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Fluorine in PDB 4d8c: Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment

Enzymatic activity of Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment

All present enzymatic activity of Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment, PDB code: 4d8c 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) 70.95 / 2.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.133, 103.505, 100.409, 90.00, 103.98, 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 Nvp-BXD552, Derived From A Co-Crystallization Experiment (pdb code 4d8c). 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 Nvp-BXD552, Derived From A Co-Crystallization Experiment, PDB code: 4d8c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4d8c

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Fluorine binding site 1 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment


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 Nvp-BXD552, Derived From A Co-Crystallization Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:34.3
occ:1.00
 F1 A:BXD501 0.0 34.3 1.0
C2 A:BXD501 1.4 35.5 1.0
F3 A:BXD501 2.2 34.6 1.0
F4 A:BXD501 2.2 37.9 1.0
C5 A:BXD501 2.4 37.2 1.0
O7 A:BXD501 2.7 32.4 1.0
C A:GLN12 2.8 28.2 1.0
C68 A:BXD501 3.0 40.9 1.0
O A:GLN12 3.0 27.8 1.0
CA A:GLN12 3.2 30.0 1.0
N A:GLY13 3.2 28.5 1.0
CD1 A:ILE110 3.5 41.9 1.0
CA A:GLY13 3.7 27.9 1.0
O A:GLY11 4.0 33.2 1.0
C8 A:BXD501 4.0 32.1 1.0
CZ2 A:TRP115 4.0 34.0 1.0
NE1 A:TRP115 4.1 32.8 1.0
N A:GLN12 4.2 30.3 1.0
O71 A:BXD501 4.3 48.3 1.0
CB A:GLN12 4.3 29.6 1.0
CE2 A:TRP115 4.4 32.7 1.0
C A:GLY11 4.4 31.8 1.0
CD1 A:LEU30 4.5 24.5 1.0
C14 A:BXD501 4.6 32.4 1.0
O A:HOH617 4.7 29.1 1.0
O A:GLY219 4.8 31.8 1.0
CD2 A:LEU30 4.9 27.0 1.0
CG1 A:ILE110 4.9 39.3 1.0
O A:HOH647 4.9 35.1 1.0

Fluorine binding site 2 out of 12 in 4d8c

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Fluorine binding site 2 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment


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 Nvp-BXD552, Derived From A Co-Crystallization Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:34.6
occ:1.00
 F3 A:BXD501 0.0 34.6 1.0
C2 A:BXD501 1.3 35.5 1.0
F1 A:BXD501 2.2 34.3 1.0
F4 A:BXD501 2.2 37.9 1.0
C5 A:BXD501 2.4 37.2 1.0
O7 A:BXD501 2.8 32.4 1.0
O A:GLY219 3.1 31.8 1.0
CD1 A:LEU30 3.3 24.5 1.0
C14 A:BXD501 3.3 32.4 1.0
CD2 A:LEU30 3.4 27.0 1.0
C8 A:BXD501 3.4 32.1 1.0
C68 A:BXD501 3.7 40.9 1.0
CA A:GLY13 3.8 27.9 1.0
C A:GLY219 3.9 30.6 1.0
O A:HOH647 3.9 35.1 1.0
CG A:LEU30 3.9 26.8 1.0
N A:GLY13 4.1 28.5 1.0
CA A:GLY219 4.2 29.3 1.0
C A:GLN12 4.3 28.2 1.0
O A:GLN12 4.3 27.8 1.0
CZ2 A:TRP115 4.5 34.0 1.0
C13 A:BXD501 4.6 32.1 1.0
C9 A:BXD501 4.8 32.5 1.0
O71 A:BXD501 4.8 48.3 1.0
O A:HOH617 4.9 29.1 1.0
NE1 A:TRP115 4.9 32.8 1.0
CE2 A:TRP115 5.0 32.7 1.0

Fluorine binding site 3 out of 12 in 4d8c

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Fluorine binding site 3 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment


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 Nvp-BXD552, Derived From A Co-Crystallization Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:37.9
occ:1.00
 F4 A:BXD501 0.0 37.9 1.0
C2 A:BXD501 1.4 35.5 1.0
F3 A:BXD501 2.2 34.6 1.0
F1 A:BXD501 2.2 34.3 1.0
C5 A:BXD501 2.4 37.2 1.0
C68 A:BXD501 3.0 40.9 1.0
O A:HOH647 3.0 35.1 1.0
O A:HOH617 3.0 29.1 1.0
N A:GLY13 3.2 28.5 1.0
O A:GLY219 3.4 31.8 1.0
OG1 A:THR221 3.4 33.5 1.0
CA A:GLY13 3.5 27.9 1.0
O7 A:BXD501 3.6 32.4 1.0
C A:GLN12 3.7 28.2 1.0
O A:GLY11 3.9 33.2 1.0
CA A:GLN12 4.0 30.0 1.0
C A:GLY219 4.2 30.6 1.0
C A:GLY11 4.2 31.8 1.0
O71 A:BXD501 4.3 48.3 1.0
N A:GLN12 4.3 30.3 1.0
O A:GLN12 4.3 27.8 1.0
N A:THR221 4.4 28.1 1.0
O A:HOH653 4.6 36.7 1.0
C8 A:BXD501 4.7 32.1 1.0
CB A:THR221 4.7 29.8 1.0
C A:THR220 4.7 30.1 1.0
C14 A:BXD501 4.8 32.4 1.0
CA A:THR221 4.8 30.4 1.0
N A:THR220 4.9 29.2 1.0
CA A:THR220 4.9 30.6 1.0
CD1 A:LEU30 4.9 24.5 1.0
C A:GLY13 5.0 28.1 1.0

