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Fluorine in PDB 3ixk: Potent Beta-Secretase 1 Inhibitor

Enzymatic activity of Potent Beta-Secretase 1 Inhibitor

All present enzymatic activity of Potent Beta-Secretase 1 Inhibitor:
3.4.23.46;

Protein crystallography data

The structure of Potent Beta-Secretase 1 Inhibitor, PDB code: 3ixk was solved by N.Borkakoti, J.D.Lindberg, S.Nystrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.26 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.838, 103.075, 100.499, 90.00, 103.32, 90.00
R / Rfree (%) 22.9 / 28.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Potent Beta-Secretase 1 Inhibitor (pdb code 3ixk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Potent Beta-Secretase 1 Inhibitor, PDB code: 3ixk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3ixk

Go back to Fluorine Binding Sites List in 3ixk
Fluorine binding site 1 out of 6 in the Potent Beta-Secretase 1 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Potent Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:44.9
occ:1.00
 F1 A:929500 0.0 44.9 1.0
C25 A:929500 1.3 43.9 1.0
C24 A:929500 2.3 46.7 1.0
C26 A:929500 2.4 44.3 1.0
CD1 A:ILE158 3.3 50.1 1.0
CG1 A:ILE158 3.4 48.7 1.0
C23 A:929500 3.6 47.3 1.0
O A:PHE156 3.6 43.2 1.0
C21 A:929500 3.6 44.9 1.0
C22 A:929500 4.1 47.7 1.0
O A:LYS155 4.2 43.7 1.0
C34 A:929500 4.5 33.9 1.0
N4 A:929500 4.5 38.3 1.0
C37 A:929500 4.6 32.1 1.0
C A:PHE156 4.6 40.6 1.0
C29 A:929500 4.6 35.2 1.0
F2 A:929500 4.6 45.8 1.0
O6 A:929500 4.8 42.3 1.0
C35 A:929500 4.8 40.9 1.0
C30 A:929500 4.9 33.0 1.0
CA A:PHE156 4.9 38.4 1.0
C20 A:929500 4.9 44.6 1.0
CB A:ILE158 5.0 49.9 1.0
CG A:GLN121 5.0 50.0 1.0

Fluorine binding site 2 out of 6 in 3ixk

Go back to Fluorine Binding Sites List in 3ixk
Fluorine binding site 2 out of 6 in the Potent Beta-Secretase 1 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Potent Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:45.8
occ:1.00
 F2 A:929500 0.0 45.8 1.0
C23 A:929500 1.3 47.3 1.0
C24 A:929500 2.4 46.7 1.0
C22 A:929500 2.4 47.7 1.0
N A:GLY122 2.4 42.9 1.0
CA A:GLY122 2.7 38.0 1.0
C A:GLN121 2.7 44.9 1.0
C A:GLY122 3.2 36.1 1.0
O A:GLY122 3.2 34.3 1.0
CA A:GLN121 3.3 44.3 1.0
O A:GLN121 3.4 47.4 1.0
N A:GLN121 3.4 41.5 1.0
CB A:GLN121 3.5 44.3 1.0
C25 A:929500 3.6 43.9 1.0
CB A:TYR119 3.6 33.4 1.0
C21 A:929500 3.7 44.9 1.0
CD2 A:TYR119 4.1 27.0 1.0
O A:LYS155 4.1 43.7 1.0
C26 A:929500 4.2 44.3 1.0
N A:LYS123 4.2 35.3 1.0
CG A:TYR119 4.2 32.3 1.0
O5 A:929500 4.3 39.4 1.0
CG A:GLN121 4.4 50.0 1.0
CD1 A:PHE156 4.4 35.0 1.0
C A:TYR119 4.6 37.3 1.0
CA A:TYR119 4.6 35.1 1.0
F1 A:929500 4.6 44.9 1.0
O A:TYR119 4.6 39.0 1.0
C A:THR120 4.7 39.9 1.0
C28 A:929500 4.8 35.0 1.0
CA A:PHE156 4.8 38.4 1.0
N A:TYR119 4.9 33.5 1.0
C20 A:929500 4.9 44.6 1.0

Fluorine binding site 3 out of 6 in 3ixk

Go back to Fluorine Binding Sites List in 3ixk
Fluorine binding site 3 out of 6 in the Potent Beta-Secretase 1 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Potent Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F500

b:64.4
occ:1.00
 F1 B:929500 0.0 64.4 1.0
C25 B:929500 1.3 61.5 1.0
C24 B:929500 2.3 58.1 1.0
C26 B:929500 2.4 58.1 1.0
CD1 B:ILE158 2.9 43.5 1.0
CZ2 B:TRP163 3.3 29.0 1.0
CG1 B:ILE158 3.4 46.5 1.0
C37 B:929500 3.5 34.6 1.0
C23 B:929500 3.6 59.5 1.0
C21 B:929500 3.6 53.0 1.0
CH2 B:TRP163 3.7 29.2 1.0
O B:PHE156 3.7 34.5 1.0
C22 B:929500 4.1 56.8 1.0
C35 B:929500 4.2 37.4 1.0
N4 B:929500 4.3 40.9 1.0
CE2 B:TRP163 4.5 27.6 1.0
C34 B:929500 4.6 38.3 1.0
F2 B:929500 4.7 64.3 1.0
CB B:ILE158 4.7 46.7 1.0
O6 B:929500 4.7 36.8 1.0
CD2 B:LEU78 4.8 27.4 1.0
C B:PHE156 4.9 33.9 1.0
C20 B:929500 4.9 54.9 1.0

