.1021/ACS.JMEDCHEM.8B01292