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Fluorine in PDB 3dm6: Beta-Secretase 1 Complexed with Statine-Based Inhibitor

Enzymatic activity of Beta-Secretase 1 Complexed with Statine-Based Inhibitor

All present enzymatic activity of Beta-Secretase 1 Complexed with Statine-Based Inhibitor:
3.4.23.46;

Protein crystallography data

The structure of Beta-Secretase 1 Complexed with Statine-Based Inhibitor, PDB code: 3dm6 was solved by J.Lindberg, N.Borkakoti, S.Nystrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.76 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.435, 103.017, 103.110, 90.00, 103.50, 90.00
R / Rfree (%) 22.3 / 28.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Beta-Secretase 1 Complexed with Statine-Based Inhibitor (pdb code 3dm6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Beta-Secretase 1 Complexed with Statine-Based Inhibitor, PDB code: 3dm6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3dm6

Go back to Fluorine Binding Sites List in 3dm6
Fluorine binding site 1 out of 6 in the Beta-Secretase 1 Complexed with Statine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Beta-Secretase 1 Complexed with Statine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:64.6
occ:1.00
 F40 A:7571000 0.0 64.6 1.0
C35 A:7571000 1.3 64.4 1.0
C34 A:7571000 2.3 64.8 1.0
C36 A:7571000 2.4 63.6 1.0
N A:GLY74 2.6 53.3 1.0
CD2 A:TYR71 3.2 47.5 1.0
CB A:TYR71 3.2 48.0 1.0
CA A:GLY74 3.2 52.9 1.0
O A:GLY74 3.2 53.5 1.0
C A:GLY74 3.3 53.1 1.0
CG A:TYR71 3.4 47.4 1.0
CB A:GLN73 3.6 53.8 1.0
C37 A:7571000 3.6 64.7 1.0
C33 A:7571000 3.6 63.2 1.0
CD1 A:PHE108 3.7 55.5 1.0
C A:GLN73 3.7 54.2 1.0
CA A:GLN73 4.0 53.9 1.0
C38 A:7571000 4.1 63.6 1.0
N A:LYS75 4.1 52.8 1.0
N A:GLN73 4.2 53.0 1.0
CE2 A:TYR71 4.2 49.6 1.0
CE1 A:PHE108 4.2 55.9 1.0
CA A:TYR71 4.4 48.7 1.0
CD1 A:TYR71 4.6 45.1 1.0
O A:LYS107 4.6 58.1 1.0
N A:TYR71 4.6 47.8 1.0
CA A:PHE108 4.7 56.3 1.0
F39 A:7571000 4.7 65.8 1.0
O19 A:7571000 4.7 51.0 1.0
O32 A:7571000 4.7 62.1 1.0
CG A:PHE108 4.7 55.9 1.0
C A:TYR71 4.8 49.7 1.0
O A:GLN73 4.8 56.3 1.0
CG A:GLN73 4.8 55.4 1.0
CB A:PHE108 4.9 56.1 1.0
CA A:LYS75 5.0 52.7 1.0

Fluorine binding site 2 out of 6 in 3dm6

Go back to Fluorine Binding Sites List in 3dm6
Fluorine binding site 2 out of 6 in the Beta-Secretase 1 Complexed with Statine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Beta-Secretase 1 Complexed with Statine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:65.8
occ:1.00
 F39 A:7571000 0.0 65.8 1.0
C37 A:7571000 1.4 64.7 1.0
C36 A:7571000 2.3 63.6 1.0
C38 A:7571000 2.4 63.6 1.0
O A:PHE108 3.2 56.4 1.0
CD1 A:ILE110 3.3 56.5 1.0
C35 A:7571000 3.6 64.4 1.0
C9 A:7571000 3.7 38.7 1.0
C33 A:7571000 3.7 63.2 1.0
CZ2 A:TRP115 3.8 50.2 1.0
CG1 A:ILE110 3.8 57.5 1.0
CH2 A:TRP115 3.9 50.8 1.0
C34 A:7571000 4.1 64.8 1.0
N8 A:7571000 4.2 43.0 1.0
C A:PHE108 4.3 56.0 1.0
C7 A:7571000 4.4 42.0 1.0
F40 A:7571000 4.7 64.6 1.0
C10 A:7571000 4.7 45.8 1.0
CA A:PHE108 4.8 56.3 1.0
O32 A:7571000 4.8 62.1 1.0
O A:LYS107 4.9 58.1 1.0
CB A:GLN73 5.0 53.8 1.0
CD1 A:PHE108 5.0 55.5 1.0