Fluorine binding site 4 out of 6 in 3ixk

Go back to Fluorine Binding Sites List in 3ixk
Fluorine binding site 4 out of 6 in the Potent Beta-Secretase 1 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Potent Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F500

b:64.3
occ:1.00
 F2 B:929500 0.0 64.3 1.0
C23 B:929500 1.3 59.5 1.0
C22 B:929500 2.3 56.8 1.0
C24 B:929500 2.3 58.1 1.0
N B:GLY122 2.7 38.9 1.0
O B:LYS155 2.9 40.3 1.0
C B:GLN121 3.0 41.9 1.0
CA B:GLY122 3.1 34.5 1.0
CB B:GLN121 3.2 44.7 1.0
CG B:GLN121 3.4 47.1 1.0
O B:GLN121 3.6 45.0 1.0
C25 B:929500 3.6 61.5 1.0
C21 B:929500 3.6 53.0 1.0
CA B:GLN121 3.6 42.6 1.0
C B:LYS155 4.0 38.1 1.0
CA B:PHE156 4.1 33.9 1.0
C26 B:929500 4.1 58.1 1.0
C B:GLY122 4.2 32.8 1.0
N B:GLN121 4.4 41.1 1.0
O B:PHE156 4.5 34.5 1.0
N B:PHE156 4.5 36.5 1.0
F1 B:929500 4.7 64.4 1.0
CD1 B:PHE156 4.7 26.6 1.0
O B:GLY122 4.7 31.9 1.0
C20 B:929500 4.8 54.9 1.0
C B:PHE156 4.8 33.9 1.0
CD B:GLN121 4.8 50.8 1.0
N B:LYS123 4.9 30.9 1.0
CB B:PHE156 4.9 30.3 1.0

Fluorine binding site 5 out of 6 in 3ixk

Go back to Fluorine Binding Sites List in 3ixk
Fluorine binding site 5 out of 6 in the Potent Beta-Secretase 1 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Potent Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F500

b:59.5
occ:1.00
 F1 C:929500 0.0 59.5 1.0
C25 C:929500 1.3 56.5 1.0
C24 C:929500 2.3 58.3 1.0
C26 C:929500 2.4 52.5 1.0
CD1 C:ILE158 3.0 48.0 1.0
CG1 C:ILE158 3.3 50.6 1.0
C37 C:929500 3.4 41.8 1.0
C23 C:929500 3.6 63.2 1.0
C21 C:929500 3.7 54.4 1.0
O C:PHE156 3.7 41.3 1.0
C35 C:929500 4.0 38.5 1.0
N4 C:929500 4.0 38.2 1.0
CZ2 C:TRP163 4.1 25.6 1.0
C22 C:929500 4.2 57.7 1.0
C34 C:929500 4.3 36.2 1.0
CH2 C:TRP163 4.5 23.8 1.0
O6 C:929500 4.5 42.7 1.0
F2 C:929500 4.7 73.0 1.0
OE1 C:GLN121 4.7 60.4 1.0
CB C:ILE158 4.8 48.9 1.0
C29 C:929500 4.8 28.9 1.0
C C:PHE156 4.9 41.0 1.0
C20 C:929500 5.0 47.7 1.0
C30 C:929500 5.0 31.0 1.0

Fluorine binding site 6 out of 6 in 3ixk

Go back to Fluorine Binding Sites List in 3ixk
Fluorine binding site 6 out of 6 in the Potent Beta-Secretase 1 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Potent Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F500

b:73.0
occ:1.00
 F2 C:929500 0.0 73.0 1.0
C23 C:929500 1.3 63.2 1.0
C24 C:929500 2.3 58.3 1.0
C22 C:929500 2.3 57.7 1.0
N C:GLY122 2.5 42.5 1.0
C C:GLN121 2.8 45.5 1.0
O C:LYS155 2.8 43.9 1.0
CA C:GLY122 2.9 38.2 1.0
O C:GLN121 3.3 48.4 1.0
CG C:GLN121 3.3 52.9 1.0
OE1 C:GLN121 3.6 60.4 1.0
C25 C:929500 3.6 56.5 1.0
C21 C:929500 3.6 54.4 1.0
CA C:GLN121 3.7 46.6 1.0
CB C:GLN121 3.8 48.5 1.0
CD C:GLN121 3.8 58.9 1.0
C C:LYS155 3.9 41.5 1.0
C26 C:929500 4.1 52.5 1.0
C C:GLY122 4.3 37.5 1.0
CA C:PHE156 4.3 40.3 1.0
N C:GLN121 4.3 42.7 1.0
N C:PHE156 4.6 40.5 1.0
CB C:LYS155 4.6 43.0 1.0
F1 C:929500 4.7 59.5 1.0
C20 C:929500 4.8 47.7 1.0
O C:GLY122 4.9 38.0 1.0
CA C:LYS155 4.9 42.1 1.0
O C:PHE156 5.0 41.3 1.0

Reference:

F.Wangsell, K.Gustafsson, I.Kvarnstrom, N.Borkakoti, M.Edlund, K.Jansson, J.Lindberg, A.Hallberg, A.Rosenquist, B.Samuelsson. Synthesis of Potent Bace-1 Inhibitors Incorporating A Hydroxyethylene Isostere As Central Core. Eur.J.Med.Chem. V. 45 870 2010.
ISSN: ISSN 0223-5234
PubMed: 20036448
DOI: 10.1016/J.EJMECH.2009.11.013
Page generated: Mon Jul 14 17:07:13 2025

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