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Fluorine in PDB 3ixj: Crystal Structure of Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor

Enzymatic activity of Crystal Structure of Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor

All present enzymatic activity of Crystal Structure of Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor:
3.4.23.46;

Protein crystallography data

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

Resolution Low / High (Å) 62.99 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.913, 102.705, 100.417, 90.00, 103.42, 90.00
R / Rfree (%) 21.2 / 24.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor (pdb code 3ixj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor, PDB code: 3ixj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3ixj

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Fluorine binding site 1 out of 6 in the Crystal Structure of Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor


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 Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:14.6
occ:1.00
 F54 A:586500 0.0 14.6 1.0
C25 A:586500 1.3 13.5 1.0
C24 A:586500 2.3 13.2 1.0
C26 A:586500 2.4 11.6 1.0
O A:HOH736 2.8 21.8 1.0
NE2 A:GLN121 3.1 19.1 1.0
O A:PHE156 3.1 17.5 1.0
CD1 A:ILE158 3.3 20.7 1.0
CG1 A:ILE158 3.6 20.9 1.0
C23 A:586500 3.6 13.1 1.0
C21 A:586500 3.6 13.0 1.0
CZ2 A:TRP163 3.8 13.1 1.0
CH2 A:TRP163 3.9 12.6 1.0
C37 A:586500 4.0 12.1 1.0
C22 A:586500 4.1 10.8 1.0
CD A:GLN121 4.3 19.2 1.0
C A:PHE156 4.3 17.9 1.0
N4 A:586500 4.3 12.8 1.0
C35 A:586500 4.5 13.8 1.0
C34 A:586500 4.6 11.2 1.0
F55 A:586500 4.7 12.4 1.0
C29 A:586500 4.7 9.5 1.0
CG A:GLN121 4.8 18.0 1.0
O2 A:586500 4.8 11.8 1.0
O A:LYS155 4.8 19.8 1.0
CA A:PHE156 4.9 17.4 1.0
O6 A:586500 4.9 14.5 1.0

Fluorine binding site 2 out of 6 in 3ixj

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Fluorine binding site 2 out of 6 in the Crystal Structure of Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor


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 Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:12.4
occ:1.00
 F55 A:586500 0.0 12.4 1.0
C23 A:586500 1.4 13.1 1.0
C24 A:586500 2.4 13.2 1.0
C22 A:586500 2.4 10.8 1.0
N A:GLY122 2.9 17.5 1.0
CA A:GLY122 3.1 17.2 1.0
C A:GLY122 3.2 17.1 1.0
CD2 A:TYR119 3.3 11.5 1.0
CD1 A:PHE156 3.3 12.8 1.0
O A:GLY122 3.3 16.8 1.0
CB A:TYR119 3.6 14.1 1.0
C25 A:586500 3.6 13.5 1.0
C21 A:586500 3.7 13.0 1.0
CG A:TYR119 3.7 11.8 1.0
N A:LYS123 3.8 17.3 1.0
C A:GLN121 4.0 18.0 1.0
CE1 A:PHE156 4.0 11.8 1.0
CA A:PHE156 4.1 17.4 1.0
C26 A:586500 4.1 11.6 1.0
CE2 A:TYR119 4.2 11.6 1.0
O A:LYS155 4.2 19.8 1.0
CG A:PHE156 4.3 15.1 1.0
CB A:PHE156 4.3 16.3 1.0
CB A:GLN121 4.4 17.5 1.0
CA A:GLN121 4.5 17.5 1.0
N A:GLN121 4.6 16.6 1.0
O5 A:586500 4.7 9.0 1.0
CA A:LYS123 4.7 18.0 1.0
F54 A:586500 4.7 14.6 1.0
CA A:TYR119 4.7 15.4 1.0
O A:PHE156 4.8 17.5 1.0
CD1 A:TYR119 4.8 9.4 1.0
O A:GLN121 4.8 19.2 1.0
O2 A:586500 4.8 11.8 1.0
C A:LYS155 4.9 19.5 1.0
N A:PHE156 4.9 18.3 1.0
N A:TYR119 5.0 15.5 1.0
CG A:GLN121 5.0 18.0 1.0
C A:PHE156 5.0 17.9 1.0