Fluorine binding site 3 out of 6 in 3dm6

Go back to Fluorine Binding Sites List in 3dm6
Fluorine binding site 3 out of 6 in the Beta-Secretase 1 Complexed with Statine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Beta-Secretase 1 Complexed with Statine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:66.3
occ:1.00
 F40 B:7571000 0.0 66.3 1.0
C35 B:7571000 1.3 65.7 1.0
C36 B:7571000 2.4 64.6 1.0
C34 B:7571000 2.4 66.2 1.0
N B:GLY74 2.6 62.2 1.0
CA B:GLY74 3.3 61.4 1.0
CB B:TYR71 3.3 57.5 1.0
O B:GLY74 3.3 60.3 1.0
CB B:GLN73 3.4 62.6 1.0
CD2 B:TYR71 3.4 57.0 1.0
C B:GLY74 3.4 61.0 1.0
C B:GLN73 3.5 62.9 1.0
CG B:TYR71 3.6 57.2 1.0
C37 B:7571000 3.6 65.7 1.0
C33 B:7571000 3.6 64.6 1.0
CA B:GLN73 3.7 62.7 1.0
N B:GLN73 3.9 62.0 1.0
CD1 B:PHE108 4.1 64.3 1.0
C38 B:7571000 4.1 66.0 1.0
N B:LYS75 4.3 60.8 1.0
CE2 B:TYR71 4.4 55.3 1.0
O B:LYS107 4.4 69.5 1.0
O19 B:7571000 4.4 50.2 1.0
CA B:TYR71 4.5 58.1 1.0
CA B:PHE108 4.6 66.7 1.0
CG B:GLN73 4.7 63.7 1.0
O B:GLN73 4.7 64.0 1.0
CD1 B:TYR71 4.7 55.4 1.0
F39 B:7571000 4.7 67.9 1.0
CE1 B:PHE108 4.7 63.7 1.0
O32 B:7571000 4.8 64.7 1.0
C B:TYR71 4.8 58.6 1.0
C18 B:7571000 4.8 52.0 1.0
N B:TYR71 4.9 57.7 1.0

Fluorine binding site 4 out of 6 in 3dm6

Go back to Fluorine Binding Sites List in 3dm6
Fluorine binding site 4 out of 6 in the Beta-Secretase 1 Complexed with Statine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Beta-Secretase 1 Complexed with Statine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:67.9
occ:1.00
 F39 B:7571000 0.0 67.9 1.0
C37 B:7571000 1.3 65.7 1.0
C38 B:7571000 2.3 66.0 1.0
C36 B:7571000 2.3 64.6 1.0
O B:PHE108 3.1 66.9 1.0
CD1 B:ILE110 3.3 68.8 1.0
CH2 B:TRP115 3.3 59.6 1.0
CZ2 B:TRP115 3.4 60.4 1.0
C35 B:7571000 3.6 65.7 1.0
C33 B:7571000 3.6 64.6 1.0
CG1 B:ILE110 3.7 67.5 1.0
C9 B:7571000 3.7 53.2 1.0
C34 B:7571000 4.1 66.2 1.0
C B:PHE108 4.2 66.8 1.0
N8 B:7571000 4.3 52.5 1.0
C7 B:7571000 4.4 54.8 1.0
CZ3 B:TRP115 4.6 58.8 1.0
F40 B:7571000 4.7 66.3 1.0
O32 B:7571000 4.7 64.7 1.0
CE2 B:TRP115 4.8 59.0 1.0
CA B:PHE108 4.8 66.7 1.0
C10 B:7571000 4.8 50.7 1.0
CD1 B:PHE108 4.9 64.3 1.0
NE2 B:GLN73 5.0 65.2 1.0

