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Fluorine in PDB 7f1g: BACE2 Xaperone Complex with N-{3-[(4R,5R,6R)-2-Amino-5-Fluoro-4,6- Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-2H,3H-[1, 4]Dioxino[2,3-C]Pyridine-7-Carboxamide

Enzymatic activity of BACE2 Xaperone Complex with N-{3-[(4R,5R,6R)-2-Amino-5-Fluoro-4,6- Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-2H,3H-[1, 4]Dioxino[2,3-C]Pyridine-7-Carboxamide

All present enzymatic activity of BACE2 Xaperone Complex with N-{3-[(4R,5R,6R)-2-Amino-5-Fluoro-4,6- Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-2H,3H-[1, 4]Dioxino[2,3-C]Pyridine-7-Carboxamide:
3.4.23.45;

Protein crystallography data

The structure of BACE2 Xaperone Complex with N-{3-[(4R,5R,6R)-2-Amino-5-Fluoro-4,6- Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-2H,3H-[1, 4]Dioxino[2,3-C]Pyridine-7-Carboxamide, PDB code: 7f1g was solved by T.Ueno, E.Matsuoka, N.Asada, S.Yamamoto, N.Kanegawa, M.Ito, H.Ito, D.Moechars, F.J.R.Rombouts, H.J.M.Gijsen, K.I.Kusakabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.17 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.438, 74.635, 106.763, 90, 90, 90
R / Rfree (%) 22.6 / 24.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the BACE2 Xaperone Complex with N-{3-[(4R,5R,6R)-2-Amino-5-Fluoro-4,6- Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-2H,3H-[1, 4]Dioxino[2,3-C]Pyridine-7-Carboxamide (pdb code 7f1g). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the BACE2 Xaperone Complex with N-{3-[(4R,5R,6R)-2-Amino-5-Fluoro-4,6- Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-2H,3H-[1, 4]Dioxino[2,3-C]Pyridine-7-Carboxamide, PDB code: 7f1g:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7f1g

Go back to Fluorine Binding Sites List in 7f1g
Fluorine binding site 1 out of 2 in the BACE2 Xaperone Complex with N-{3-[(4R,5R,6R)-2-Amino-5-Fluoro-4,6- Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-2H,3H-[1, 4]Dioxino[2,3-C]Pyridine-7-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of BACE2 Xaperone Complex with N-{3-[(4R,5R,6R)-2-Amino-5-Fluoro-4,6- Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-2H,3H-[1, 4]Dioxino[2,3-C]Pyridine-7-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.6
occ:1.00
 F24 A:0QQ401 0.0 30.6 1.0
C23 A:0QQ401 1.3 29.4 1.0
C22 A:0QQ401 2.3 29.6 1.0
C05 A:0QQ401 2.4 28.5 1.0
H16 A:0QQ401 2.5 29.0 1.0
H12 A:0QQ401 2.5 29.6 1.0
HE1 A:PHE124 2.6 39.1 1.0
H15 A:0QQ401 2.7 28.5 1.0
HD1 A:PHE124 2.9 39.6 1.0
C04 A:0QQ401 3.0 28.4 1.0
HE2 A:TYR87 3.1 41.5 1.0
C25 A:0QQ401 3.1 28.6 1.0
C26 A:0QQ401 3.1 28.9 1.0
CE2 A:TYR87 3.2 41.4 1.0
CE1 A:PHE124 3.2 39.4 1.0
H14 A:0QQ401 3.2 29.1 1.0
CD1 A:PHE124 3.4 39.4 1.0
CZ A:TYR87 3.5 41.7 1.0
C21 A:0QQ401 3.6 29.7 1.0
C06 A:0QQ401 3.7 28.9 1.0
H17 A:0QQ401 3.7 29.0 1.0
CD2 A:TYR87 3.7 41.8 1.0
HD12 A:ILE134 3.8 25.7 1.0
OH A:TYR87 3.8 38.9 1.0
HD11 A:ILE134 3.9 25.7 1.0
HD2 A:TYR87 3.9 42.2 1.0
C28 A:0QQ401 4.0 28.8 1.0
HD13 A:ILE134 4.0 25.5 1.0
CD1 A:ILE134 4.1 26.2 1.0
H13 A:0QQ401 4.1 28.4 1.0
C07 A:0QQ401 4.1 29.1 1.0
F27 A:0QQ401 4.2 29.8 1.0
CE1 A:TYR87 4.3 40.7 1.0
N03 A:0QQ401 4.4 26.1 1.0
CZ A:PHE124 4.4 39.0 1.0
H11 A:0QQ401 4.4 29.6 1.0
CG A:TYR87 4.5 43.5 1.0
H4 A:0QQ401 4.5 28.6 1.0
HA A:PHE124 4.6 45.7 1.0
H18 A:0QQ401 4.6 29.7 1.0
CG A:PHE124 4.7 40.5 1.0
CD1 A:TYR87 4.7 42.1 1.0
HZ A:PHE124 4.7 38.4 1.0
C30 A:0QQ401 4.8 29.7 1.0
HD1 A:TRP92 4.8 34.9 1.0
H20 A:0QQ401 4.8 29.5 1.0
HH2 A:TRP131 4.8 34.1 1.0
HE1 A:TYR87 4.9 41.2 1.0

