Fluorine in PDB 4azy: Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10)

Enzymatic activity of Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10)

All present enzymatic activity of Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10):
3.4.23.46;

Protein crystallography data

The structure of Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10), PDB code: 4azy was solved by B.M.Swahn, K.Kolmodin, S.Karlstrom, S.Von Berg, P.Soderman, J.Holenz, S.Berg, J.Lindstrom, M.Sundstrom, D.Turek, J.Kihlstrom, C.Slivo, L.Andersson, D.Pyring, L.Ohberg, A.Kers, K.Bogar, M.Bergh, L.L.Olsson, J.Janson, S.Eketjall, B.Georgievska, F.Jeppsson, J.Falting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.87 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.540, 76.390, 104.340, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.1

Other elements in 4azy:

The structure of Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10) (pdb code 4azy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10), PDB code: 4azy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 4azy

Go back to Fluorine Binding Sites List in 4azy
Fluorine binding site 1 out of 5 in the Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10)


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 BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1507

b:11.4
occ:1.00
F7 A:7F31507 0.0 11.4 1.0
C5 A:7F31507 1.4 14.3 1.0
C4 A:7F31507 2.4 13.1 1.0
C6 A:7F31507 2.4 15.9 1.0
OG1 A:THR231 2.9 12.8 1.0
OD2 A:ASP228 2.9 13.9 1.0
O A:HOH2271 3.0 19.3 1.0
N34 A:7F31507 3.1 12.7 1.0
C8 A:7F31507 3.1 13.8 1.0
O A:HOH2057 3.2 27.2 1.0
O A:HOH2279 3.3 22.2 1.0
C3 A:7F31507 3.7 14.9 1.0
C1 A:7F31507 3.7 16.0 1.0
CG A:ASP228 4.1 11.4 1.0
C2 A:7F31507 4.2 16.1 1.0
O A:HOH2270 4.2 24.9 1.0
CB A:THR231 4.3 13.4 1.0
N9 A:7F31507 4.3 11.3 1.0
O A:HOH2047 4.4 30.6 1.0
O A:GLY230 4.4 13.3 1.0
O A:HOH2123 4.5 38.7 1.0
O A:HOH2048 4.7 44.1 1.0
OD1 A:ASP228 4.7 11.8 1.0
C10 A:7F31507 4.8 15.2 1.0
C A:GLY230 4.8 14.9 1.0
CA A:THR231 4.9 11.4 1.0
N A:THR231 4.9 10.7 1.0

Fluorine binding site 2 out of 5 in 4azy

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Fluorine binding site 2 out of 5 in the Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10)


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 BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1507

b:16.4
occ:1.00
F23 A:7F31507 0.0 16.4 1.0
C14 A:7F31507 1.3 15.8 1.0
C13 A:7F31507 2.4 16.4 1.0
C15 A:7F31507 2.4 15.9 1.0
C17 A:7F31507 2.9 17.3 1.0
C18 A:7F31507 3.0 20.8 1.0
O A:HOH2160 3.0 21.6 1.0
O A:PHE108 3.2 19.4 1.0
CZ2 A:TRP115 3.2 17.7 1.0
CH2 A:TRP115 3.3 18.2 1.0
CD1 A:ILE110 3.5 28.2 1.0
C12 A:7F31507 3.6 14.3 1.0
C16 A:7F31507 3.6 14.4 1.0
CG1 A:ILE110 4.0 25.6 1.0
C22 A:7F31507 4.1 14.5 1.0
C11 A:7F31507 4.1 14.8 1.0
N19 A:7F31507 4.1 20.8 1.0
C A:PHE108 4.4 20.8 1.0
O A:HOH2119 4.4 38.2 1.0
CE2 A:TRP115 4.6 18.7 1.0
CZ3 A:TRP115 4.6 18.0 1.0
O A:HOH2043 4.6 36.6 1.0
CD1 A:ILE118 4.8 15.6 1.0
CD1 A:LEU30 5.0 20.3 1.0
C20 A:7F31507 5.0 16.2 1.0

Fluorine binding site 3 out of 5 in 4azy

Go back to Fluorine Binding Sites List in 4azy
Fluorine binding site 3 out of 5 in the Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10)


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 BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1507

b:22.2
occ:1.00
F31 A:7F31507 0.0 22.2 1.0
C30 A:7F31507 1.4 19.0 1.0
F32 A:7F31507 2.2 17.6 1.0
F33 A:7F31507 2.3 21.5 1.0
C28 A:7F31507 2.4 15.3 1.0
N27 A:7F31507 3.0 16.0 1.0
NE1 A:TRP76 3.2 17.0 1.0
C29 A:7F31507 3.4 14.2 1.0
CB A:ALA39 3.5 15.2 1.0
CE1 A:PHE108 3.5 20.4 1.0
CE2 A:TRP76 3.5 18.3 1.0
CZ A:PHE108 3.6 18.6 1.0
CZ2 A:TRP76 3.8 17.6 1.0
CD1 A:TRP76 4.0 18.2 1.0
C26 A:7F31507 4.2 16.7 1.0
CB A:ILE118 4.3 13.2 1.0
CD1 A:ILE118 4.4 15.6 1.0
CD2 A:TRP76 4.5 15.7 1.0
C24 A:7F31507 4.6 15.9 1.0
CG2 A:ILE118 4.7 13.6 1.0
CG A:TRP76 4.7 16.2 1.0
CG1 A:ILE118 4.7 13.0 1.0
CA A:ALA39 4.8 14.5 1.0
CB A:ASN37 4.8 12.8 1.0
CH2 A:TRP76 4.8 18.3 1.0
CD1 A:PHE108 4.8 19.9 1.0
C25 A:7F31507 4.8 16.9 1.0
O A:ASN37 4.9 12.2 1.0
CE2 A:PHE108 4.9 20.7 1.0
OG A:SER35 4.9 26.2 1.0

