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Fluorine in PDB 3i25: Potent Beta-Secretase 1 Hydroxyethylene Inhibitor

Enzymatic activity of Potent Beta-Secretase 1 Hydroxyethylene Inhibitor

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

Protein crystallography data

The structure of Potent Beta-Secretase 1 Hydroxyethylene Inhibitor, PDB code: 3i25 was solved by J.D.Lindberg, N.Borkakoti, S.Nystrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.16 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.417, 102.483, 100.186, 90.00, 103.53, 90.00
R / Rfree (%) 20 / 23.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Potent Beta-Secretase 1 Hydroxyethylene Inhibitor (pdb code 3i25). 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 Hydroxyethylene Inhibitor, PDB code: 3i25:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3i25

Go back to Fluorine Binding Sites List in 3i25
Fluorine binding site 1 out of 6 in the Potent Beta-Secretase 1 Hydroxyethylene 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 Hydroxyethylene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F531

b:34.1
occ:1.00
 F2 A:MV7531 0.0 34.1 1.0
C26 A:MV7531 1.3 32.8 1.0
C27 A:MV7531 2.3 32.2 1.0
C25 A:MV7531 2.4 32.3 1.0
O A:HOH430 3.2 35.5 1.0
O A:PHE108 3.2 36.9 1.0
CD1 A:ILE110 3.3 38.8 1.0
NE2 A:GLN73 3.4 37.5 1.0
C22 A:MV7531 3.6 30.7 1.0
C24 A:MV7531 3.6 31.6 1.0
CG1 A:ILE110 3.6 38.7 1.0
CZ2 A:TRP115 3.8 30.1 1.0
CH2 A:TRP115 3.9 29.9 1.0
C39 A:MV7531 3.9 31.2 1.0
C23 A:MV7531 4.1 32.4 1.0
N5 A:MV7531 4.2 34.8 1.0
C A:PHE108 4.4 36.5 1.0
CD A:GLN73 4.4 37.0 1.0
C37 A:MV7531 4.4 32.4 1.0
C38 A:MV7531 4.5 33.6 1.0
C35 A:MV7531 4.6 27.2 1.0
O6 A:MV7531 4.7 31.9 1.0
F1 A:MV7531 4.7 33.7 1.0
CG A:GLN73 4.8 35.1 1.0
O10 A:MV7531 4.8 39.5 1.0
C36 A:MV7531 4.9 29.7 1.0
O A:LYS107 4.9 39.2 1.0
CA A:PHE108 5.0 36.2 1.0

Fluorine binding site 2 out of 6 in 3i25

Go back to Fluorine Binding Sites List in 3i25
Fluorine binding site 2 out of 6 in the Potent Beta-Secretase 1 Hydroxyethylene 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 Hydroxyethylene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F531

b:33.7
occ:1.00
 F1 A:MV7531 0.0 33.7 1.0
C24 A:MV7531 1.3 31.6 1.0
C25 A:MV7531 2.3 32.3 1.0
C23 A:MV7531 2.4 32.4 1.0
N A:GLY74 2.9 33.9 1.0
O A:GLY74 3.2 31.1 1.0
C A:GLY74 3.3 32.7 1.0
CA A:GLY74 3.3 33.2 1.0
CD2 A:TYR71 3.4 29.9 1.0
CD1 A:PHE108 3.5 30.7 1.0
CB A:TYR71 3.5 29.7 1.0
C26 A:MV7531 3.6 32.8 1.0
C22 A:MV7531 3.7 30.7 1.0
CG A:TYR71 3.7 28.3 1.0
C A:GLN73 3.8 34.4 1.0
CB A:GLN73 4.0 34.5 1.0
N A:LYS75 4.1 33.2 1.0
CE1 A:PHE108 4.1 29.0 1.0
C27 A:MV7531 4.1 32.2 1.0
O A:LYS107 4.2 39.2 1.0
CA A:GLN73 4.2 33.8 1.0
N A:GLN73 4.2 32.7 1.0
CE2 A:TYR71 4.3 25.1 1.0
CA A:PHE108 4.3 36.2 1.0
O7 A:MV7531 4.4 26.5 1.0
CG A:PHE108 4.5 33.3 1.0
CB A:PHE108 4.6 34.9 1.0
O A:GLN73 4.6 35.5 1.0
CA A:TYR71 4.7 31.4 1.0
F2 A:MV7531 4.7 34.1 1.0
CG A:GLN73 4.7 35.1 1.0
CD1 A:TYR71 4.8 26.5 1.0
O6 A:MV7531 4.8 31.9 1.0
C A:TYR71 4.9 31.9 1.0
C28 A:MV7531 4.9 28.6 1.0
N A:TYR71 4.9 31.3 1.0
CA A:LYS75 4.9 32.5 1.0
C A:LYS107 5.0 38.3 1.0
O A:PHE108 5.0 36.9 1.0

Fluorine binding site 3 out of 6 in 3i25

Go back to Fluorine Binding Sites List in 3i25
Fluorine binding site 3 out of 6 in the Potent Beta-Secretase 1 Hydroxyethylene 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 Hydroxyethylene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F531

b:33.0
occ:1.00
 F2 B:MV7531 0.0 33.0 1.0
C26 B:MV7531 1.3 29.3 1.0
C27 B:MV7531 2.3 28.6 1.0
C25 B:MV7531 2.4 29.1 1.0
O B:HOH422 3.1 35.1 1.0
CD1 B:ILE110 3.3 33.8 1.0
O B:PHE108 3.3 31.6 1.0
C22 B:MV7531 3.6 29.4 1.0
NE2 B:GLN73 3.6 34.4 1.0
CZ2 B:TRP115 3.6 25.1 1.0
CG1 B:ILE110 3.6 33.2 1.0
C24 B:MV7531 3.6 31.7 1.0
CH2 B:TRP115 3.6 26.1 1.0
C39 B:MV7531 3.8 26.7 1.0
C23 B:MV7531 4.1 26.7 1.0
N5 B:MV7531 4.3 29.8 1.0
C38 B:MV7531 4.5 28.9 1.0
C B:PHE108 4.5 32.4 1.0
C37 B:MV7531 4.5 29.1 1.0
CD B:GLN73 4.5 36.5 1.0
C35 B:MV7531 4.6 23.9 1.0
O6 B:MV7531 4.7 28.5 1.0
F1 B:MV7531 4.7 32.3 1.0
CG B:GLN73 4.7 32.8 1.0
O10 B:MV7531 4.8 32.0 1.0
CB B:ILE110 4.9 34.4 1.0
CZ3 B:TRP115 4.9 26.2 1.0
CE2 B:TRP115 4.9 25.7 1.0
C36 B:MV7531 5.0 23.3 1.0

Fluorine binding site 4 out of 6 in 3i25

Go back to Fluorine Binding Sites List in 3i25
Fluorine binding site 4 out of 6 in the Potent Beta-Secretase 1 Hydroxyethylene 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 Hydroxyethylene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F531

b:32.3
occ:1.00
 F1 B:MV7531 0.0 32.3 1.0
C24 B:MV7531 1.3 31.7 1.0
C25 B:MV7531 2.4 29.1 1.0
C23 B:MV7531 2.4 26.7 1.0
N B:GLY74 2.9 29.2 1.0
CA B:GLY74 3.2 28.1 1.0
C B:GLY74 3.3 27.7 1.0
CD2 B:TYR71 3.3 23.3 1.0
CD1 B:PHE108 3.3 29.0 1.0
O B:GLY74 3.3 27.4 1.0
CB B:TYR71 3.6 25.5 1.0
C26 B:MV7531 3.6 29.3 1.0
C22 B:MV7531 3.7 29.4 1.0
CG B:TYR71 3.7 24.6 1.0
C B:GLN73 3.8 30.6 1.0
CE1 B:PHE108 3.9 25.1 1.0
N B:LYS75 4.0 27.2 1.0
C27 B:MV7531 4.2 28.6 1.0
CE2 B:TYR71 4.2 24.7 1.0
CA B:GLN73 4.2 30.8 1.0
CB B:GLN73 4.3 31.8 1.0
CA B:PHE108 4.3 31.7 1.0
O B:LYS107 4.3 33.0 1.0
N B:GLN73 4.3 29.8 1.0
CG B:PHE108 4.4 29.8 1.0
O7 B:MV7531 4.5 24.0 1.0
CB B:PHE108 4.6 30.7 1.0
O B:GLN73 4.6 31.4 1.0
CG B:GLN73 4.7 32.8 1.0
F2 B:MV7531 4.7 33.0 1.0
CD1 B:TYR71 4.7 23.8 1.0
CA B:TYR71 4.8 26.9 1.0
O6 B:MV7531 4.8 28.5 1.0
CA B:LYS75 4.9 27.8 1.0
N B:TYR71 4.9 26.8 1.0
C28 B:MV7531 4.9 26.5 1.0
O B:PHE108 4.9 31.6 1.0

Fluorine binding site 5 out of 6 in 3i25

Go back to Fluorine Binding Sites List in 3i25
Fluorine binding site 5 out of 6 in the Potent Beta-Secretase 1 Hydroxyethylene 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 Hydroxyethylene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F531

b:34.0
occ:1.00
 F2 C:MV7531 0.0 34.0 1.0
C26 C:MV7531 1.3 33.0 1.0
C25 C:MV7531 2.3 32.7 1.0
C27 C:MV7531 2.3 32.1 1.0
O C:HOH428 3.1 37.5 1.0
CD1 C:ILE110 3.2 40.4 1.0
O C:PHE108 3.3 36.8 1.0
OE1 C:GLN73 3.5 48.6 1.0
C24 C:MV7531 3.6 33.9 1.0
CG1 C:ILE110 3.6 40.8 1.0
C22 C:MV7531 3.6 30.8 1.0
C39 C:MV7531 3.7 30.3 1.0
CZ2 C:TRP115 3.7 28.4 1.0
CH2 C:TRP115 3.9 28.2 1.0
C23 C:MV7531 4.1 31.8 1.0
N5 C:MV7531 4.2 30.8 1.0
C37 C:MV7531 4.3 31.3 1.0
C38 C:MV7531 4.3 30.3 1.0
CD C:GLN73 4.4 45.0 1.0
C C:PHE108 4.5 37.5 1.0
C35 C:MV7531 4.6 26.8 1.0
O10 C:MV7531 4.6 37.0 1.0
F1 C:MV7531 4.7 36.6 1.0
CG C:GLN73 4.7 39.5 1.0
O6 C:MV7531 4.7 31.6 1.0
C36 C:MV7531 4.9 28.3 1.0
O C:LYS107 4.9 39.9 1.0

Fluorine binding site 6 out of 6 in 3i25

Go back to Fluorine Binding Sites List in 3i25
Fluorine binding site 6 out of 6 in the Potent Beta-Secretase 1 Hydroxyethylene 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 Hydroxyethylene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F531

b:36.6
occ:1.00
 F1 C:MV7531 0.0 36.6 1.0
C24 C:MV7531 1.3 33.9 1.0
C23 C:MV7531 2.4 31.8 1.0
C25 C:MV7531 2.4 32.7 1.0
N C:GLY74 3.0 35.8 1.0
CA C:GLY74 3.2 35.0 1.0
C C:GLY74 3.3 34.6 1.0
CD1 C:PHE108 3.5 33.0 1.0
CD2 C:TYR71 3.5 27.8 1.0
O C:GLY74 3.5 33.9 1.0
C26 C:MV7531 3.6 33.0 1.0
C22 C:MV7531 3.6 30.8 1.0
CB C:TYR71 3.7 28.9 1.0
C C:GLN73 3.8 36.8 1.0
CG C:TYR71 3.8 28.4 1.0
CB C:GLN73 4.0 37.0 1.0
N C:LYS75 4.0 33.9 1.0
O C:LYS107 4.0 39.9 1.0
CE1 C:PHE108 4.1 34.5 1.0
C27 C:MV7531 4.1 32.1 1.0
CA C:PHE108 4.2 37.4 1.0
CA C:GLN73 4.3 36.2 1.0
CE2 C:TYR71 4.3 28.3 1.0
N C:GLN73 4.4 35.2 1.0
CG C:PHE108 4.5 35.8 1.0
O7 C:MV7531 4.6 33.3 1.0
CG C:GLN73 4.6 39.5 1.0
CB C:PHE108 4.6 37.0 1.0
O C:GLN73 4.6 38.5 1.0
F2 C:MV7531 4.7 34.0 1.0
O6 C:MV7531 4.8 31.6 1.0
CA C:TYR71 4.8 30.0 1.0
C C:LYS107 4.8 38.7 1.0
O C:HOH428 4.9 37.5 1.0
CD1 C:TYR71 4.9 27.6 1.0
C28 C:MV7531 4.9 29.7 1.0
O C:PHE108 4.9 36.8 1.0
N C:PHE108 5.0 37.9 1.0
CA C:LYS75 5.0 33.8 1.0

Reference:

C.Bjorklund, H.Adolfsson, K.Jansson, J.Lindberg, L.Vrang, A.Hallberg, A.Rosenquist, B.Samuelsson. Discovery of Potent Bace-1 Inhibitors Containing A New Hydroxyethylene (He) Scaffold: Exploration of P1' Alkoxy Residues and An Aminoethylene (Ae) Central Core Bioorg.Med.Chem. V. 18 1711 2010.
ISSN: ISSN 0968-0896
PubMed: 20122837
DOI: 10.1016/J.BMC.2009.12.051
Page generated: Wed Jul 31 19:24:21 2024

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