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Fluorine in PDB 5t1w: Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality

Enzymatic activity of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality

All present enzymatic activity of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality:
3.4.23.46;

Protein crystallography data

The structure of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality, PDB code: 5t1w was solved by K.D.Parris, F.Vajdos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.65 / 2.96
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.460, 101.460, 170.660, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 25

Other elements in 5t1w:

The structure of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality also contains other interesting chemical elements:

Iodine (I) 3 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality (pdb code 5t1w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality, PDB code: 5t1w:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5t1w

Go back to Fluorine Binding Sites List in 5t1w
Fluorine binding site 1 out of 6 in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:11.2
occ:1.00
 F1 A:74B401 0.0 11.2 1.0
C14 A:74B401 1.4 8.1 1.0
C9 A:74B401 2.3 8.4 1.0
O1 A:74B401 2.6 9.3 1.0
C10 A:74B401 3.7 8.9 1.0
NH2 A:ARG128 3.8 27.1 1.0
CG1 A:VAL69 3.8 4.7 1.0
C8 A:74B401 3.9 8.4 1.0
CZ A:ARG128 4.0 34.6 1.0
CB A:SER35 4.1 12.3 1.0
NH1 A:ARG128 4.3 7.4 1.0
NE A:ARG128 4.5 27.2 1.0
CB A:TYR71 4.6 10.0 1.0
NE1 A:TRP76 4.7 10.6 1.0
CG A:TYR71 4.8 12.5 1.0
C11 A:74B401 4.8 7.0 1.0
CD1 A:TYR71 4.9 14.2 1.0

Fluorine binding site 2 out of 6 in 5t1w

Go back to Fluorine Binding Sites List in 5t1w
Fluorine binding site 2 out of 6 in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:11.5
occ:1.00
 F2 A:74B401 0.0 11.5 1.0
C5 A:74B401 1.4 12.5 1.0
C4 A:74B401 2.3 16.8 1.0
C6 A:74B401 2.4 9.7 1.0
C8 A:74B401 2.9 8.4 1.0
C7 A:74B401 2.9 7.9 1.0
OH A:TYR71 3.0 29.1 1.0
C11 A:74B401 3.1 7.0 1.0
CZ A:TYR71 3.1 22.8 1.0
CE1 A:PHE108 3.2 7.7 1.0
CD1 A:PHE108 3.3 7.1 1.0
CE2 A:TYR71 3.4 14.2 1.0
C3 A:74B401 3.6 18.5 1.0
C1 A:74B401 3.6 9.8 1.0
CE1 A:TYR71 3.7 13.7 1.0
C9 A:74B401 3.8 8.4 1.0
O1 A:74B401 3.8 9.3 1.0
C10 A:74B401 4.0 8.9 1.0
C2 A:74B401 4.1 12.9 1.0
C12 A:74B401 4.2 4.6 1.0
CD2 A:TYR71 4.2 12.9 1.0
N1 A:74B401 4.3 7.2 1.0
CZ A:PHE108 4.4 5.0 1.0
CD1 A:TYR71 4.5 14.2 1.0
CG A:PHE108 4.6 4.8 1.0
F3 A:74B401 4.7 24.2 1.0
CD1 A:ILE118 4.7 16.1 1.0
CG A:TYR71 4.7 12.5 1.0
CD1 A:TRP76 4.7 11.7 1.0

Fluorine binding site 3 out of 6 in 5t1w

Go back to Fluorine Binding Sites List in 5t1w
Fluorine binding site 3 out of 6 in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:24.2
occ:1.00
 F3 A:74B401 0.0 24.2 1.0
C3 A:74B401 1.4 18.5 1.0
C4 A:74B401 2.3 16.8 1.0
C2 A:74B401 2.4 12.9 1.0
C15 A:74B401 2.8 13.3 1.0
O A:PHE108 3.3 8.9 1.0
CH2 A:TRP115 3.4 14.6 1.0
CZ2 A:TRP115 3.5 14.1 1.0
CD1 A:ILE110 3.5 3.0 1.0
C5 A:74B401 3.6 12.5 1.0
C1 A:74B401 3.6 9.8 1.0
CG1 A:ILE110 3.9 8.7 1.0
N3 A:74B401 4.1 17.5 1.0
C6 A:74B401 4.1 9.7 1.0
F4 A:74B401 4.5 23.4 1.0
C A:PHE108 4.5 9.4 1.0
C16 A:74B401 4.5 20.2 1.0
CZ3 A:TRP115 4.7 13.8 1.0
F2 A:74B401 4.7 11.5 1.0
CE2 A:TRP115 4.8 14.8 1.0