Fluorine binding site 4 out of 12 in 4d8c

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Fluorine binding site 4 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment


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 Nvp-BXD552, Derived From A Co-Crystallization Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:36.5
occ:1.00
 F64 A:BXD501 0.0 36.5 1.0
C10 A:BXD501 1.3 32.8 1.0
C11 A:BXD501 2.4 33.5 1.0
C9 A:BXD501 2.4 32.5 1.0
N65 A:BXD501 2.8 30.2 1.0
CD1 A:PHE108 3.1 28.9 1.0
O A:GLN73 3.2 45.0 1.0
CA A:PHE108 3.5 33.2 1.0
C13 A:BXD501 3.7 32.1 1.0
C8 A:BXD501 3.7 32.1 1.0
O A:PHE108 3.7 34.1 1.0
CA A:GLY74 3.7 36.0 1.0
CE1 A:PHE108 3.8 29.7 1.0
O A:LYS107 3.8 35.6 1.0
O A:HOH705 3.8 42.7 1.0
CG A:PHE108 3.9 30.2 1.0
CD2 A:TYR71 4.0 29.0 1.0
CB A:PHE108 4.0 31.3 1.0
C A:PHE108 4.1 34.0 1.0
C A:GLN73 4.1 42.3 1.0
C14 A:BXD501 4.1 32.4 1.0
C A:GLY74 4.2 33.3 1.0
O A:HOH719 4.3 45.8 1.0
N A:GLY74 4.4 40.0 1.0
CG A:TYR71 4.4 30.7 1.0
CE2 A:TYR71 4.5 29.1 1.0
N A:PHE108 4.5 33.8 1.0
O A:GLY74 4.5 31.8 1.0
C A:LYS107 4.6 35.3 1.0
CB A:TYR71 4.7 31.3 1.0
N A:LYS75 4.8 31.6 1.0
O7 A:BXD501 4.8 32.4 1.0
C16 A:BXD501 4.9 30.7 1.0

Fluorine binding site 5 out of 12 in 4d8c

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Fluorine binding site 5 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment


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 Nvp-BXD552, Derived From A Co-Crystallization Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:38.0
occ:1.00
 F1 B:BXD501 0.0 38.0 1.0
C2 B:BXD501 1.4 38.1 1.0
F3 B:BXD501 2.2 39.4 1.0
F4 B:BXD501 2.2 40.5 1.0
C5 B:BXD501 2.4 39.1 1.0
O7 B:BXD501 2.7 35.7 1.0
C B:GLN12 2.8 35.4 1.0
O B:GLN12 2.9 35.1 1.0
C68 B:BXD501 3.0 42.5 1.0
CA B:GLN12 3.2 36.8 1.0
N B:GLY13 3.2 34.6 1.0
CD1 B:ILE110 3.5 43.6 1.0
CA B:GLY13 3.6 32.5 1.0
CZ2 B:TRP115 3.9 31.9 1.0
C8 B:BXD501 4.0 35.1 1.0
NE1 B:TRP115 4.0 31.3 1.0
O B:GLY11 4.2 38.4 1.0
CB B:GLN12 4.2 37.0 1.0
N B:GLN12 4.2 36.5 1.0
O71 B:BXD501 4.3 49.3 1.0
CE2 B:TRP115 4.3 30.9 1.0
CD1 B:LEU30 4.4 26.9 1.0
C B:GLY11 4.6 38.1 1.0
C14 B:BXD501 4.6 32.3 1.0
O B:HOH646 4.7 34.4 1.0
O B:HOH679 4.8 39.9 1.0
CD2 B:LEU30 4.8 26.2 1.0
CG1 B:ILE110 4.9 42.1 1.0
O B:GLY219 4.9 33.7 1.0
C B:GLY13 4.9 32.3 1.0

Fluorine binding site 6 out of 12 in 4d8c

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Fluorine binding site 6 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment


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 Nvp-BXD552, Derived From A Co-Crystallization Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:39.4
occ:1.00
 F3 B:BXD501 0.0 39.4 1.0
C2 B:BXD501 1.4 38.1 1.0
F1 B:BXD501 2.2 38.0 1.0
F4 B:BXD501 2.2 40.5 1.0
C5 B:BXD501 2.4 39.1 1.0
O7 B:BXD501 2.8 35.7 1.0
O B:GLY219 3.2 33.7 1.0
CD1 B:LEU30 3.2 26.9 1.0
CD2 B:LEU30 3.3 26.2 1.0
C14 B:BXD501 3.4 32.3 1.0
C8 B:BXD501 3.5 35.1 1.0
CA B:GLY13 3.7 32.5 1.0
O B:HOH679 3.7 39.9 1.0
C68 B:BXD501 3.7 42.5 1.0
CG B:LEU30 3.9 27.9 1.0
C B:GLY219 4.0 32.2 1.0
N B:GLY13 4.0 34.6 1.0
C B:GLN12 4.2 35.4 1.0
CA B:GLY219 4.2 30.0 1.0
O B:GLN12 4.2 35.1 1.0
CZ2 B:TRP115 4.4 31.9 1.0
C13 B:BXD501 4.7 32.9 1.0
O71 B:BXD501 4.8 49.3 1.0
C9 B:BXD501 4.8 33.6 1.0
NE1 B:TRP115 4.8 31.3 1.0
CE2 B:TRP115 4.9 30.9 1.0
O B:HOH646 4.9 34.4 1.0
C B:GLY13 4.9 32.3 1.0
O B:HOH618 5.0 28.8 1.0

Fluorine binding site 7 out of 12 in 4d8c

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Fluorine binding site 7 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment


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 Nvp-BXD552, Derived From A Co-Crystallization Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:40.5
occ:1.00
 F4 B:BXD501 0.0 40.5 1.0
C2 B:BXD501 1.4 38.1 1.0
F3 B:BXD501 2.2 39.4 1.0
F1 B:BXD501 2.2 38.0 1.0
C5 B:BXD501 2.4 39.1 1.0
O B:HOH679 2.8 39.9 1.0
C68 B:BXD501 2.9 42.5 1.0
O B:HOH646 3.0 34.4 1.0
N B:GLY13 3.1 34.6 1.0
CA B:GLY13 3.4 32.5 1.0
OG1 B:THR221 3.4 33.6 1.0
C B:GLN12 3.5 35.4 1.0
O B:GLY219 3.5 33.7 1.0
O7 B:BXD501 3.6 35.7 1.0
O B:GLY11 3.9 38.4 1.0
CA B:GLN12 3.9 36.8 1.0
O B:GLN12 4.2 35.1 1.0
N B:GLN12 4.2 36.5 1.0
C B:GLY11 4.2 38.1 1.0
O71 B:BXD501 4.3 49.3 1.0
C B:GLY219 4.3 32.2 1.0
N B:THR221 4.5 31.8 1.0
O B:HOH647 4.7 36.9 1.0
C8 B:BXD501 4.7 35.1 1.0
CB B:THR221 4.7 32.5 1.0
C14 B:BXD501 4.8 32.3 1.0
C B:THR220 4.8 31.6 1.0
CA B:THR221 4.9 31.4 1.0
C B:GLY13 4.9 32.3 1.0
CD1 B:LEU30 4.9 26.9 1.0

Fluorine binding site 8 out of 12 in 4d8c

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Fluorine binding site 8 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment


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 Nvp-BXD552, Derived From A Co-Crystallization Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:35.8
occ:1.00
 F64 B:BXD501 0.0 35.8 1.0
C10 B:BXD501 1.3 34.9 1.0
C11 B:BXD501 2.4 32.9 1.0
C9 B:BXD501 2.4 33.6 1.0
N65 B:BXD501 2.8 35.1 1.0
CD1 B:PHE108 3.1 32.6 1.0
O B:GLN73 3.2 40.9 1.0
CA B:PHE108 3.5 35.4 1.0
C13 B:BXD501 3.7 32.9 1.0
C8 B:BXD501 3.7 35.1 1.0
O B:PHE108 3.7 35.9 1.0
CA B:GLY74 3.7 33.3 1.0
CE1 B:PHE108 3.8 32.0 1.0
O B:LYS107 3.8 37.7 1.0
O B:HOH704 3.9 43.8 1.0
CG B:PHE108 3.9 32.6 1.0
CD2 B:TYR71 4.0 28.3 1.0
C B:PHE108 4.0 36.2 1.0
CB B:PHE108 4.0 33.8 1.0
C14 B:BXD501 4.1 32.3 1.0
C B:GLN73 4.2 40.1 1.0
C B:GLY74 4.3 32.4 1.0
O B:HOH658 4.3 37.7 1.0
CE2 B:TYR71 4.4 26.6 1.0
CG B:TYR71 4.5 29.8 1.0
N B:GLY74 4.5 36.7 1.0
N B:PHE108 4.5 35.9 1.0
C B:LYS107 4.6 37.6 1.0
CB B:TYR71 4.7 30.0 1.0
O B:GLY74 4.7 30.9 1.0
N B:LYS75 4.8 29.5 1.0
O7 B:BXD501 4.8 35.7 1.0
C16 B:BXD501 4.9 30.1 1.0

