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Fluorine in PDB 3ivi: Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents

Enzymatic activity of Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents

All present enzymatic activity of Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents:
3.4.23.46;

Protein crystallography data

The structure of Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents, PDB code: 3ivi was solved by H.Pan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.35 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.711, 104.480, 100.616, 90.00, 104.83, 90.00
R / Rfree (%) 19.5 / 22.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents (pdb code 3ivi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents, PDB code: 3ivi:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3ivi

Go back to Fluorine Binding Sites List in 3ivi
Fluorine binding site 1 out of 6 in the Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:56.5
occ:1.00
 F34 A:2LI1 0.0 56.5 1.0
C29 A:2LI1 1.3 53.2 1.0
C30 A:2LI1 2.4 51.8 1.0
C28 A:2LI1 2.4 51.0 1.0
CZ2 A:TRP176 3.3 34.9 1.0
C1 A:GOL901 3.3 85.4 1.0
O2 A:GOL901 3.4 85.9 1.0
C2 A:GOL901 3.5 85.8 1.0
CD1 A:LEU91 3.5 37.6 1.0
C31 A:2LI1 3.6 52.3 1.0
C27 A:2LI1 3.6 49.2 1.0
CD1 A:ILE171 3.7 36.5 1.0
O1 A:GOL901 3.8 84.1 1.0
CH2 A:TRP176 3.9 35.1 1.0
C32 A:2LI1 4.1 51.5 1.0
CE2 A:TRP176 4.2 35.0 1.0
O A:GLN73 4.4 37.2 1.0
NE1 A:TRP176 4.6 35.1 1.0
C A:GLN73 4.7 36.4 1.0
F33 A:2LI1 4.8 52.4 1.0
O A:PHE169 4.8 32.7 1.0
CG1 A:ILE171 4.9 37.2 1.0
CG A:LEU91 4.9 35.1 1.0
C26 A:2LI1 4.9 45.5 1.0
C3 A:GOL901 5.0 86.1 1.0

Fluorine binding site 2 out of 6 in 3ivi

Go back to Fluorine Binding Sites List in 3ivi
Fluorine binding site 2 out of 6 in the Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:52.4
occ:1.00
 F33 A:2LI1 0.0 52.4 1.0
C31 A:2LI1 1.3 52.3 1.0
C32 A:2LI1 2.4 51.5 1.0
C30 A:2LI1 2.4 51.8 1.0
O A:HOH33 3.2 59.7 1.0
CD1 A:PHE169 3.2 30.4 1.0
C29 A:2LI1 3.6 53.2 1.0
C27 A:2LI1 3.6 49.2 1.0
CE1 A:PHE169 3.8 30.2 1.0
CA A:PHE169 3.9 32.4 1.0
CA A:GLY135 3.9 32.9 1.0
CD2 A:TYR132 4.0 30.2 1.0
O A:LYS168 4.1 32.3 1.0
O A:PHE169 4.1 32.7 1.0
C28 A:2LI1 4.1 51.0 1.0
N A:GLY135 4.2 33.8 1.0
CG A:PHE169 4.2 31.0 1.0
CB A:TYR132 4.2 32.5 1.0
CG A:TYR132 4.2 31.4 1.0
C A:GLY135 4.3 32.0 1.0
CB A:PHE169 4.4 32.1 1.0
O25 A:2LI1 4.5 45.4 1.0
C A:PHE169 4.5 32.8 1.0
O A:GLY135 4.5 30.7 1.0
CE2 A:TYR132 4.7 30.9 1.0
F34 A:2LI1 4.8 56.5 1.0
C22 A:2LI1 4.8 45.3 1.0
N A:PHE169 4.9 32.2 1.0
C26 A:2LI1 4.9 45.5 1.0
C A:LYS168 4.9 32.2 1.0
N A:LYS136 4.9 31.3 1.0