Fluorine binding site 4 out of 6 in 5t1w

Go back to Fluorine Binding Sites List in 5t1w
Fluorine binding site 4 out of 6 in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:23.4
occ:1.00
 F4 A:74B401 0.0 23.4 1.0
C17 A:74B401 1.3 23.1 1.0
F5 A:74B401 2.1 26.7 1.0
F6 A:74B401 2.2 22.2 1.0
C16 A:74B401 2.4 20.2 1.0
N3 A:74B401 2.9 17.5 1.0
C15 A:74B401 3.0 13.3 1.0
C A:GLN12 3.3 11.9 1.0
N A:GLY13 3.4 7.2 1.0
O A:GLY11 3.5 23.4 1.0
CA A:GLN12 3.7 10.2 1.0
O A:GLN12 3.7 10.5 1.0
CD1 A:ILE110 3.7 3.0 1.0
CA A:GLY13 3.9 7.5 1.0
C A:GLY11 4.1 21.9 1.0
N A:GLN12 4.2 12.7 1.0
C2 A:74B401 4.4 12.9 1.0
F3 A:74B401 4.5 24.2 1.0
OG1 A:THR232 4.8 20.1 1.0
CD1 A:LEU30 4.9 10.3 1.0
O3 A:GOL407 4.9 29.5 1.0
C3 A:74B401 4.9 18.5 1.0

Fluorine binding site 5 out of 6 in 5t1w

Go back to Fluorine Binding Sites List in 5t1w
Fluorine binding site 5 out of 6 in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:26.7
occ:1.00
 F5 A:74B401 0.0 26.7 1.0
C17 A:74B401 1.3 23.1 1.0
F4 A:74B401 2.1 23.4 1.0
F6 A:74B401 2.1 22.2 1.0
C16 A:74B401 2.4 20.2 1.0
OG1 A:THR232 2.7 20.1 1.0
O A:GLY11 3.1 23.4 1.0
N3 A:74B401 3.6 17.5 1.0
C A:GLY11 3.7 21.9 1.0
O3 A:GOL407 3.7 29.5 1.0
N A:THR232 4.0 5.5 1.0
CB A:THR232 4.0 11.6 1.0
C3 A:GOL407 4.1 26.4 1.0
N A:GLY13 4.1 7.2 1.0
CA A:GLY11 4.4 21.7 1.0
C15 A:74B401 4.4 13.3 1.0
N A:GLN12 4.4 12.7 1.0
CA A:THR232 4.5 5.3 1.0
C A:GLN12 4.5 11.9 1.0
CA A:GLN12 4.6 10.2 1.0
CA A:GLY13 4.7 7.5 1.0
C A:THR231 4.7 9.0 1.0
CA A:THR231 4.9 4.3 1.0
O A:GLY230 5.0 8.7 1.0

Fluorine binding site 6 out of 6 in 5t1w

Go back to Fluorine Binding Sites List in 5t1w
Fluorine binding site 6 out of 6 in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:22.2
occ:1.00
 F6 A:74B401 0.0 22.2 1.0
C17 A:74B401 1.3 23.1 1.0
F5 A:74B401 2.1 26.7 1.0
F4 A:74B401 2.2 23.4 1.0
C16 A:74B401 2.4 20.2 1.0
N3 A:74B401 2.7 17.5 1.0
O3 A:GOL407 3.3 29.5 1.0
CA A:GLY13 3.3 7.5 1.0
N A:GLY13 3.5 7.2 1.0
C15 A:74B401 3.6 13.3 1.0
C A:GLY230 3.9 9.8 1.0
O A:GLY230 4.1 8.7 1.0
OG1 A:THR232 4.1 20.1 1.0
C A:GLN12 4.1 11.9 1.0
N A:THR231 4.1 5.5 1.0
C3 A:GOL407 4.1 26.4 1.0
CA A:GLY230 4.2 6.8 1.0
O A:SER229 4.3 12.6 1.0
N A:THR232 4.4 5.5 1.0
CA A:THR231 4.6 4.3 1.0
C A:THR231 4.6 9.0 1.0
O A:GLN12 4.6 10.5 1.0
O A:GLY11 4.6 23.4 1.0
C A:GLY13 4.8 13.0 1.0
CD1 A:LEU30 4.8 10.3 1.0
C A:GLY11 4.9 21.9 1.0
CA A:GLN12 4.9 10.2 1.0
O2 A:GOL407 4.9 33.5 1.0
C2 A:74B401 5.0 12.9 1.0

Reference:

C.R.Butler, K.Ogilvie, L.Martinez-Alsina, G.Barreiro, E.M.Beck, C.E.Nolan, K.Atchison, E.Benvenuti, L.Buzon, S.Doran, C.Gonzales, C.J.Helal, X.Hou, M.H.Hsu, E.F.Johnson, K.Lapham, L.Lanyon, K.Parris, B.T.O'neill, D.Riddell, A.Robshaw, F.Vajdos, M.A.Brodney. Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality. J. Med. Chem. V. 60 386 2017.
ISSN: ISSN 1520-4804
PubMed: 27997172
DOI: 10.1021/ACS.JMEDCHEM.6B01451
Page generated: Thu Aug 1 15:01:42 2024

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