Fluorine binding site 5 out of 6 in 3dm6

Go back to Fluorine Binding Sites List in 3dm6
Fluorine binding site 5 out of 6 in the Beta-Secretase 1 Complexed with Statine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Beta-Secretase 1 Complexed with Statine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1000

b:59.4
occ:1.00
 F40 C:7571000 0.0 59.4 1.0
C35 C:7571000 1.3 58.6 1.0
C36 C:7571000 2.4 57.7 1.0
C34 C:7571000 2.4 56.9 1.0
N C:GLY74 3.0 58.7 1.0
O C:GLY74 3.0 56.8 1.0
C C:GLY74 3.2 57.5 1.0
CA C:GLY74 3.2 57.5 1.0
CD2 C:TYR71 3.2 51.8 1.0
CD1 C:PHE108 3.4 54.2 1.0
CB C:TYR71 3.4 54.9 1.0
CG C:TYR71 3.5 52.8 1.0
C37 C:7571000 3.6 58.1 1.0
C33 C:7571000 3.6 55.2 1.0
C C:GLN73 3.8 59.5 1.0
CE1 C:PHE108 4.0 53.4 1.0
N C:LYS75 4.0 57.6 1.0
C38 C:7571000 4.1 57.8 1.0
CE2 C:TYR71 4.1 51.2 1.0
CA C:PHE108 4.3 58.6 1.0
CG C:PHE108 4.4 55.8 1.0
CA C:GLN73 4.5 59.5 1.0
N C:GLN73 4.5 58.8 1.0
O C:LYS107 4.5 62.9 1.0
O C:GLN73 4.6 60.7 1.0
CB C:GLN73 4.6 59.8 1.0
CB C:PHE108 4.6 56.9 1.0
CD1 C:TYR71 4.6 50.6 1.0
CA C:TYR71 4.6 55.8 1.0
F39 C:7571000 4.7 59.0 1.0
O32 C:7571000 4.8 57.4 1.0
CA C:LYS75 4.8 58.3 1.0
N C:TYR71 4.9 56.5 1.0
O C:PHE108 4.9 58.6 1.0
O19 C:7571000 5.0 45.5 1.0
C C:TYR71 5.0 56.2 1.0

Fluorine binding site 6 out of 6 in 3dm6

Go back to Fluorine Binding Sites List in 3dm6
Fluorine binding site 6 out of 6 in the Beta-Secretase 1 Complexed with Statine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Beta-Secretase 1 Complexed with Statine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1000

b:59.0
occ:1.00
 F39 C:7571000 0.0 59.0 1.0
C37 C:7571000 1.3 58.1 1.0
C36 C:7571000 2.3 57.7 1.0
C38 C:7571000 2.4 57.8 1.0
CD1 C:ILE110 3.0 57.4 1.0
O C:PHE108 3.3 58.6 1.0
C35 C:7571000 3.6 58.6 1.0
C33 C:7571000 3.6 55.2 1.0
CZ2 C:TRP115 3.7 49.2 1.0
C9 C:7571000 3.8 38.6 1.0
CH2 C:TRP115 3.9 50.0 1.0
NE2 C:GLN73 3.9 65.3 1.0
CG1 C:ILE110 3.9 57.0 1.0
N8 C:7571000 4.0 45.6 1.0
C34 C:7571000 4.1 56.9 1.0
C7 C:7571000 4.3 42.6 1.0
C C:PHE108 4.4 58.1 1.0
C10 C:7571000 4.6 46.0 1.0
F40 C:7571000 4.7 59.4 1.0
O32 C:7571000 4.7 57.4 1.0

Reference:

M.Back, J.Nyhlen, I.Kvarnstrom, S.Appelgren, N.Borkakoti, K.Jansson, J.Lindberg, S.Nystrom, A.Hallberg, S.Rosenquist, B.Samuelsson. Design, Synthesis and Sar of Potent Statine-Based Bace-1 Inhibitors: Exploration of P1 Phenoxy and Benzyloxy Residues Bioorg.Med.Chem. V. 16 9471 2008.
ISSN: ISSN 0968-0896
PubMed: 18842420
DOI: 10.1016/J.BMC.2008.09.041
Page generated: Wed Jul 31 18:00:26 2024

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