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Fluorine in PDB 4lxk: Crystal Structure of Human Beta Secretase in Complex with Compound 11D

Enzymatic activity of Crystal Structure of Human Beta Secretase in Complex with Compound 11D

All present enzymatic activity of Crystal Structure of Human Beta Secretase in Complex with Compound 11D:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Human Beta Secretase in Complex with Compound 11D, PDB code: 4lxk was solved by J.M.Rondeau, E.Bourgier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.88 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.291, 103.540, 100.428, 90.00, 104.27, 90.00
R / Rfree (%) n/a / n/a

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D (pdb code 4lxk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D, PDB code: 4lxk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4lxk

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Fluorine binding site 1 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D


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 Beta Secretase in Complex with Compound 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:40.9
occ:1.00
 F1 A:1YT501 0.0 40.9 1.0
C2 A:1YT501 1.4 41.6 1.0
F4 A:1YT501 2.2 40.4 1.0
F3 A:1YT501 2.2 43.5 1.0
C5 A:1YT501 2.4 41.7 1.0
O7 A:1YT501 2.8 38.5 1.0
O A:GLY230 3.2 33.3 1.0
CD1 A:LEU30 3.5 31.3 1.0
C14 A:1YT501 3.5 35.3 1.0
CA A:GLY13 3.6 33.7 1.0
O A:HOH686 3.6 37.3 1.0
C8 A:1YT501 3.6 38.1 1.0
CD2 A:LEU30 3.6 33.7 1.0
C67 A:1YT501 3.8 45.9 1.0
N A:GLY13 3.8 33.4 1.0
C A:GLY230 4.0 32.2 1.0
C A:GLN12 4.1 35.0 1.0
CG A:LEU30 4.2 31.8 1.0
O A:GLN12 4.2 34.6 1.0
CA A:GLY230 4.3 30.9 1.0
CZ2 A:TRP115 4.6 37.0 1.0
O A:HOH658 4.6 31.5 1.0
C13 A:1YT501 4.8 35.2 1.0
O70 A:1YT501 4.8 51.9 1.0
CA A:GLN12 4.9 37.7 1.0
O A:HOH654 4.9 31.9 1.0
C A:GLY13 4.9 34.5 1.0
C9 A:1YT501 4.9 38.2 1.0

Fluorine binding site 2 out of 12 in 4lxk

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Fluorine binding site 2 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D


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 Beta Secretase in Complex with Compound 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:43.5
occ:1.00
 F3 A:1YT501 0.0 43.5 1.0
C2 A:1YT501 1.4 41.6 1.0
F1 A:1YT501 2.2 40.9 1.0
F4 A:1YT501 2.2 40.4 1.0
C5 A:1YT501 2.4 41.7 1.0
C67 A:1YT501 2.9 45.9 1.0
O A:HOH658 3.0 31.5 1.0
O A:HOH686 3.1 37.3 1.0
OG1 A:THR232 3.2 35.1 1.0
N A:GLY13 3.3 33.4 1.0
O A:GLY11 3.6 40.4 1.0
O A:GLY230 3.6 33.3 1.0
O7 A:1YT501 3.6 38.5 1.0
C A:GLN12 3.7 35.0 1.0
CA A:GLY13 3.7 33.7 1.0
CA A:GLN12 3.9 37.7 1.0
C A:GLY11 4.0 41.1 1.0
N A:GLN12 4.1 38.8 1.0
O70 A:1YT501 4.2 51.9 1.0
O A:HOH703 4.4 39.3 1.0
O A:GLN12 4.4 34.6 1.0
N A:THR232 4.5 30.8 1.0
C A:GLY230 4.5 32.2 1.0
CB A:THR232 4.5 33.0 1.0
C8 A:1YT501 4.7 38.1 1.0
CA A:THR232 4.8 32.3 1.0
C14 A:1YT501 4.9 35.3 1.0
C A:THR231 4.9 32.2 1.0
CA A:GLY11 5.0 42.6 1.0