Fluorine binding site 2 out of 2 in 7f1g

Go back to Fluorine Binding Sites List in 7f1g
Fluorine binding site 2 out of 2 in the BACE2 Xaperone Complex with N-{3-[(4R,5R,6R)-2-Amino-5-Fluoro-4,6- Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-2H,3H-[1, 4]Dioxino[2,3-C]Pyridine-7-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of BACE2 Xaperone Complex with N-{3-[(4R,5R,6R)-2-Amino-5-Fluoro-4,6- Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-2H,3H-[1, 4]Dioxino[2,3-C]Pyridine-7-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:29.8
occ:1.00
 F27 A:0QQ401 0.0 29.8 1.0
C26 A:0QQ401 1.4 28.9 1.0
H16 A:0QQ401 2.0 29.0 1.0
C28 A:0QQ401 2.4 28.8 1.0
C04 A:0QQ401 2.4 28.4 1.0
H14 A:0QQ401 2.5 29.1 1.0
H18 A:0QQ401 2.6 29.7 1.0
N03 A:0QQ401 2.8 26.1 1.0
C30 A:0QQ401 2.9 29.7 1.0
C25 A:0QQ401 2.9 28.6 1.0
C02 A:0QQ401 3.0 26.2 1.0
S29 A:0QQ401 3.1 28.6 1.0
HE1 A:TYR87 3.1 41.2 1.0
CE1 A:TYR87 3.1 40.7 1.0
HD1 A:TYR87 3.2 42.1 1.0
CD1 A:TYR87 3.2 42.1 1.0
H17 A:0QQ401 3.3 29.0 1.0
H19 A:0QQ401 3.3 29.5 1.0
H13 A:0QQ401 3.4 28.4 1.0
C05 A:0QQ401 3.8 28.5 1.0
H15 A:0QQ401 3.9 28.5 1.0
H20 A:0QQ401 3.9 29.5 1.0
CZ A:TYR87 3.9 41.7 1.0
CG A:TYR87 4.0 43.5 1.0
N01 A:0QQ401 4.1 23.9 1.0
O A:HOH650 4.1 43.7 1.0
HB3 A:SER51 4.2 17.5 1.0
F24 A:0QQ401 4.2 30.6 1.0
H3 A:0QQ401 4.3 24.5 1.0
HB3 A:TYR87 4.4 46.2 1.0
C23 A:0QQ401 4.4 29.4 1.0
OH A:TYR87 4.6 38.9 1.0
CE2 A:TYR87 4.6 41.4 1.0
CD2 A:TYR87 4.6 41.8 1.0
C06 A:0QQ401 4.8 28.9 1.0
H4 A:0QQ401 4.8 28.6 1.0
CB A:TYR87 4.8 46.7 1.0
H2 A:0QQ401 4.8 24.4 1.0

Reference:

T.Ueno, E.Matsuoka, N.Asada, S.Yamamoto, N.Kanegawa, M.Ito, H.Ito, D.Moechars, F.J.R.Rombouts, H.J.M.Gijsen, K.I.Kusakabe. Discovery of Extremely Selective Fused Pyridine-Derived Beta-Site Amyloid Precursor Protein-Cleaving Enzyme (BACE1) Inhibitors with High in Vivo Efficacy Through 10S Loop Interactions. J.Med.Chem. V. 64 14165 2021.
ISSN: ISSN 0022-2623
PubMed: 34553947
DOI: 10.1021/ACS.JMEDCHEM.1C00359
Page generated: Tue Jul 15 19:22:57 2025

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