Fluorine in PDB 7b1p: Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854)

All present enzymatic activity of Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854):
3.4.23.46;

The structure of Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854), PDB code: 7b1p was solved by J.M.Rondeau, E.Wirth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.92 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.576, 74.805, 104.974, 90, 90, 90
R / Rfree (%)	18.6 / 21.1

The structure of Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854) also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854) (pdb code 7b1p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854), PDB code: 7b1p:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:14.7 occ:1.00 F34 A:SL8501 0.0 14.7 1.0 C33 A:SL8501 1.4 13.5 1.0 F35 A:SL8501 2.2 15.9 1.0 F36 A:SL8501 2.2 17.3 1.0 C28 A:SL8501 2.4 12.5 1.0 C27 A:SL8501 2.9 10.5 1.0 O29 A:SL8501 3.0 12.2 1.0 C30 A:SL8501 3.2 9.9 1.0 O A:HOH907 3.2 22.3 1.0 O A:HOH910 3.3 33.5 1.0 O A:HOH930 3.3 19.0 1.0 N41 A:SL8501 3.3 10.4 1.0 O A:HOH901 3.4 28.7 1.0 N26 A:SL8501 3.5 8.8 1.0 O A:HOH726 3.6 14.6 1.0 O A:HOH778 3.6 16.1 1.0 O A:GLY34 3.6 7.6 1.0 C37 A:SL8501 3.8 12.5 1.0 C25 A:SL8501 3.9 8.7 1.0 O A:HOH693 4.5 21.3 1.0 C A:GLY34 4.5 6.7 1.0 C44 A:SL8501 4.6 8.8 1.0 O A:HOH855 4.6 26.3 1.0 OD2 A:ASP228 4.7 6.7 1.0 O A:HOH891 4.8 24.6 1.0 CB A:SER35 5.0 5.7 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:15.9 occ:1.00 F35 A:SL8501 0.0 15.9 1.0 C33 A:SL8501 1.4 13.5 1.0 F34 A:SL8501 2.2 14.7 1.0 F36 A:SL8501 2.2 17.3 1.0 C28 A:SL8501 2.4 12.5 1.0 O A:HOH778 2.8 16.1 1.0 C37 A:SL8501 2.8 12.5 1.0 O A:HOH901 2.9 28.7 1.0 N41 A:SL8501 2.9 10.4 1.0 OD2 A:ASP228 3.0 6.7 1.0 C27 A:SL8501 3.1 10.5 1.0 O A:HOH891 3.3 24.6 1.0 O29 A:SL8501 3.6 12.2 1.0 O A:HOH738 3.7 14.1 1.0 OG1 A:THR231 3.8 9.2 1.0 CG A:ASP228 4.1 7.1 1.0 O A:HOH910 4.2 33.5 1.0 N26 A:SL8501 4.3 8.8 1.0 O A:GLY34 4.3 7.6 1.0 C30 A:SL8501 4.5 9.9 1.0 OD1 A:ASP228 4.7 5.8 1.0 O A:HOH915 4.9 28.4 1.0 O A:HOH907 4.9 22.3 1.0 C A:GLY34 5.0 6.7 1.0 O A:HOH882 5.0 38.4 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Bace-1 in Complex with Compound 38A (Nb- 854) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:17.3 occ:1.00 F36 A:SL8501 0.0 17.3 1.0 C33 A:SL8501 1.4 13.5 1.0 F34 A:SL8501 2.2 14.7 1.0 F35 A:SL8501 2.2 15.9 1.0 C28 A:SL8501 2.4 12.5 1.0 O29 A:SL8501 2.7 12.2 1.0 C37 A:SL8501 3.0 12.5 1.0 O A:HOH855 3.1 26.3 1.0 O A:HOH910 3.2 33.5 1.0 O A:HOH907 3.3 22.3 1.0 O A:HOH901 3.4 28.7 1.0 O A:HOH891 3.5 24.6 1.0 O A:HOH882 3.6 38.4 1.0 C30 A:SL8501 3.6 9.9 1.0 C27 A:SL8501 3.8 10.5 1.0 O A:HOH738 4.2 14.1 1.0 O A:HOH915 4.2 28.4 1.0 N41 A:SL8501 4.4 10.4 1.0 N26 A:SL8501 4.7 8.8 1.0 O A:HOH778 4.7 16.1 1.0 C25 A:SL8501 4.7 8.7 1.0 O A:HOH930 4.8 19.0 1.0

H.Rueeger, R.Lueoend, R.Machauer, S.J.Veenstra, P.Holzer, K.Hurth, M.Voegtle, M.Frederiksen, J.M.Rondeau, M.Tintelnot-Blomley, L.H.Jacobson, M.Staufenbiel, G.Laue, U.Neumann. Synthesis of the Potent, Selective, and Efficacious Beta-Secretase (BACE1) Inhibitor Nb-360. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 33844524
DOI: 10.1021/ACS.JMEDCHEM.0C02143