Fluorine binding site 3 out of 6 in 3ivi

Go back to Fluorine Binding Sites List in 3ivi
Fluorine binding site 3 out of 6 in the Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:53.9
occ:1.00
 F34 B:2LI2 0.0 53.9 1.0
C29 B:2LI2 1.3 52.2 1.0
C30 B:2LI2 2.3 53.8 1.0
C28 B:2LI2 2.4 51.6 1.0
O2 B:GOL901 3.3 82.0 1.0
CZ2 B:TRP176 3.4 29.3 1.0
C2 B:GOL901 3.4 82.0 1.0
CD1 B:LEU91 3.5 34.5 1.0
C1 B:GOL901 3.5 82.0 1.0
C31 B:2LI2 3.6 52.0 1.0
C27 B:2LI2 3.6 50.5 1.0
O1 B:GOL901 3.6 80.3 1.0
CD1 B:ILE171 3.9 33.8 1.0
CH2 B:TRP176 3.9 29.4 1.0
C32 B:2LI2 4.1 51.0 1.0
CE2 B:TRP176 4.4 29.9 1.0
O B:HOH469 4.5 49.4 1.0
O B:GLN73 4.7 32.9 1.0
F33 B:2LI2 4.7 54.8 1.0
CG B:LEU91 4.8 32.8 1.0
NE1 B:TRP176 4.8 29.6 1.0
O B:PHE169 4.8 29.9 1.0
C3 B:GOL901 4.9 82.9 1.0
C26 B:2LI2 4.9 47.4 1.0
O B:GLY291 4.9 31.9 1.0
CG1 B:ILE171 4.9 33.5 1.0
C B:GLN73 4.9 33.4 1.0
CD2 B:LEU91 5.0 34.1 1.0

Fluorine binding site 4 out of 6 in 3ivi

Go back to Fluorine Binding Sites List in 3ivi
Fluorine binding site 4 out of 6 in the Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:54.8
occ:1.00
 F33 B:2LI2 0.0 54.8 1.0
C31 B:2LI2 1.3 52.0 1.0
C32 B:2LI2 2.3 51.0 1.0
C30 B:2LI2 2.4 53.8 1.0
O B:HOH11 3.2 47.2 1.0
CD1 B:PHE169 3.3 26.9 1.0
C29 B:2LI2 3.6 52.2 1.0
C27 B:2LI2 3.6 50.5 1.0
CA B:GLY135 3.7 33.2 1.0
CE1 B:PHE169 3.9 26.6 1.0
CD2 B:TYR132 3.9 30.2 1.0
O B:HOH469 4.0 49.4 1.0
N B:GLY135 4.0 33.8 1.0
CA B:PHE169 4.1 29.2 1.0
C28 B:2LI2 4.1 51.6 1.0
O B:LYS168 4.1 28.9 1.0
C B:GLY135 4.2 32.8 1.0
CB B:TYR132 4.2 31.3 1.0
CG B:TYR132 4.2 30.2 1.0
CG B:PHE169 4.3 28.2 1.0
O B:PHE169 4.4 29.9 1.0
O B:GLY135 4.4 31.4 1.0
CB B:PHE169 4.5 28.8 1.0
O25 B:2LI2 4.6 48.8 1.0
CE2 B:TYR132 4.6 30.3 1.0
F34 B:2LI2 4.7 53.9 1.0
C B:PHE169 4.8 29.8 1.0
C22 B:2LI2 4.8 46.2 1.0
N B:LYS136 4.8 32.8 1.0
C26 B:2LI2 4.9 47.4 1.0
NE2 B:GLN134 4.9 40.8 1.0
C B:LYS168 5.0 29.0 1.0