Fluorine binding site 3 out of 6 in 3ixj

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Fluorine binding site 3 out of 6 in the Crystal Structure of Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor


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 Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F500

b:10.7
occ:1.00
 F54 B:586500 0.0 10.7 1.0
C25 B:586500 1.3 9.9 1.0
C26 B:586500 2.3 10.0 1.0
C24 B:586500 2.4 9.4 1.0
O B:HOH785 3.1 19.9 1.0
CD1 B:ILE158 3.2 15.7 1.0
O B:PHE156 3.3 15.4 1.0
CG1 B:ILE158 3.5 16.9 1.0
C21 B:586500 3.6 9.8 1.0
C23 B:586500 3.6 10.9 1.0
CZ2 B:TRP163 3.7 10.0 1.0
CH2 B:TRP163 3.9 8.7 1.0
C37 B:586500 3.9 10.4 1.0
C22 B:586500 4.1 8.5 1.0
N4 B:586500 4.4 10.2 1.0
CG B:GLN121 4.4 18.0 1.0
C34 B:586500 4.5 8.7 1.0
C B:PHE156 4.5 15.8 1.0
C35 B:586500 4.5 11.9 1.0
O6 B:586500 4.7 9.9 1.0
C29 B:586500 4.7 6.2 1.0
O2 B:586500 4.7 8.5 1.0
F55 B:586500 4.8 11.8 1.0
NE2 B:GLN121 4.8 25.3 1.0
CB B:GLN121 4.8 15.1 1.0
CB B:ILE158 4.9 18.3 1.0
O B:LYS155 5.0 16.2 1.0

Fluorine binding site 4 out of 6 in 3ixj

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Fluorine binding site 4 out of 6 in the Crystal Structure of Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor


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 Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F500

b:11.8
occ:1.00
 F55 B:586500 0.0 11.8 1.0
C23 B:586500 1.4 10.9 1.0
C22 B:586500 2.4 8.5 1.0
C24 B:586500 2.4 9.4 1.0
N B:GLY122 2.9 14.2 1.0
CA B:GLY122 3.2 12.8 1.0
CD1 B:PHE156 3.3 11.8 1.0
C B:GLY122 3.3 12.5 1.0
CD2 B:TYR119 3.3 5.3 1.0
O B:GLY122 3.4 11.7 1.0
CB B:TYR119 3.6 7.4 1.0
C25 B:586500 3.6 9.9 1.0
CG B:TYR119 3.7 8.3 1.0
C21 B:586500 3.7 9.8 1.0
C B:GLN121 3.9 14.7 1.0
CE1 B:PHE156 3.9 9.1 1.0
N B:LYS123 4.0 12.4 1.0
CB B:GLN121 4.1 15.1 1.0
C26 B:586500 4.1 10.0 1.0
CE2 B:TYR119 4.2 5.2 1.0
CA B:PHE156 4.2 15.7 1.0
O B:LYS155 4.3 16.2 1.0
CG B:PHE156 4.3 13.3 1.0
CA B:GLN121 4.4 14.7 1.0
N B:GLN121 4.5 12.7 1.0
CB B:PHE156 4.5 14.3 1.0
O5 B:586500 4.6 10.3 1.0
CA B:TYR119 4.7 9.5 1.0
CD1 B:TYR119 4.8 5.2 1.0
F54 B:586500 4.8 10.7 1.0
O2 B:586500 4.8 8.5 1.0
O B:PHE156 4.8 15.4 1.0
O B:GLN121 4.8 16.2 1.0
CA B:LYS123 4.9 13.2 1.0
CG B:GLN121 4.9 18.0 1.0
N B:TYR119 4.9 9.5 1.0

Fluorine binding site 5 out of 6 in 3ixj

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Fluorine binding site 5 out of 6 in the Crystal Structure of Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor


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 Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F500

b:13.8
occ:1.00
 F54 C:586500 0.0 13.8 1.0
C25 C:586500 1.3 11.2 1.0
C26 C:586500 2.4 8.8 1.0
C24 C:586500 2.4 10.9 1.0
O C:HOH731 3.1 19.0 1.0
OE1 C:GLN121 3.2 28.9 1.0
O C:PHE156 3.3 20.6 1.0
CD1 C:ILE158 3.3 22.9 1.0
C23 C:586500 3.6 12.8 1.0
C21 C:586500 3.6 9.9 1.0
CG1 C:ILE158 3.6 23.8 1.0
CZ2 C:TRP163 3.9 11.6 1.0
C37 C:586500 4.0 8.4 1.0
CH2 C:TRP163 4.1 11.5 1.0
C22 C:586500 4.1 9.8 1.0
CD C:GLN121 4.2 23.9 1.0
CG C:GLN121 4.3 21.9 1.0
N4 C:586500 4.4 10.4 1.0
C C:PHE156 4.4 20.4 1.0
C34 C:586500 4.4 12.3 1.0
C35 C:586500 4.6 11.8 1.0
O6 C:586500 4.6 15.9 1.0
C29 C:586500 4.6 9.7 1.0
O C:LYS155 4.7 22.4 1.0
F55 C:586500 4.7 14.2 1.0
O2 C:586500 4.8 9.0 1.0
C30 C:586500 4.9 9.8 1.0
CA C:PHE156 5.0 20.1 1.0

Fluorine binding site 6 out of 6 in 3ixj

Go back to Fluorine Binding Sites List in 3ixj
Fluorine binding site 6 out of 6 in the Crystal Structure of Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor


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 Beta-Secretase 1 in Complex with Selective Beta-Secretase 1 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F500

b:14.2
occ:1.00
 F55 C:586500 0.0 14.2 1.0
C23 C:586500 1.3 12.8 1.0
C24 C:586500 2.3 10.9 1.0
C22 C:586500 2.4 9.8 1.0
CA C:GLY122 3.0 17.8 1.0
N C:GLY122 3.0 18.5 1.0
C C:GLY122 3.2 16.6 1.0
CD2 C:TYR119 3.2 10.6 1.0
O C:GLY122 3.3 15.6 1.0
CD1 C:PHE156 3.4 15.8 1.0
CB C:TYR119 3.5 12.8 1.0
C25 C:586500 3.6 11.2 1.0
CG C:TYR119 3.6 12.4 1.0
C21 C:586500 3.7 9.9 1.0
N C:LYS123 3.9 15.9 1.0
C C:GLN121 4.0 19.6 1.0
CA C:PHE156 4.1 20.1 1.0
CE2 C:TYR119 4.1 10.8 1.0
C26 C:586500 4.1 8.8 1.0
CE1 C:PHE156 4.2 15.6 1.0
O C:LYS155 4.2 22.4 1.0
CG C:PHE156 4.3 17.6 1.0
CB C:PHE156 4.4 19.4 1.0
CG C:GLN121 4.5 21.9 1.0
O C:GLN121 4.6 20.4 1.0
N C:GLN121 4.7 18.6 1.0
O5 C:586500 4.7 10.1 1.0
CA C:TYR119 4.7 14.9 1.0
F54 C:586500 4.7 13.8 1.0
CD1 C:TYR119 4.7 10.4 1.0
CA C:GLN121 4.7 20.4 1.0
O2 C:586500 4.8 9.0 1.0
O C:PHE156 4.9 20.6 1.0
CA C:LYS123 4.9 15.9 1.0
N C:PHE156 4.9 20.0 1.0
C C:LYS155 4.9 21.8 1.0
N C:TYR119 4.9 13.0 1.0

Reference:

C.Bjorklund, S.Oscarson, K.Benkestock, N.Borkakoti, K.Jansson, J.Lindberg, L.Vrang, A.Hallberg, A.Rosenquist, B.Samuelsson. Design and Synthesis of Potent and Selective Bace-1 Inhibitors. J.Med.Chem. V. 53 1458 2010.
ISSN: ISSN 0022-2623
PubMed: 20128595
DOI: 10.1021/JM901168F
Page generated: Wed Jul 31 19:37:24 2024

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