Atomistry » Fluorine » PDB 3hky-3ig6 » 3i25
Atomistry »
  Fluorine »
    PDB 3hky-3ig6 »
      3i25 »

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

Last articles

Cl in 4CQG
Cl in 4CQD
Cl in 4CQC
Cl in 4CR5
Cl in 4CQ1
Cl in 4CQA
Cl in 4CQB
Cl in 4CPX
Cl in 4CPW
Cl in 4CPU
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy