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Fluorine in PDB 5t1u: 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: 5t1u 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) 44.38 / 1.78
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.497, 102.497, 171.693, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 20.6

Other elements in 5t1u:

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

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 5t1u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality, PDB code: 5t1u:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 5t1u

Go back to Fluorine Binding Sites List in 5t1u
Fluorine binding site 1 out of 5 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:32.4
occ:1.00
 F1 A:P6U401 0.0 32.4 1.0
C11 A:P6U401 1.4 33.6 1.0
C10 A:P6U401 2.3 30.7 1.0
C6 A:P6U401 2.4 28.8 1.0
C2 A:P6U401 2.9 31.6 1.0
C1 A:P6U401 2.9 29.9 1.0
C3 A:P6U401 3.1 27.4 1.0
CE2 A:TYR71 3.3 36.8 1.0
CD2 A:TYR71 3.4 37.2 1.0
CE1 A:PHE108 3.4 30.2 1.0
C9 A:P6U401 3.6 29.4 1.0
CD1 A:PHE108 3.6 28.6 1.0
C7 A:P6U401 3.6 26.4 1.0
C4 A:P6U401 4.0 28.7 1.0
CZ A:TYR71 4.0 38.8 1.0
CG A:TYR71 4.1 37.5 1.0
C8 A:P6U401 4.1 25.9 1.0
N1 A:P6U401 4.3 28.0 1.0
CE1 A:TYR71 4.6 47.1 1.0
CD1 A:TYR71 4.7 44.9 1.0
OH A:TYR71 4.7 41.5 1.0
F2 A:P6U401 4.7 30.6 1.0
CZ A:PHE108 4.7 28.6 1.0
CD1 A:ILE118 4.8 31.9 1.0
CB A:TYR71 4.9 37.9 1.0
CG A:PHE108 5.0 24.9 1.0

Fluorine binding site 2 out of 5 in 5t1u

Go back to Fluorine Binding Sites List in 5t1u
Fluorine binding site 2 out of 5 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:30.6
occ:1.00
 F2 A:P6U401 0.0 30.6 1.0
C9 A:P6U401 1.4 29.4 1.0
C8 A:P6U401 2.3 25.9 1.0
C10 A:P6U401 2.3 30.7 1.0
C12 A:P6U401 2.8 27.0 1.0
O A:HOH592 2.9 36.6 1.0
O A:HOH522 3.1 34.6 1.0
N3 A:P6U401 3.3 28.4 1.0
CH2 A:TRP115 3.4 27.1 1.0
CZ2 A:TRP115 3.5 24.8 1.0
C11 A:P6U401 3.6 33.6 1.0
C7 A:P6U401 3.6 26.4 1.0
C14 A:P6U401 3.8 32.6 1.0
O A:PHE108 3.9 26.6 1.0
C13 A:P6U401 4.1 32.3 1.0
C6 A:P6U401 4.1 28.8 1.0
CD1 A:ILE110 4.4 32.9 1.0
C15 A:P6U401 4.6 42.3 1.0
CZ3 A:TRP115 4.7 23.7 1.0
F1 A:P6U401 4.7 32.4 1.0
CE2 A:TRP115 4.7 24.5 1.0
CG1 A:ILE110 4.8 29.7 1.0
CD1 A:LEU30 4.9 30.7 1.0

Fluorine binding site 3 out of 5 in 5t1u

Go back to Fluorine Binding Sites List in 5t1u
Fluorine binding site 3 out of 5 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:33.0
occ:1.00
 F3 A:P6U401 0.0 33.0 1.0
C16 A:P6U401 1.3 34.0 1.0
F5 A:P6U401 2.1 30.2 1.0
F4 A:P6U401 2.1 35.1 1.0
C13 A:P6U401 2.3 32.3 1.0
C15 A:P6U401 2.8 42.3 1.0
C14 A:P6U401 2.8 32.6 1.0
O1 A:EDO405 3.0 26.7 0.8
H21 A:EDO405 3.0 29.8 0.8
N A:GLY13 3.2 26.8 1.0
CA A:GLY13 3.3 30.6 1.0
OG1 A:THR232 3.4 28.7 1.0
H22 A:EDO405 3.6 29.8 0.8
C2 A:EDO405 3.6 24.9 0.8
N3 A:P6U401 3.7 28.4 1.0
HO1 A:EDO405 3.7 32.0 0.8
C A:GLN12 3.8 28.3 1.0
C1 A:EDO405 3.8 36.4 0.8
O A:GLY11 3.8 32.1 1.0
O A:HOH548 3.9 32.8 1.0
C A:GLY11 4.1 28.5 1.0
O A:HOH533 4.2 41.2 1.0
C12 A:P6U401 4.3 27.0 1.0
N A:GLN12 4.3 26.8 1.0
CA A:GLN12 4.4 24.9 1.0
O A:GLN12 4.4 28.5 1.0
H11 A:EDO405 4.5 43.6 0.8
H12 A:EDO405 4.6 43.6 0.8
CB A:THR232 4.7 29.2 1.0
C A:GLY13 4.7 24.3 1.0
N A:THR232 4.8 28.1 1.0
CA A:GLY11 4.9 32.4 1.0
O2 A:EDO405 5.0 34.8 0.8
O A:GLY230 5.0 26.1 1.0
C A:GLY230 5.0 27.4 1.0
CA A:THR232 5.0 22.8 1.0

