Fluorine in PDB 6e3z: Structure of Bace-1 in Complex with Ligand 8

All present enzymatic activity of Structure of Bace-1 in Complex with Ligand 8:
3.4.23.46;

The structure of Structure of Bace-1 in Complex with Ligand 8, PDB code: 6e3z was solved by P.L.Shaffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.45 / 1.94
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	232.178, 100.500, 63.968, 90.00, 103.22, 90.00
R / Rfree (%)	17.9 / 21.3

The structure of Structure of Bace-1 in Complex with Ligand 8 also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Fluorine atom in the Structure of Bace-1 in Complex with Ligand 8 (pdb code 6e3z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 16 binding sites of Fluorine where determined in the Structure of Bace-1 in Complex with Ligand 8, PDB code: 6e3z:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in the Structure of Bace-1 in Complex with Ligand 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Bace-1 in Complex with Ligand 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.6 occ:1.00 F11 A:HRV401 0.0 32.6 1.0 C10 A:HRV401 1.4 31.9 1.0 F13 A:HRV401 2.2 32.6 1.0 F12 A:HRV401 2.2 32.3 1.0 C8 A:HRV401 2.3 29.5 1.0 O7 A:HRV401 2.8 29.6 1.0 C2 A:HRV401 3.7 29.8 1.0 CB A:TYR71 3.8 54.3 1.0 C6 A:HRV401 4.0 29.6 1.0 CG A:TYR71 4.1 51.9 1.0 CD1 A:TYR71 4.3 50.0 1.0 C1 A:HRV401 4.3 30.4 1.0 C14 A:HRV401 4.3 30.3 1.0 O A:HOH703 4.5 47.6 1.0 O A:GLN73 4.6 77.9 1.0 F31 A:HRV401 4.7 32.6 1.0 CD2 A:TYR71 4.7 50.2 1.0 C30 A:HRV401 4.8 31.5 1.0 N3 A:HRV401 4.8 28.6 1.0 N A:THR72 4.8 68.3 1.0 O A:HOH805 4.9 55.2 1.0 C4 A:HRV401 4.9 28.8 1.0 N A:GLN73 4.9 78.4 1.0

Fluorine binding site 2 out of 16 in the Structure of Bace-1 in Complex with Ligand 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Bace-1 in Complex with Ligand 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.3 occ:1.00 F12 A:HRV401 0.0 32.3 1.0 C10 A:HRV401 1.4 31.9 1.0 F13 A:HRV401 2.2 32.6 1.0 F11 A:HRV401 2.2 32.6 1.0 C8 A:HRV401 2.4 29.5 1.0 O7 A:HRV401 2.7 29.6 1.0 C14 A:HRV401 2.8 30.3 1.0 C30 A:HRV401 3.0 31.5 1.0 C2 A:HRV401 3.1 29.8 1.0 O A:HOH703 3.2 47.6 1.0 F31 A:HRV401 3.2 32.6 1.0 O A:HOH805 3.4 55.2 1.0 C15 A:HRV401 3.4 30.5 1.0 C29 A:HRV401 3.7 30.6 1.0 C1 A:HRV401 3.9 30.4 1.0 C16 A:HRV401 4.1 30.6 1.0 C6 A:HRV401 4.1 29.6 1.0 C28 A:HRV401 4.2 30.8 1.0 N3 A:HRV401 4.3 28.6 1.0 O A:GLN73 4.5 77.9 1.0 O A:HOH652 4.5 41.5 1.0 O A:HOH666 4.6 39.0 1.0 C4 A:HRV401 4.7 28.8 1.0 CG A:TYR71 4.7 51.9 1.0 CD2 A:TYR71 4.8 50.2 1.0 CB A:TYR71 4.9 54.3 1.0