Fluorine binding site 3 out of 12 in 4lxk

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Fluorine binding site 3 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D


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 Beta Secretase in Complex with Compound 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:40.4
occ:1.00
 F4 A:1YT501 0.0 40.4 1.0
C2 A:1YT501 1.4 41.6 1.0
F1 A:1YT501 2.2 40.9 1.0
F3 A:1YT501 2.2 43.5 1.0
C5 A:1YT501 2.4 41.7 1.0
O7 A:1YT501 2.7 38.5 1.0
C A:GLN12 2.8 35.0 1.0
C67 A:1YT501 3.0 45.9 1.0
O A:GLN12 3.0 34.6 1.0
CA A:GLN12 3.1 37.7 1.0
N A:GLY13 3.2 33.4 1.0
CA A:GLY13 3.7 33.7 1.0
O A:GLY11 3.8 40.4 1.0
CZ2 A:TRP115 4.0 37.0 1.0
N A:GLN12 4.0 38.8 1.0
C8 A:1YT501 4.0 38.1 1.0
NE1 A:TRP115 4.2 36.1 1.0
CB A:GLN12 4.2 38.1 1.0
O70 A:1YT501 4.3 51.9 1.0
C A:GLY11 4.3 41.1 1.0
CE2 A:TRP115 4.5 36.6 1.0
O A:HOH658 4.7 31.5 1.0
CD1 A:LEU30 4.7 31.3 1.0
C14 A:1YT501 4.7 35.3 1.0
CG1 A:ILE110 4.7 45.0 1.0
O A:HOH686 4.8 37.3 1.0
O A:GLY230 5.0 33.3 1.0

Fluorine binding site 4 out of 12 in 4lxk

Go back to Fluorine Binding Sites List in 4lxk
Fluorine binding site 4 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D


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 Beta Secretase in Complex with Compound 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:43.2
occ:1.00
 F63 A:1YT501 0.0 43.2 1.0
C10 A:1YT501 1.3 39.2 1.0
C11 A:1YT501 2.4 37.7 1.0
C9 A:1YT501 2.4 38.2 1.0
N64 A:1YT501 2.8 38.7 1.0
CD1 A:PHE108 3.1 32.9 1.0
O A:GLN73 3.3 49.5 0.5
CA A:PHE108 3.5 36.6 1.0
O A:HOH749 3.6 47.7 1.0
CA A:GLY74 3.6 44.5 0.5
C8 A:1YT501 3.7 38.1 1.0
C13 A:1YT501 3.7 35.2 1.0
O A:PHE108 3.7 37.5 1.0
O A:LYS107 3.7 38.2 1.0
CA A:GLY74 3.7 44.4 0.5
CE1 A:PHE108 3.8 33.9 1.0
CG A:PHE108 3.9 34.4 1.0
N A:GLY74 3.9 47.0 0.5
CB A:PHE108 4.0 33.7 1.0
CD2 A:TYR71 4.0 32.4 1.0
C A:PHE108 4.1 38.3 1.0
C14 A:1YT501 4.2 35.3 1.0
C A:GLN73 4.2 49.0 0.5
C A:GLY74 4.2 42.4 0.5
C A:GLY74 4.2 42.3 0.5
N A:GLY74 4.4 46.8 0.5
N A:PHE108 4.5 36.5 1.0
CG A:TYR71 4.5 34.3 1.0
C A:LYS107 4.5 38.5 1.0
CE2 A:TYR71 4.6 32.5 1.0
O A:GLY74 4.6 42.0 0.5
CB A:TYR71 4.6 35.2 1.0
O A:GLY74 4.7 41.6 0.5
N A:LYS75 4.8 40.9 1.0
O7 A:1YT501 4.8 38.5 1.0
C16 A:1YT501 5.0 33.6 1.0