Fluorine binding site 4 out of 5 in 5t1u

Go back to Fluorine Binding Sites List in 5t1u
Fluorine binding site 4 out of 5 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:35.1
occ:1.00
 F4 A:P6U401 0.0 35.1 1.0
C16 A:P6U401 1.3 34.0 1.0
F3 A:P6U401 2.1 33.0 1.0
F5 A:P6U401 2.2 30.2 1.0
C13 A:P6U401 2.3 32.3 1.0
N3 A:P6U401 3.0 28.4 1.0
O A:GLY230 3.1 26.1 1.0
C A:GLY230 3.1 27.4 1.0
C15 A:P6U401 3.2 42.3 1.0
OG1 A:THR232 3.3 28.7 1.0
N A:THR232 3.3 28.1 1.0
N A:THR231 3.3 25.6 1.0
C A:THR231 3.4 29.7 1.0
CA A:THR231 3.5 28.5 1.0
O1 A:EDO405 3.6 26.7 0.8
O A:HOH548 3.6 32.8 1.0
O A:HOH692 3.6 30.4 1.0
C14 A:P6U401 3.7 32.6 1.0
C12 A:P6U401 3.8 27.0 1.0
HO1 A:EDO405 3.8 32.0 0.8
O A:HOH579 4.0 37.2 1.0
CA A:GLY230 4.0 21.4 1.0
O A:THR231 4.0 24.9 1.0
CA A:THR232 4.0 22.8 1.0
CB A:THR232 4.3 29.2 1.0
O A:SER229 4.5 24.1 1.0
H21 A:EDO405 4.7 29.8 0.8
O A:HOH533 4.8 41.2 1.0
O A:HOH743 4.8 41.7 1.0
C1 A:EDO405 4.9 36.4 0.8
N A:GLY230 4.9 22.6 1.0

Fluorine binding site 5 out of 5 in 5t1u

Go back to Fluorine Binding Sites List in 5t1u
Fluorine binding site 5 out of 5 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:30.2
occ:1.00
 F5 A:P6U401 0.0 30.2 1.0
C16 A:P6U401 1.3 34.0 1.0
F3 A:P6U401 2.1 33.0 1.0
F4 A:P6U401 2.2 35.1 1.0
C13 A:P6U401 2.3 32.3 1.0
C12 A:P6U401 2.9 27.0 1.0
N3 A:P6U401 2.9 28.4 1.0
C14 A:P6U401 3.2 32.6 1.0
CA A:GLY13 3.5 30.6 1.0
C A:GLY230 3.6 27.4 1.0
C15 A:P6U401 3.7 42.3 1.0
O A:GLY230 3.7 26.1 1.0
CA A:GLY230 3.7 21.4 1.0
CD1 A:LEU30 3.7 30.7 1.0
O A:HOH652 3.9 24.0 1.0
O A:HOH548 3.9 32.8 1.0
O A:SER229 3.9 24.1 1.0
N A:GLY13 4.2 26.8 1.0
H21 A:EDO405 4.3 29.8 0.8
O1 A:EDO405 4.3 26.7 0.8
N A:THR231 4.3 25.6 1.0
C8 A:P6U401 4.4 25.9 1.0
CD2 A:LEU30 4.5 28.2 1.0
CG A:LEU30 4.6 25.7 1.0
N A:GLY230 4.7 22.6 1.0
C A:GLN12 4.7 28.3 1.0
C A:SER229 4.7 21.1 1.0
C A:GLY13 4.8 24.3 1.0
HO1 A:EDO405 4.8 32.0 0.8
O A:GLN12 4.9 28.5 1.0
N A:TYR14 5.0 20.6 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 15:01:11 2024

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