Fluorine binding site 3 out of 16 in the Structure of Bace-1 in Complex with Ligand 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Bace-1 in Complex with Ligand 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.6 occ:1.00 F13 A:HRV401 0.0 32.6 1.0 C10 A:HRV401 1.3 31.9 1.0 F12 A:HRV401 2.2 32.3 1.0 F11 A:HRV401 2.2 32.6 1.0 C8 A:HRV401 2.4 29.5 1.0 F31 A:HRV401 2.8 32.6 1.0 CG A:TYR71 2.8 51.9 1.0 C1 A:HRV401 2.9 30.4 1.0 C2 A:HRV401 2.9 29.8 1.0 CD1 A:TYR71 3.0 50.0 1.0 CD2 A:TYR71 3.0 50.2 1.0 CB A:TYR71 3.3 54.3 1.0 C30 A:HRV401 3.3 31.5 1.0 C14 A:HRV401 3.4 30.3 1.0 CE1 A:TYR71 3.4 46.1 1.0 CE2 A:TYR71 3.4 47.1 1.0 O A:HOH703 3.5 47.6 1.0 O7 A:HRV401 3.6 29.6 1.0 CZ A:TYR71 3.6 44.8 1.0 N3 A:HRV401 4.3 28.6 1.0 C29 A:HRV401 4.5 30.6 1.0 O A:GLN73 4.5 77.9 1.0 C15 A:HRV401 4.6 30.5 1.0 OH A:TYR71 4.6 43.7 1.0 C6 A:HRV401 4.7 29.6 1.0 CA A:TYR71 4.8 58.4 1.0

Fluorine binding site 4 out of 16 in the Structure of Bace-1 in Complex with Ligand 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Bace-1 in Complex with Ligand 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.6 occ:1.00 F31 A:HRV401 0.0 32.6 1.0 C30 A:HRV401 1.3 31.5 1.0 C29 A:HRV401 2.3 30.6 1.0 C14 A:HRV401 2.4 30.3 1.0 C1 A:HRV401 2.7 30.4 1.0 F13 A:HRV401 2.8 32.6 1.0 C2 A:HRV401 2.9 29.8 1.0 F12 A:HRV401 3.2 32.3 1.0 CE1 A:PHE108 3.3 32.8 1.0 CE2 A:TYR71 3.3 47.1 1.0 C10 A:HRV401 3.4 31.9 1.0 O A:HOH703 3.4 47.6 1.0 CZ A:TYR71 3.5 44.8 1.0 C15 A:HRV401 3.6 30.5 1.0 C28 A:HRV401 3.6 30.8 1.0 C8 A:HRV401 3.7 29.5 1.0 CD1 A:PHE108 3.8 35.0 1.0 OH A:TYR71 3.8 43.7 1.0 CD2 A:TYR71 3.9 50.2 1.0 C16 A:HRV401 4.1 30.6 1.0 CE1 A:TYR71 4.2 46.1 1.0 CD1 A:ILE118 4.2 29.4 1.0 N3 A:HRV401 4.3 28.6 1.0 CG A:TYR71 4.5 51.9 1.0 CZ A:PHE108 4.5 31.8 1.0 O A:HOH652 4.6 41.5 1.0 CD1 A:TYR71 4.6 50.0 1.0 F11 A:HRV401 4.7 32.6 1.0 O7 A:HRV401 4.7 29.6 1.0

Fluorine binding site 5 out of 16 in the Structure of Bace-1 in Complex with Ligand 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Bace-1 in Complex with Ligand 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:41.5 occ:1.00 F11 B:HRV401 0.0 41.5 1.0 C10 B:HRV401 1.4 41.5 1.0 F12 B:HRV401 2.2 41.3 1.0 F13 B:HRV401 2.2 41.6 1.0 C8 B:HRV401 2.3 41.0 1.0 O7 B:HRV401 2.8 40.7 1.0 C2 B:HRV401 3.8 41.9 1.0 CB B:TYR71 3.9 58.4 1.0 C6 B:HRV401 4.0 39.9 1.0 O B:GLN73 4.1 70.2 1.0 C14 B:HRV401 4.3 42.9 1.0 CG B:TYR71 4.3 55.3 1.0 C1 B:HRV401 4.4 42.4 1.0 O B:HOH588 4.4 55.4 1.0 N B:GLN73 4.5 73.2 1.0 N B:THR72 4.5 66.7 1.0 CD1 B:TYR71 4.6 52.1 1.0 F31 B:HRV401 4.6 43.8 1.0 C30 B:HRV401 4.7 43.5 1.0 N3 B:HRV401 4.8 40.9 1.0 CB B:THR72 4.9 71.2 1.0 O B:HOH683 5.0 56.3 1.0 C4 B:HRV401 5.0 39.7 1.0

