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Fluorine in PDB 4d89: Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Soaking Experiment

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

All present enzymatic activity of Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Soaking 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 Soaking Experiment, PDB code: 4d89 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) 42.45 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.771, 73.501, 103.992, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Soaking Experiment (pdb code 4d89). 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 Beta Secretase in Complex with Nvp-BXD552, Derived From A Soaking Experiment, PDB code: 4d89:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4d89

Go back to Fluorine Binding Sites List in 4d89
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Soaking 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 Soaking Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:20.7
occ:1.00
 F1 A:BXD501 0.0 20.7 1.0
C2 A:BXD501 1.4 21.4 1.0
F3 A:BXD501 2.2 20.3 1.0
F4 A:BXD501 2.2 21.3 1.0
C5 A:BXD501 2.4 21.1 1.0
O7 A:BXD501 2.7 18.6 1.0
C A:GLN60 2.9 16.2 1.0
C68 A:BXD501 2.9 24.6 1.0
O A:GLN60 3.1 16.0 1.0
CA A:GLN60 3.2 16.6 1.0
N A:GLY61 3.3 15.5 1.0
CD1 A:ILE158 3.3 21.8 0.5
CZ2 A:TRP163 3.7 14.0 1.0
CA A:GLY61 3.7 15.8 1.0
NE1 A:TRP163 3.9 12.8 1.0
C8 A:BXD501 3.9 19.0 1.0
O A:GLY59 4.0 16.9 1.0
CE2 A:TRP163 4.2 13.3 1.0
N A:GLN60 4.2 16.0 1.0
O71 A:BXD501 4.3 27.0 0.5
CB A:GLN60 4.3 20.4 1.0
O71 A:BXD501 4.3 27.8 0.5
C A:GLY59 4.5 15.5 1.0
CD1 A:LEU78 4.5 13.5 1.0
C14 A:BXD501 4.6 16.8 1.0
CG1 A:ILE158 4.7 22.6 0.5
CG1 A:ILE158 4.7 22.3 0.5
O A:GLY278 4.8 17.6 1.0
CH2 A:TRP163 4.8 13.7 1.0
O A:HOH617 4.9 17.5 1.0
CD2 A:LEU78 4.9 15.1 1.0
C9 A:BXD501 5.0 20.1 1.0
N65 A:BXD501 5.0 20.7 1.0

Fluorine binding site 2 out of 4 in 4d89

Go back to Fluorine Binding Sites List in 4d89
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Soaking 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 Soaking Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:20.3
occ:1.00
 F3 A:BXD501 0.0 20.3 1.0
C2 A:BXD501 1.4 21.4 1.0
F1 A:BXD501 2.2 20.7 1.0
F4 A:BXD501 2.2 21.3 1.0
C5 A:BXD501 2.4 21.1 1.0
O7 A:BXD501 2.7 18.6 1.0
O A:GLY278 3.1 17.6 1.0
C14 A:BXD501 3.3 16.8 1.0
CD2 A:LEU78 3.3 15.1 1.0
CD1 A:LEU78 3.3 13.5 1.0
C8 A:BXD501 3.3 19.0 1.0
CA A:GLY61 3.7 15.8 1.0
C68 A:BXD501 3.8 24.6 1.0
CG A:LEU78 3.9 11.3 1.0
C A:GLY278 4.0 17.1 1.0
O A:HOH669 4.0 24.4 1.0
N A:GLY61 4.0 15.5 1.0
CZ2 A:TRP163 4.1 14.0 1.0
C A:GLN60 4.2 16.2 1.0
O A:GLN60 4.3 16.0 1.0
CA A:GLY278 4.3 15.0 1.0
C13 A:BXD501 4.6 16.2 1.0
CE2 A:TRP163 4.6 13.3 1.0
NE1 A:TRP163 4.6 12.8 1.0
C9 A:BXD501 4.6 20.1 1.0
O71 A:BXD501 4.7 27.0 0.5
O71 A:BXD501 4.8 27.8 0.5
CH2 A:TRP163 4.9 13.7 1.0