Fluorine binding site 4 out of 5 in 4azy

Go back to Fluorine Binding Sites List in 4azy
Fluorine binding site 4 out of 5 in the Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10)


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 BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1507

b:17.6
occ:1.00
F32 A:7F31507 0.0 17.6 1.0
C30 A:7F31507 1.4 19.0 1.0
F33 A:7F31507 2.2 21.5 1.0
F31 A:7F31507 2.2 22.2 1.0
C28 A:7F31507 2.4 15.3 1.0
C29 A:7F31507 2.7 14.2 1.0
OG A:SER35 2.9 26.2 1.0
CG2 A:ILE118 3.1 13.6 1.0
CB A:ILE118 3.4 13.2 1.0
N27 A:7F31507 3.6 16.0 1.0
CB A:SER35 3.6 15.2 1.0
OD2 A:ASP32 3.7 13.2 1.0
O A:ASN37 3.9 12.2 1.0
CD1 A:ILE118 3.9 15.6 1.0
C24 A:7F31507 4.1 15.9 1.0
CG1 A:ILE118 4.3 13.0 1.0
O A:ILE118 4.6 11.6 1.0
C26 A:7F31507 4.7 16.7 1.0
CA A:ILE118 4.7 11.1 1.0
C A:ILE118 4.7 11.4 1.0
CG A:ASP32 4.7 12.6 1.0
CB A:ALA39 4.8 15.2 1.0
C A:ASN37 4.9 14.2 1.0
CB A:ASN37 4.9 12.8 1.0
N A:GLY120 4.9 10.9 1.0
C25 A:7F31507 4.9 16.9 1.0
CZ A:PHE108 4.9 18.6 1.0
CE1 A:PHE108 5.0 20.4 1.0
N9 A:7F31507 5.0 11.3 1.0
CA A:GLY120 5.0 10.6 1.0

Fluorine binding site 5 out of 5 in 4azy

Go back to Fluorine Binding Sites List in 4azy
Fluorine binding site 5 out of 5 in the Design and Synthesis of BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10)


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 BACE1 Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides (Compound 10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1507

b:21.5
occ:1.00
F33 A:7F31507 0.0 21.5 1.0
C30 A:7F31507 1.4 19.0 1.0
F32 A:7F31507 2.2 17.6 1.0
F31 A:7F31507 2.3 22.2 1.0
C28 A:7F31507 2.4 15.3 1.0
N27 A:7F31507 2.8 16.0 1.0
C29 A:7F31507 3.5 14.2 1.0
CB A:ASN37 3.5 12.8 1.0
OG A:SER35 3.6 26.2 1.0
CB A:SER35 3.6 15.2 1.0
CZ2 A:TRP76 4.0 17.6 1.0
NE1 A:TRP76 4.0 17.0 1.0
C26 A:7F31507 4.1 16.7 1.0
O A:ASN37 4.1 12.2 1.0
O A:HOH2060 4.1 19.6 1.0
O A:HOH2024 4.2 35.2 1.0
N A:ASN37 4.2 9.5 1.0
OD1 A:ASN37 4.2 15.1 1.0
CG A:ASN37 4.3 15.2 1.0
CE2 A:TRP76 4.3 18.3 1.0
CA A:ASN37 4.3 10.3 1.0
C A:ASN37 4.6 14.2 1.0
C24 A:7F31507 4.7 15.9 1.0
CB A:ALA39 4.7 15.2 1.0
C25 A:7F31507 4.9 16.9 1.0
N A:SER36 5.0 10.9 1.0
CA A:SER35 5.0 11.1 1.0

Reference:

B.M.Swahn, K.Kolmodin, S.Karlstrom, S.Von Berg, P.Soderman, J.Holenz, S.Berg, J.Lindstrom, M.Sundstrom, D.Turek, J.Kihlstrom, C.Slivo, L.Andersson, D.Pyring, D.Rotticci, L.Ohberg, A.Kers, K.Bogar, F.Von Kieseritzky, M.Bergh, L.L.Olsson, J.Janson, S.Eketjall, B.Georgievska, F.Jeppsson, J.Falting. Design and Synthesis of Beta-Site Amyloid Precursor Protein Cleaving Enzyme (BACE1) Inhibitors with in Vivo Brain Reduction of Beta-Amyloid Peptides. J. Med. Chem. V. 55 9346 2012.
ISSN: ISSN 1520-4804
PubMed: 22924815
DOI: 10.1021/JM3009025
Page generated: Sun Dec 13 11:59:01 2020

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