Fluorine binding site 5 out of 6 in 3ivi

Go back to Fluorine Binding Sites List in 3ivi
Fluorine binding site 5 out of 6 in the Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3

b:57.2
occ:1.00
 F34 C:2LI3 0.0 57.2 1.0
C29 C:2LI3 1.3 55.0 1.0
C30 C:2LI3 2.3 55.4 1.0
C28 C:2LI3 2.4 53.4 1.0
O2 C:GOL901 2.7 88.1 1.0
C2 C:GOL901 3.2 87.9 1.0
CZ2 C:TRP176 3.3 32.9 1.0
CD1 C:LEU91 3.4 37.4 1.0
O1 C:GOL901 3.4 87.0 1.0
C31 C:2LI3 3.6 54.8 1.0
C27 C:2LI3 3.6 51.7 1.0
CH2 C:TRP176 3.8 33.2 1.0
CD1 C:ILE171 3.9 37.5 1.0
C1 C:GOL901 3.9 87.5 1.0
C32 C:2LI3 4.1 53.2 1.0
CE2 C:TRP176 4.2 33.3 1.0
C3 C:GOL901 4.5 87.7 1.0
O C:GLN73 4.5 37.1 1.0
O3 C:GOL901 4.5 87.6 1.0
NE1 C:TRP176 4.6 33.2 1.0
F33 C:2LI3 4.7 57.2 1.0
O C:PHE169 4.7 33.4 1.0
C C:GLN73 4.8 37.0 1.0
CG C:LEU91 4.8 35.3 1.0
C26 C:2LI3 4.9 50.0 1.0

Fluorine binding site 6 out of 6 in 3ivi

Go back to Fluorine Binding Sites List in 3ivi
Fluorine binding site 6 out of 6 in the Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Design and Synthesis of Potent Bace-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3

b:57.2
occ:1.00
 F33 C:2LI3 0.0 57.2 1.0
C31 C:2LI3 1.3 54.8 1.0
C30 C:2LI3 2.3 55.4 1.0
C32 C:2LI3 2.4 53.2 1.0
CD1 C:PHE169 3.1 33.5 1.0
O C:HOH39 3.4 51.8 1.0
C29 C:2LI3 3.6 55.0 1.0
C27 C:2LI3 3.6 51.7 1.0
CA C:PHE169 3.7 33.4 1.0
O C:LYS168 3.8 33.4 1.0
CA C:GLY135 3.8 32.7 1.0
CE1 C:PHE169 3.9 33.8 1.0
CG C:PHE169 4.0 33.2 1.0
O C:PHE169 4.1 33.4 1.0
C28 C:2LI3 4.1 53.4 1.0
CD2 C:TYR132 4.1 28.8 1.0
N C:GLY135 4.2 33.0 1.0
CB C:PHE169 4.2 33.3 1.0
CG C:TYR132 4.3 29.0 1.0
C C:GLY135 4.4 32.3 1.0
C C:PHE169 4.4 33.4 1.0
CB C:TYR132 4.4 30.2 1.0
C C:LYS168 4.6 33.2 1.0
N C:PHE169 4.6 33.3 1.0
F34 C:2LI3 4.7 57.2 1.0
CE2 C:TYR132 4.7 28.7 1.0
O C:GLY135 4.7 31.9 1.0
O25 C:2LI3 4.8 48.4 1.0
C26 C:2LI3 4.9 50.0 1.0
N C:LYS136 4.9 31.8 1.0
C22 C:2LI3 4.9 48.0 1.0

Reference:

J.M.Sealy, A.P.Truong, L.Tso, G.D.Probst, J.Aquino, R.K.Hom, B.M.Jagodzinska, D.Dressen, D.W.Wone, L.Brogley, V.John, J.S.Tung, M.A.Pleiss, J.A.Tucker, A.W.Konradi, M.S.Dappen, G.Toth, H.Pan, L.Ruslim, J.Miller, M.P.Bova, S.Sinha, K.P.Quinn, J.M.Sauer. Design and Synthesis of Cell Potent Bace-1 Inhibitors: Structure-Activity Relationship of P1' Substituents. Bioorg.Med.Chem.Lett. V. 19 6386 2009.
ISSN: ISSN 0960-894X
PubMed: 19811916
DOI: 10.1016/J.BMCL.2009.09.061
Page generated: Mon Jul 14 17:06:18 2025

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