Fluorine in PDB 7n66: Bace-1 in Complex with Ligand 12

All present enzymatic activity of Bace-1 in Complex with Ligand 12:
3.4.23.46;

The structure of Bace-1 in Complex with Ligand 12, PDB code: 7n66 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)	19.91 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.13, 102.13, 170.523, 90, 90, 120
R / Rfree (%)	19.6 / 23

The structure of Bace-1 in Complex with Ligand 12 also contains other interesting chemical elements:

Iodine

(I)

5 atoms

The binding sites of Fluorine atom in the Bace-1 in Complex with Ligand 12 (pdb code 7n66). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Bace-1 in Complex with Ligand 12, PDB code: 7n66:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Bace-1 in Complex with Ligand 12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bace-1 in Complex with Ligand 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:F510 b:26.4 occ:1.00 F3 A:0EW510 0.0 26.4 1.0 C19 A:0EW510 1.3 26.4 1.0 F2 A:0EW510 2.2 26.5 1.0 O4 A:0EW510 2.2 25.7 1.0 O3 A:0EW510 2.2 26.6 1.0 C20 A:0EW510 3.1 25.9 1.0 C18 A:0EW510 3.1 26.1 1.0 N A:GLY13 3.5 26.6 1.0 CE1 A:TYR14 3.5 23.5 1.0 CA A:GLY13 3.6 24.7 1.0 CD1 A:TYR14 3.9 23.3 1.0 N A:GLY11 4.1 35.7 1.0 NH2 A:ARG307 4.3 28.5 1.0 N A:GLN12 4.3 26.4 1.0 C A:GLY13 4.3 25.1 1.0 C21 A:0EW510 4.3 25.3 1.0 CA A:GLY11 4.4 31.9 1.0 OE2 A:GLU339 4.4 29.0 1.0 C17 A:0EW510 4.4 25.7 1.0 CZ A:TYR14 4.4 26.6 1.0 C A:GLY11 4.5 27.7 1.0 O A:LYS9 4.5 43.9 1.0 CB A:ALA335 4.5 20.3 1.0 C A:GLN12 4.7 31.1 1.0 OH A:TYR14 4.7 30.6 1.0 O A:GLY13 4.7 25.2 1.0 OG1 A:THR232 4.9 19.6 1.0 N A:TYR14 5.0 19.4 1.0

Fluorine binding site 2 out of 4 in the Bace-1 in Complex with Ligand 12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bace-1 in Complex with Ligand 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:F510 b:26.5 occ:1.00 F2 A:0EW510 0.0 26.5 1.0 C19 A:0EW510 1.3 26.4 1.0 F3 A:0EW510 2.2 26.4 1.0 O4 A:0EW510 2.3 25.7 1.0 O3 A:0EW510 2.3 26.6 1.0 C20 A:0EW510 3.2 25.9 1.0 C18 A:0EW510 3.2 26.1 1.0 OG1 A:THR232 3.3 19.6 1.0 NH2 A:ARG307 3.3 28.5 1.0 CG2 A:THR232 3.4 25.8 1.0 CB A:THR232 3.7 26.3 1.0 O A:HOH635 3.8 43.5 1.0 CZ A:ARG307 3.8 31.8 1.0 CB A:ALA335 3.8 20.3 1.0 CA A:THR232 3.9 26.0 1.0 NE A:ARG307 4.0 33.7 1.0 CA A:GLY11 4.1 31.9 1.0 N A:GLY11 4.2 35.7 1.0 OE2 A:GLU339 4.4 29.0 1.0 O A:HOH645 4.5 37.7 1.0 C21 A:0EW510 4.5 25.3 1.0 C17 A:0EW510 4.6 25.7 1.0 C A:GLY11 4.7 27.7 1.0 NH1 A:ARG307 4.7 33.1 1.0 O A:THR232 4.8 25.9 1.0 C A:THR232 4.8 23.9 1.0 N A:THR232 4.9 24.4 1.0