Fluorine binding site 5 out of 12 in 4lxk

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Fluorine binding site 5 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Beta Secretase in Complex with Compound 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:43.1
occ:1.00
 F1 B:1YT502 0.0 43.1 1.0
C2 B:1YT502 1.4 43.6 1.0
F4 B:1YT502 2.2 43.8 1.0
F3 B:1YT502 2.2 44.9 1.0
C5 B:1YT502 2.4 42.6 1.0
O7 B:1YT502 2.8 39.6 1.0
O B:GLY230 3.2 33.0 1.0
CD1 B:LEU30 3.3 32.5 1.0
CD2 B:LEU30 3.5 31.8 1.0
C14 B:1YT502 3.5 35.4 1.0
CA B:GLY13 3.5 35.3 1.0
C8 B:1YT502 3.6 39.5 1.0
O B:HOH717 3.6 38.8 1.0
C67 B:1YT502 3.8 45.7 1.0
N B:GLY13 3.8 36.8 1.0
CG B:LEU30 4.0 33.7 1.0
C B:GLY230 4.0 32.9 1.0
C B:GLN12 4.1 38.3 1.0
O B:GLN12 4.2 38.5 1.0
CA B:GLY230 4.2 31.9 1.0
CZ2 B:TRP115 4.5 36.0 1.0
O B:HOH690 4.8 35.2 1.0
O B:HOH675 4.8 31.9 1.0
C13 B:1YT502 4.8 35.2 1.0
O70 B:1YT502 4.8 50.5 1.0
C B:GLY13 4.9 35.3 1.0
CA B:GLN12 4.9 39.6 1.0
C9 B:1YT502 4.9 39.8 1.0
NE1 B:TRP115 5.0 36.0 1.0
O B:SER229 5.0 29.6 1.0

Fluorine binding site 6 out of 12 in 4lxk

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Fluorine binding site 6 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Beta Secretase in Complex with Compound 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:44.9
occ:1.00
 F3 B:1YT502 0.0 44.9 1.0
C2 B:1YT502 1.4 43.6 1.0
F1 B:1YT502 2.2 43.1 1.0
F4 B:1YT502 2.2 43.8 1.0
C5 B:1YT502 2.4 42.6 1.0
C67 B:1YT502 2.9 45.7 1.0
O B:HOH717 3.0 38.8 1.0
O B:HOH690 3.1 35.2 1.0
N B:GLY13 3.2 36.8 1.0
OG1 B:THR232 3.3 36.4 1.0
CA B:GLY13 3.6 35.3 1.0
O B:GLY230 3.6 33.0 1.0
C B:GLN12 3.6 38.3 1.0
O7 B:1YT502 3.6 39.6 1.0
O B:GLY11 3.7 40.3 1.0
CA B:GLN12 3.9 39.6 1.0
C B:GLY11 4.1 39.6 1.0
N B:GLN12 4.1 38.9 1.0
O70 B:1YT502 4.2 50.5 1.0
O B:GLN12 4.3 38.5 1.0
O B:HOH779 4.4 53.9 1.0
C B:GLY230 4.5 32.9 1.0
O B:HOH704 4.5 38.5 1.0
N B:THR232 4.6 33.0 1.0
CB B:THR232 4.6 34.9 1.0
C8 B:1YT502 4.7 39.5 1.0
C14 B:1YT502 4.9 35.4 1.0
CA B:THR232 4.9 34.6 1.0
C B:THR231 5.0 33.5 1.0

