Fluorine in PDB 7b1q: Crystal Structure of Human Bace-1 in Complex with Compound Nb-360 (Compound 54)

All present enzymatic activity of Crystal Structure of Human Bace-1 in Complex with Compound Nb-360 (Compound 54):
3.4.23.46;

The structure of Crystal Structure of Human Bace-1 in Complex with Compound Nb-360 (Compound 54), PDB code: 7b1q 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)	60.48 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.747, 74.158, 104.512, 90, 90, 90
R / Rfree (%)	18.9 / 21.8

The binding sites of Fluorine atom in the Crystal Structure of Human Bace-1 in Complex with Compound Nb-360 (Compound 54) (pdb code 7b1q). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human Bace-1 in Complex with Compound Nb-360 (Compound 54), PDB code: 7b1q:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Human Bace-1 in Complex with Compound Nb-360 (Compound 54)


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 Nb-360 (Compound 54) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:32.8 occ:1.00 F7 A:SLK501 0.0 32.8 1.0 C4 A:SLK501 1.3 28.4 1.0 C3 A:SLK501 2.3 28.2 1.0 C5 A:SLK501 2.4 27.0 1.0 C9 A:SLK501 3.0 28.0 1.0 CD2 A:TYR71 3.1 51.5 1.0 CE2 A:TYR71 3.1 52.8 1.0 C12 A:SLK501 3.1 26.0 1.0 CE1 A:PHE108 3.1 37.1 1.0 C11 A:SLK501 3.2 24.7 1.0 CD1 A:PHE108 3.5 36.7 1.0 C2 A:SLK501 3.6 26.1 1.0 C6 A:SLK501 3.7 25.8 1.0 CG A:TYR71 3.9 50.3 1.0 CZ A:TYR71 4.0 52.8 1.0 CD1 A:ILE118 4.0 24.3 1.0 C1 A:SLK501 4.1 27.9 1.0 O13 A:SLK501 4.2 27.4 1.0 CZ A:PHE108 4.3 37.2 1.0 N10 A:SLK501 4.5 25.1 1.0 CD1 A:TYR71 4.6 51.3 1.0 OH A:TYR71 4.6 54.8 1.0 CE1 A:TYR71 4.6 53.1 1.0 CB A:TYR71 4.7 49.2 1.0 CG A:PHE108 4.9 37.4 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Human Bace-1 in Complex with Compound Nb-360 (Compound 54)


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 Nb-360 (Compound 54) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:35.8 occ:1.00 F18 A:SLK501 0.0 35.8 1.0 C15 A:SLK501 1.4 31.6 1.0 F19 A:SLK501 2.2 30.4 1.0 F20 A:SLK501 2.2 34.4 1.0 C14 A:SLK501 2.4 28.4 1.0 O13 A:SLK501 2.7 27.4 1.0 C21 A:SLK501 3.0 31.1 1.0 C11 A:SLK501 3.5 24.7 1.0 C16 A:SLK501 3.7 26.6 1.0 O A:HOH725 4.2 27.1 1.0 O A:HOH750 4.4 40.3 1.0 N17 A:SLK501 4.4 20.4 1.0 N10 A:SLK501 4.6 25.1 1.0 C9 A:SLK501 4.7 28.0 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Human Bace-1 in Complex with Compound Nb-360 (Compound 54)


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 Nb-360 (Compound 54) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:30.4 occ:1.00 F19 A:SLK501 0.0 30.4 1.0 C15 A:SLK501 1.4 31.6 1.0 F20 A:SLK501 2.2 34.4 1.0 F18 A:SLK501 2.2 35.8 1.0 C14 A:SLK501 2.4 28.4 1.0 C16 A:SLK501 2.9 26.6 1.0 O13 A:SLK501 3.0 27.4 1.0 C11 A:SLK501 3.1 24.7 1.0 O A:HOH718 3.3 27.7 1.0 N17 A:SLK501 3.4 20.4 1.0 O A:HOH750 3.4 40.3 1.0 O A:GLY34 3.5 20.7 1.0 N10 A:SLK501 3.5 25.1 1.0 C21 A:SLK501 3.8 31.1 1.0 C9 A:SLK501 3.8 28.0 1.0 C A:GLY34 4.4 21.1 1.0 C12 A:SLK501 4.5 26.0 1.0 CE1 A:TYR71 4.5 53.1 1.0 OD2 A:ASP228 4.8 25.8 1.0 CD1 A:TYR71 4.9 51.3 1.0 CB A:SER35 4.9 20.1 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Human Bace-1 in Complex with Compound Nb-360 (Compound 54)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Bace-1 in Complex with Compound Nb-360 (Compound 54) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:34.4 occ:1.00 F20 A:SLK501 0.0 34.4 1.0 C15 A:SLK501 1.4 31.6 1.0 F19 A:SLK501 2.2 30.4 1.0 F18 A:SLK501 2.2 35.8 1.0 O A:HOH750 2.3 40.3 1.0 C14 A:SLK501 2.4 28.4 1.0 C21 A:SLK501 2.8 31.1 1.0 N17 A:SLK501 2.9 20.4 1.0 OD2 A:ASP228 3.0 25.8 1.0 C16 A:SLK501 3.0 26.6 1.0 O13 A:SLK501 3.6 27.4 1.0 O A:HOH725 3.9 27.1 1.0 OG1 A:THR231 4.1 26.3 1.0 O A:GLY34 4.1 20.7 1.0 CG A:ASP228 4.1 26.3 1.0 N10 A:SLK501 4.2 25.1 1.0 C11 A:SLK501 4.4 24.7 1.0 OD1 A:ASP228 4.7 24.9 1.0 C A:GLY34 4.8 21.1 1.0 CA A:GLY34 4.8 18.6 1.0 CD1 A:ILE226 4.9 24.3 1.0 C9 A:SLK501 5.0 28.0 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