Fluorine binding site 3 out of 4 in the Bace-1 in Complex with Ligand 12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Bace-1 in Complex with Ligand 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:F510 b:27.5 occ:1.00 F1 A:0EW510 0.0 27.5 1.0 C14 A:0EW510 1.3 27.4 1.0 C13 A:0EW510 2.4 26.8 1.0 C9 A:0EW510 2.5 27.6 1.0 C7 A:0EW510 3.0 28.4 1.0 C6 A:0EW510 3.0 29.1 1.0 CE1 A:PHE108 3.1 27.3 1.0 C5 A:0EW510 3.2 29.8 1.0 CD1 A:PHE108 3.2 24.5 1.0 CE2 A:TYR71 3.4 34.1 1.0 C1 A:DMS507 3.4 53.2 1.0 CZ A:TYR71 3.6 28.6 1.0 C12 A:0EW510 3.6 26.3 1.0 C10 A:0EW510 3.7 27.1 1.0 OH A:TYR71 3.7 32.8 1.0 S A:DMS507 3.9 69.4 1.0 CD2 A:TYR71 4.0 32.7 1.0 F A:0EW510 4.1 29.3 1.0 C11 A:0EW510 4.2 26.6 1.0 CE1 A:TYR71 4.4 34.8 1.0 C4 A:0EW510 4.4 32.9 1.0 CZ A:PHE108 4.4 21.9 1.0 N A:0EW510 4.4 29.3 1.0 CG A:PHE108 4.5 26.2 1.0 CD1 A:ILE118 4.7 30.1 1.0 CG A:TYR71 4.7 37.0 1.0 CD1 A:TYR71 4.9 33.7 1.0 O A:DMS507 4.9 63.5 1.0 C2 A:DMS507 5.0 59.6 1.0 O A:HOH606 5.0 30.2 1.0

Fluorine binding site 4 out of 4 in the Bace-1 in Complex with Ligand 12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Bace-1 in Complex with Ligand 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:F510 b:29.3 occ:1.00 F A:0EW510 0.0 29.3 1.0 C7 A:0EW510 1.4 28.4 1.0 C6 A:0EW510 2.4 29.1 1.0 N A:0EW510 2.8 29.3 1.0 C5 A:0EW510 2.9 29.8 1.0 OH A:TYR71 3.1 32.8 1.0 O A:HOH702 3.3 25.4 1.0 CB A:SER35 3.3 15.3 1.0 OD2 A:ASP32 3.4 18.6 1.0 CE1 A:TYR71 3.4 34.8 1.0 OG A:SER35 3.5 19.8 1.0 O1 A:0EW510 3.5 42.7 1.0 CZ A:TYR71 3.5 28.6 1.0 C9 A:0EW510 3.7 27.6 1.0 C8 A:0EW510 3.7 32.1 1.0 F1 A:0EW510 4.1 27.5 1.0 C4 A:0EW510 4.1 32.9 1.0 O A:HOH643 4.2 20.6 1.0 C2 A:0EW510 4.3 35.4 1.0 C14 A:0EW510 4.4 27.4 1.0 CD1 A:TYR71 4.5 33.7 1.0 S A:0EW510 4.5 42.8 1.0 CG A:ASP32 4.6 19.0 1.0 N1 A:0EW510 4.6 30.0 1.0 CE2 A:TYR71 4.6 34.1 1.0 CA A:SER35 4.8 19.5 1.0 C10 A:0EW510 4.8 27.1 1.0 CG2 A:ILE118 4.8 27.7 1.0

F.J.R.Rombouts, K.I.Kusakabe, R.Alexander, N.Austin, H.Borghys, M.De Cleyn, D.Dhuyvetter, H.J.M.Gijsen, B.Hrupka, T.Jacobs, S.Jerhaoui, L.Lammens, L.Leclercq, K.Tsubone, T.Ueno, K.Morimoto, S.Einaru, H.Sumiyoshi, A.Van Den Bergh, A.Vos, M.Surkyn, A.Teisman, D.Moechars. Jnj-67569762, A 2-Aminotetrahydropyridine-Based Selective BACE1 Inhibitor Targeting the S3 Pocket: From Discovery to Clinical Candidate. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34553934
DOI: 10.1021/ACS.JMEDCHEM.1C00935