Fluorine binding site 7 out of 12 in 4lxk

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Fluorine binding site 7 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Beta Secretase in Complex with Compound 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:43.8
occ:1.00
 F4 B:1YT502 0.0 43.8 1.0
C2 B:1YT502 1.4 43.6 1.0
F1 B:1YT502 2.2 43.1 1.0
F3 B:1YT502 2.2 44.9 1.0
C5 B:1YT502 2.4 42.6 1.0
O7 B:1YT502 2.7 39.6 1.0
C B:GLN12 2.7 38.3 1.0
O B:GLN12 2.9 38.5 1.0
C67 B:1YT502 3.0 45.7 1.0
CA B:GLN12 3.1 39.6 1.0
N B:GLY13 3.2 36.8 1.0
CA B:GLY13 3.6 35.3 1.0
CZ2 B:TRP115 3.9 36.0 1.0
NE1 B:TRP115 4.0 36.0 1.0
C8 B:1YT502 4.1 39.5 1.0
O B:GLY11 4.1 40.3 1.0
N B:GLN12 4.1 38.9 1.0
CB B:GLN12 4.2 41.7 1.0
O70 B:1YT502 4.3 50.5 1.0
CE2 B:TRP115 4.3 34.7 1.0
CD1 B:LEU30 4.4 32.5 1.0
C B:GLY11 4.5 39.6 1.0
C14 B:1YT502 4.7 35.4 1.0
O B:HOH690 4.7 35.2 1.0
CG1 B:ILE110 4.8 46.5 1.0
O B:HOH717 4.9 38.8 1.0
CD2 B:LEU30 4.9 31.8 1.0
C B:GLY13 4.9 35.3 1.0
O B:GLY230 5.0 33.0 1.0

Fluorine binding site 8 out of 12 in 4lxk

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Fluorine binding site 8 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human Beta Secretase in Complex with Compound 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:41.2
occ:1.00
 F63 B:1YT502 0.0 41.2 1.0
C10 B:1YT502 1.3 40.3 1.0
C9 B:1YT502 2.4 39.8 1.0
C11 B:1YT502 2.4 36.4 1.0
N64 B:1YT502 2.8 41.3 1.0
CD1 B:PHE108 3.0 35.5 1.0
O B:GLN73 3.3 41.0 0.5
CA B:PHE108 3.5 37.9 1.0
O B:HOH727 3.5 43.0 1.0
CA B:GLY74 3.6 38.9 0.5
CA B:GLY74 3.6 38.2 0.5
C8 B:1YT502 3.7 39.5 1.0
C13 B:1YT502 3.7 35.2 1.0
O B:PHE108 3.7 37.2 1.0
CE1 B:PHE108 3.8 34.5 1.0
O B:LYS107 3.8 41.0 1.0
CG B:PHE108 3.9 34.9 1.0
N B:GLY74 3.9 41.1 0.5
CD2 B:TYR71 4.0 32.1 1.0
CB B:PHE108 4.0 36.6 1.0
C B:PHE108 4.1 38.1 1.0
C14 B:1YT502 4.2 35.4 1.0
C B:GLN73 4.2 42.5 0.5
C B:GLY74 4.3 37.7 0.5
C B:GLY74 4.3 37.3 0.5
N B:GLY74 4.4 39.8 0.5
CG B:TYR71 4.4 32.6 1.0
N B:PHE108 4.5 38.8 1.0
O B:HOH785 4.5 48.7 1.0
CE2 B:TYR71 4.5 29.9 1.0
C B:LYS107 4.6 40.6 1.0
CB B:TYR71 4.6 33.0 1.0
N B:LYS75 4.8 35.8 1.0
O B:GLY74 4.8 37.0 0.5
O B:GLY74 4.8 36.6 0.5
O7 B:1YT502 4.8 39.6 1.0
C16 B:1YT502 5.0 31.4 1.0