Fluorine binding site 6 out of 16 in the Structure of Bace-1 in Complex with Ligand 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Bace-1 in Complex with Ligand 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:41.3 occ:1.00 F12 B:HRV401 0.0 41.3 1.0 C10 B:HRV401 1.4 41.5 1.0 F11 B:HRV401 2.2 41.5 1.0 F13 B:HRV401 2.2 41.6 1.0 C8 B:HRV401 2.4 41.0 1.0 O7 B:HRV401 2.8 40.7 1.0 C14 B:HRV401 2.9 42.9 1.0 C30 B:HRV401 3.1 43.5 1.0 C2 B:HRV401 3.1 41.9 1.0 O B:HOH588 3.2 55.4 1.0 F31 B:HRV401 3.4 43.8 1.0 C15 B:HRV401 3.4 43.7 1.0 C29 B:HRV401 3.8 43.6 1.0 O B:HOH683 4.0 56.3 1.0 C1 B:HRV401 4.1 42.4 1.0 C16 B:HRV401 4.1 44.9 1.0 C6 B:HRV401 4.2 39.9 1.0 C28 B:HRV401 4.2 44.2 1.0 O B:GLN73 4.3 70.2 1.0 N3 B:HRV401 4.4 40.9 1.0 O B:HOH609 4.4 56.5 1.0 C4 B:HRV401 4.8 39.7 1.0 CG B:TYR71 4.9 55.3 1.0 CB B:TYR71 4.9 58.4 1.0

Fluorine binding site 7 out of 16 in the Structure of Bace-1 in Complex with Ligand 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Bace-1 in Complex with Ligand 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:41.6 occ:1.00 F13 B:HRV401 0.0 41.6 1.0 C10 B:HRV401 1.4 41.5 1.0 F11 B:HRV401 2.2 41.5 1.0 F12 B:HRV401 2.2 41.3 1.0 C8 B:HRV401 2.4 41.0 1.0 F31 B:HRV401 2.7 43.8 1.0 CG B:TYR71 2.8 55.3 1.0 C2 B:HRV401 3.0 41.9 1.0 C1 B:HRV401 3.0 42.4 1.0 CD1 B:TYR71 3.1 52.1 1.0 CB B:TYR71 3.2 58.4 1.0 CD2 B:TYR71 3.2 56.2 1.0 C30 B:HRV401 3.3 43.5 1.0 O B:HOH588 3.3 55.4 1.0 C14 B:HRV401 3.4 42.9 1.0 O7 B:HRV401 3.6 40.7 1.0 CE1 B:TYR71 3.8 50.1 1.0 CE2 B:TYR71 3.8 54.6 1.0 O B:GLN73 3.9 70.2 1.0 CZ B:TYR71 4.0 51.2 1.0 C29 B:HRV401 4.4 43.6 1.0 N3 B:HRV401 4.4 40.9 1.0 C15 B:HRV401 4.5 43.7 1.0 CA B:TYR71 4.6 59.7 1.0 C6 B:HRV401 4.7 39.9 1.0

