Fluorine in PDB 6od6: Structure of Bace-1 in Complex with Ligand 13

All present enzymatic activity of Structure of Bace-1 in Complex with Ligand 13:
3.4.23.46;

The structure of Structure of Bace-1 in Complex with Ligand 13, PDB code: 6od6 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)	48.26 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	232.398, 100.391, 64.606, 90.00, 103.67, 90.00
R / Rfree (%)	22.3 / 24.8

The binding sites of Fluorine atom in the Structure of Bace-1 in Complex with Ligand 13 (pdb code 6od6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Bace-1 in Complex with Ligand 13, PDB code: 6od6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of Bace-1 in Complex with Ligand 13


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 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:74.5 occ:1.00 F16 A:M7D401 0.0 74.5 1.0 C15 A:M7D401 1.3 70.2 1.0 C17 A:M7D401 2.4 68.5 1.0 C14 A:M7D401 2.4 69.0 1.0 C20 A:M7D401 2.9 65.0 1.0 C19 A:M7D401 2.9 66.0 1.0 CE2 A:TYR71 3.1 64.7 1.0 C29 A:M7D401 3.1 68.1 1.0 CE1 A:PHE108 3.3 55.4 1.0 CD2 A:TYR71 3.4 60.7 1.0 CZ A:TYR71 3.4 68.5 1.0 CD1 A:PHE108 3.5 54.1 1.0 C13 A:M7D401 3.6 66.5 1.0 C18 A:M7D401 3.6 70.6 1.0 OH A:TYR71 3.9 72.9 1.0 CG A:TYR71 4.0 57.5 1.0 CE1 A:TYR71 4.0 62.6 1.0 C12 A:M7D401 4.1 68.2 1.0 CD1 A:ILE118 4.1 54.9 1.0 N28 A:M7D401 4.2 71.2 1.0 CD1 A:TYR71 4.3 61.0 1.0 N21 A:M7D401 4.3 68.5 1.0 CZ A:PHE108 4.5 57.0 1.0 C27 A:M7D401 4.9 72.8 1.0 CG A:PHE108 4.9 56.2 1.0 O A:HOH526 5.0 61.0 1.0 CB A:TYR71 5.0 51.4 1.0

Fluorine binding site 2 out of 3 in the Structure of Bace-1 in Complex with Ligand 13


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 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:78.0 occ:1.00 F16 B:M7D401 0.0 78.0 1.0 C15 B:M7D401 1.3 81.8 1.0 C17 B:M7D401 2.4 78.7 1.0 C14 B:M7D401 2.4 78.0 1.0 C19 B:M7D401 2.9 75.7 1.0 C20 B:M7D401 2.9 72.6 1.0 C29 B:M7D401 3.0 71.9 1.0 CE2 B:TYR71 3.0 63.7 1.0 CZ B:TYR71 3.3 65.5 1.0 CE1 B:PHE108 3.3 65.7 1.0 CD2 B:TYR71 3.4 61.7 1.0 CD1 B:PHE108 3.6 67.6 1.0 C13 B:M7D401 3.6 80.0 1.0 C18 B:M7D401 3.6 80.4 1.0 OH B:TYR71 3.7 69.1 1.0 CE1 B:TYR71 3.8 59.8 1.0 CG B:TYR71 3.9 60.8 1.0 CD1 B:TYR71 4.0 58.6 1.0 N28 B:M7D401 4.1 74.0 1.0 C12 B:M7D401 4.1 81.3 1.0 CD1 B:ILE118 4.3 59.0 1.0 N21 B:M7D401 4.3 73.7 1.0 CZ B:PHE108 4.5 65.0 1.0 C27 B:M7D401 4.8 71.8 1.0 CB B:TYR71 4.9 61.4 1.0 CG B:PHE108 5.0 66.2 1.0 O B:HOH611 5.0 73.1 1.0

Fluorine binding site 3 out of 3 in the Structure of Bace-1 in Complex with Ligand 13


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 13 within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:95.5 occ:1.00 F16 C:M7D401 0.0 95.5 1.0 C15 C:M7D401 1.3 93.9 1.0 C14 C:M7D401 2.4 92.4 1.0 C17 C:M7D401 2.4 93.7 1.0 C20 C:M7D401 2.8 90.2 1.0 C19 C:M7D401 2.9 92.4 1.0 C29 C:M7D401 3.1 96.3 1.0 CE2 C:TYR71 3.2 91.4 1.0 CE1 C:PHE108 3.4 95.5 1.0 CD2 C:TYR71 3.6 90.3 1.0 C13 C:M7D401 3.6 92.4 1.0 C18 C:M7D401 3.6 93.5 1.0 CD1 C:PHE108 3.7 96.5 1.0 CZ C:TYR71 3.7 89.4 1.0 CD1 C:ILE118 3.9 94.7 0.0 OH C:TYR71 4.1 86.6 1.0 C12 C:M7D401 4.1 92.0 1.0 N28 C:M7D401 4.2 97.4 1.0 N21 C:M7D401 4.3 92.7 1.0 CG C:TYR71 4.3 91.7 1.0 CE1 C:TYR71 4.5 90.9 1.0 CZ C:PHE108 4.6 95.3 1.0 CD1 C:TYR71 4.7 91.2 1.0 C27 C:M7D401 4.9 97.4 1.0

D.Oehlrich, A.Peschiulli, G.Tresadern, M.Van Gool, J.A.Vega, A.I.De Lucas, S.A.Alonso De Diego, H.Prokopcova, N.Austin, S.Van Brandt, M.Surkyn, M.De Cleyn, A.Vos, F.J.R.Rombouts, G.Macdonald, D.Moechars, H.J.M.Gijsen, A.A.Trabanco. Evaluation of A Series of Beta-Secretase 1 Inhibitors Containing Novel Heteroaryl-Fused-Piperazine Amidine Warheads. Acs Med.Chem.Lett. V. 10 1159 2019.
ISSN: ISSN 1948-5875
PubMed: 31413800
DOI: 10.1021/ACSMEDCHEMLETT.9B00181