Fluorine binding site 9 out of 12 in 4lxk

Go back to Fluorine Binding Sites List in 4lxk
Fluorine binding site 9 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Beta Secretase in Complex with Compound 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:42.5
occ:1.00
 F1 C:1YT501 0.0 42.5 1.0
C2 C:1YT501 1.4 41.5 1.0
F4 C:1YT501 2.2 40.0 1.0
F3 C:1YT501 2.2 40.9 1.0
C5 C:1YT501 2.4 41.6 1.0
O7 C:1YT501 2.8 38.4 1.0
O C:GLY230 3.3 32.3 1.0
CD1 C:LEU30 3.4 32.3 1.0
C14 C:1YT501 3.5 35.3 1.0
CD2 C:LEU30 3.5 31.6 1.0
CA C:GLY13 3.5 34.4 1.0
C8 C:1YT501 3.6 38.5 1.0
O C:HOH621 3.6 47.1 1.0
C67 C:1YT501 3.8 44.9 1.0
N C:GLY13 3.8 34.7 1.0
CG C:LEU30 4.0 32.4 1.0
C C:GLN12 4.1 35.4 1.0
C C:GLY230 4.1 31.8 1.0
O C:GLN12 4.2 34.8 1.0
CA C:GLY230 4.3 29.9 1.0
CZ2 C:TRP115 4.4 35.9 1.0
O C:HOH672 4.7 31.6 1.0
O70 C:1YT501 4.8 51.2 1.0
C13 C:1YT501 4.8 35.6 1.0
C C:GLY13 4.9 35.1 1.0
CA C:GLN12 4.9 38.3 1.0
NE1 C:TRP115 4.9 36.9 1.0
CE2 C:TRP115 4.9 37.9 1.0
C9 C:1YT501 4.9 37.8 1.0
O C:HOH688 5.0 35.6 1.0

Fluorine binding site 10 out of 12 in 4lxk

Go back to Fluorine Binding Sites List in 4lxk
Fluorine binding site 10 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Compound 11D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human Beta Secretase in Complex with Compound 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:40.9
occ:1.00
 F3 C:1YT501 0.0 40.9 1.0
C2 C:1YT501 1.4 41.5 1.0
F1 C:1YT501 2.2 42.5 1.0
F4 C:1YT501 2.2 40.0 1.0
C5 C:1YT501 2.4 41.6 1.0
C67 C:1YT501 2.9 44.9 1.0
O C:HOH672 3.0 31.6 1.0
O C:HOH621 3.1 47.1 1.0
N C:GLY13 3.1 34.7 1.0
OG1 C:THR232 3.4 36.0 1.0
O C:GLY11 3.5 41.8 1.0
C C:GLN12 3.6 35.4 1.0
CA C:GLY13 3.6 34.4 1.0
O7 C:1YT501 3.6 38.4 1.0
O C:GLY230 3.7 32.3 1.0
CA C:GLN12 3.8 38.3 1.0
C C:GLY11 3.9 42.7 1.0
N C:GLN12 4.1 39.9 1.0
O70 C:1YT501 4.2 51.2 1.0
O C:GLN12 4.3 34.8 1.0
O C:HOH804 4.4 55.5 1.0
C C:GLY230 4.6 31.8 1.0
N C:THR232 4.6 33.2 1.0
O C:HOH784 4.7 50.3 1.0
CB C:THR232 4.7 35.2 1.0
C8 C:1YT501 4.7 38.5 1.0
C14 C:1YT501 4.9 35.3 1.0
CA C:THR232 5.0 34.4 1.0
CA C:GLY11 5.0 44.4 1.0

Reference:

H.Rueeger, R.Lueoend, R.Machauer, S.J.Veenstra, L.H.Jacobson, M.Staufenbiel, S.Desrayaud, J.M.Rondeau, H.Mobitz, U.Neumann. Discovery of Cyclic Sulfoxide Hydroxyethylamines As Potent and Selective Beta-Site App-Cleaving Enzyme 1 (BACE1) Inhibitors: Structure Based Design and in Vivo Reduction of Amyloid Beta-Peptides. Bioorg.Med.Chem.Lett. V. 23 5300 2013.
ISSN: ISSN 0960-894X
PubMed: 23981898
DOI: 10.1016/J.BMCL.2013.07.071
Page generated: Thu Aug 1 03:32:18 2024

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