Fluorine binding site 9 out of 12 in 4d8c

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Fluorine binding site 9 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment


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 Nvp-BXD552, Derived From A Co-Crystallization Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:35.5
occ:1.00
 F1 C:BXD401 0.0 35.5 1.0
C2 C:BXD401 1.4 36.6 1.0
F3 C:BXD401 2.2 37.2 1.0
F4 C:BXD401 2.2 39.6 1.0
C5 C:BXD401 2.4 37.8 1.0
O7 C:BXD401 2.7 34.0 1.0
C C:GLN12 2.8 32.5 1.0
O C:GLN12 2.9 30.7 1.0
C68 C:BXD401 3.0 41.4 1.0
CA C:GLN12 3.2 35.0 1.0
N C:GLY13 3.2 31.3 1.0
CD1 C:ILE110 3.5 43.7 1.0
CA C:GLY13 3.6 31.8 1.0
CZ2 C:TRP115 3.9 32.6 1.0
O C:GLY11 4.0 39.5 1.0
NE1 C:TRP115 4.0 32.4 1.0
C8 C:BXD401 4.0 32.8 1.0
N C:GLN12 4.2 36.8 1.0
CB C:GLN12 4.2 36.7 1.0
O71 C:BXD401 4.3 45.8 1.0
CE2 C:TRP115 4.3 31.6 1.0
CD1 C:LEU30 4.4 28.4 1.0
C C:GLY11 4.5 39.4 1.0
O C:HOH603 4.6 43.2 1.0
C14 C:BXD401 4.6 30.1 1.0
O C:HOH514 4.7 29.4 1.0
CD2 C:LEU30 4.8 28.9 1.0
CG1 C:ILE110 4.9 40.9 1.0
C C:GLY13 5.0 30.9 1.0
O C:GLY223 5.0 32.1 1.0

Fluorine binding site 10 out of 12 in 4d8c

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Fluorine binding site 10 out of 12 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Co-Crystallization Experiment


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 Nvp-BXD552, Derived From A Co-Crystallization Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:37.2
occ:1.00
 F3 C:BXD401 0.0 37.2 1.0
C2 C:BXD401 1.4 36.6 1.0
F1 C:BXD401 2.2 35.5 1.0
F4 C:BXD401 2.2 39.6 1.0
C5 C:BXD401 2.4 37.8 1.0
O7 C:BXD401 2.8 34.0 1.0
O C:GLY223 3.2 32.1 1.0
CD1 C:LEU30 3.2 28.4 1.0
CD2 C:LEU30 3.3 28.9 1.0
C14 C:BXD401 3.4 30.1 1.0
C8 C:BXD401 3.5 32.8 1.0
O C:HOH603 3.5 43.2 1.0
CA C:GLY13 3.7 31.8 1.0
C68 C:BXD401 3.7 41.4 1.0
CG C:LEU30 3.9 27.5 1.0
N C:GLY13 4.0 31.3 1.0
C C:GLY223 4.1 31.7 1.0
C C:GLN12 4.2 32.5 1.0
O C:GLN12 4.2 30.7 1.0
CA C:GLY223 4.3 29.9 1.0
CZ2 C:TRP115 4.4 32.6 1.0
C13 C:BXD401 4.7 30.9 1.0
NE1 C:TRP115 4.8 32.4 1.0
O71 C:BXD401 4.8 45.8 1.0
C9 C:BXD401 4.8 32.1 1.0
CE2 C:TRP115 4.9 31.6 1.0
O C:HOH510 4.9 27.9 1.0
O C:HOH514 4.9 29.4 1.0
C C:GLY13 5.0 30.9 1.0

Reference:

H.Rueeger, R.Lueoend, O.Rogel, J.M.Rondeau, H.Mobitz, R.Machauer, L.Jacobson, M.Staufenbiel, S.Desrayaud, U.Neumann. Discovery of Cyclic Sulfone Hydroxyethylamines As Potent and Selective Beta-Site App-Cleaving Enzyme 1 (BACE1) Inhibitors: Structure Based Design and in Vivo Reduction of Amyloid Beta-Peptides J.Med.Chem. V. 55 3364 2012.
ISSN: ISSN 0022-2623
PubMed: 22380629
DOI: 10.1021/JM300069Y
Page generated: Thu Aug 1 00:55:46 2024

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