Fluorine binding site 8 out of 16 in the Structure of Bace-1 in Complex with Ligand 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Bace-1 in Complex with Ligand 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:43.8 occ:1.00 F31 B:HRV401 0.0 43.8 1.0 C30 B:HRV401 1.3 43.5 1.0 C14 B:HRV401 2.4 42.9 1.0 C29 B:HRV401 2.4 43.6 1.0 C1 B:HRV401 2.6 42.4 1.0 F13 B:HRV401 2.7 41.6 1.0 C2 B:HRV401 2.9 41.9 1.0 C10 B:HRV401 3.4 41.5 1.0 F12 B:HRV401 3.4 41.3 1.0 CE2 B:TYR71 3.4 54.6 1.0 CE1 B:PHE108 3.4 51.6 1.0 O B:HOH588 3.5 55.4 1.0 CZ B:TYR71 3.5 51.2 1.0 C15 B:HRV401 3.6 43.7 1.0 C8 B:HRV401 3.7 41.0 1.0 C28 B:HRV401 3.7 44.2 1.0 CD2 B:TYR71 3.8 56.2 1.0 CD1 B:PHE108 3.9 53.8 1.0 OH B:TYR71 3.9 48.9 1.0 CE1 B:TYR71 4.0 50.1 1.0 CD1 B:ILE118 4.1 39.8 1.0 C16 B:HRV401 4.1 44.9 1.0 N3 B:HRV401 4.2 40.9 1.0 CG B:TYR71 4.2 55.3 1.0 CD1 B:TYR71 4.3 52.1 1.0 CZ B:PHE108 4.5 51.0 1.0 O B:HOH609 4.6 56.5 1.0 F11 B:HRV401 4.6 41.5 1.0 O7 B:HRV401 4.7 40.7 1.0

Fluorine binding site 9 out of 16 in the Structure of Bace-1 in Complex with Ligand 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of Bace-1 in Complex with Ligand 8 within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:47.3 occ:1.00 F11 C:HRV401 0.0 47.3 1.0 C10 C:HRV401 1.4 47.2 1.0 F13 C:HRV401 2.2 49.3 1.0 F12 C:HRV401 2.2 47.4 1.0 C8 C:HRV401 2.4 44.8 1.0 O7 C:HRV401 2.8 44.2 1.0 C2 C:HRV401 3.7 43.6 1.0 C6 C:HRV401 4.0 44.0 1.0 CB C:TYR71 4.0 72.1 1.0 CG C:TYR71 4.1 71.0 1.0 C14 C:HRV401 4.3 42.7 1.0 CD1 C:TYR71 4.3 69.5 1.0 C1 C:HRV401 4.3 43.8 1.0 F31 C:HRV401 4.6 43.7 1.0 C30 C:HRV401 4.7 42.9 1.0 O C:GLN73 4.7 88.2 1.0 CD2 C:TYR71 4.7 71.1 1.0 N3 C:HRV401 4.8 43.4 1.0 C4 C:HRV401 4.9 43.3 1.0 N C:THR72 5.0 81.4 1.0 C15 C:HRV401 5.0 43.0 1.0

Fluorine binding site 10 out of 16 in the Structure of Bace-1 in Complex with Ligand 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of Bace-1 in Complex with Ligand 8 within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:47.4 occ:1.00 F12 C:HRV401 0.0 47.4 1.0 C10 C:HRV401 1.4 47.2 1.0 F13 C:HRV401 2.2 49.3 1.0 F11 C:HRV401 2.2 47.3 1.0 C8 C:HRV401 2.4 44.8 1.0 C14 C:HRV401 2.7 42.7 1.0 O7 C:HRV401 2.7 44.2 1.0 C30 C:HRV401 2.9 42.9 1.0 C2 C:HRV401 3.0 43.6 1.0 C15 C:HRV401 3.2 43.0 1.0 F31 C:HRV401 3.3 43.7 1.0 C29 C:HRV401 3.6 42.7 1.0 C1 C:HRV401 3.8 43.8 1.0 C16 C:HRV401 3.8 42.6 1.0 C28 C:HRV401 4.0 42.7 1.0 C6 C:HRV401 4.1 44.0 1.0 N3 C:HRV401 4.2 43.4 1.0 O C:HOH671 4.2 47.2 1.0 C4 C:HRV401 4.6 43.3 1.0 N17 C:HRV401 4.9 41.5 1.0

H.J.M.Gijsen, J.Lin, Y.Houpis. Discovery and Chemical Development of Jnj-50138803, A Clinical Candidate Bace Inhibitor To Be Published.