Fluorine binding site 3 out of 4 in 4d89

Go back to Fluorine Binding Sites List in 4d89
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Soaking 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 Soaking Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:21.3
occ:1.00
 F4 A:BXD501 0.0 21.3 1.0
C2 A:BXD501 1.4 21.4 1.0
F3 A:BXD501 2.2 20.3 1.0
F1 A:BXD501 2.2 20.7 1.0
C5 A:BXD501 2.4 21.1 1.0
C68 A:BXD501 3.0 24.6 1.0
N A:GLY61 3.0 15.5 1.0
O A:HOH617 3.1 17.5 1.0
O A:HOH669 3.1 24.4 1.0
CA A:GLY61 3.3 15.8 1.0
OG1 A:THR280 3.4 14.8 1.0
O A:GLY278 3.4 17.6 1.0
C A:GLN60 3.5 16.2 1.0
O7 A:BXD501 3.6 18.6 1.0
O A:GLY59 3.8 16.9 1.0
O71 A:BXD501 3.9 27.0 0.5
CA A:GLN60 3.9 16.6 1.0
O71 A:BXD501 4.2 27.8 0.5
C A:GLY59 4.2 15.5 1.0
N A:GLN60 4.2 16.0 1.0
O A:GLN60 4.2 16.0 1.0
C A:GLY278 4.4 17.1 1.0
N A:THR280 4.5 13.0 1.0
C8 A:BXD501 4.6 19.0 1.0
O A:HOH657 4.6 24.6 1.0
CB A:THR280 4.7 14.1 1.0
C14 A:BXD501 4.7 16.8 1.0
C A:GLY61 4.8 14.1 1.0
CD1 A:LEU78 4.9 13.5 1.0
CA A:THR280 4.9 12.8 1.0
C72 A:BXD501 5.0 27.2 0.5
C A:THR279 5.0 14.7 1.0

Fluorine binding site 4 out of 4 in 4d89

Go back to Fluorine Binding Sites List in 4d89
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXD552, Derived From A Soaking 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 Soaking Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:23.4
occ:1.00
 F64 A:BXD501 0.0 23.4 1.0
C10 A:BXD501 1.3 19.9 1.0
C9 A:BXD501 2.4 20.1 1.0
C11 A:BXD501 2.4 18.7 1.0
N65 A:BXD501 2.8 20.7 1.0
CD1 A:PHE156 3.0 18.1 1.0
O A:GLN121 3.2 29.4 1.0
CA A:PHE156 3.5 19.6 1.0
CE1 A:PHE156 3.6 16.1 1.0
O A:PHE156 3.6 18.3 1.0
C8 A:BXD501 3.7 19.0 1.0
C13 A:BXD501 3.7 16.2 1.0
CA A:GLY122 3.8 23.3 1.0
O A:HOH707 3.8 39.7 1.0
CG A:PHE156 3.9 17.5 1.0
O A:LYS155 3.9 23.2 1.0
CD2 A:TYR119 4.0 18.7 1.0
C A:PHE156 4.0 18.4 1.0
CB A:PHE156 4.1 16.8 1.0
C14 A:BXD501 4.1 16.8 1.0
O A:HOH735 4.2 33.6 1.0
C A:GLN121 4.2 28.6 1.0
C A:GLY122 4.3 21.2 1.0
CG A:TYR119 4.5 16.3 1.0
CE2 A:TYR119 4.5 18.2 1.0
N A:GLY122 4.5 26.0 1.0
N A:PHE156 4.5 20.6 1.0
C A:LYS155 4.6 23.2 1.0
O A:GLY122 4.6 21.2 1.0
CB A:TYR119 4.7 17.3 1.0
O7 A:BXD501 4.8 18.6 1.0
N A:LYS123 4.9 20.4 1.0
CZ A:PHE156 4.9 16.8 1.0
C16 A:BXD501 5.0 17.2 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 00:54:56 2024

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