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Fluorine in PDB 7f1d: Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in 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: 7f1d 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) 20.00 / 2.05
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.057, 102.057, 170.262, 90, 90, 120
R / Rfree (%) 19.8 / 22.2

Other elements in 7f1d:

The structure of Crystal Structure of BACE1 in 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 also contains other interesting chemical elements:

Iodine (I) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of BACE1 in 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 7f1d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of BACE1 in 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: 7f1d:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7f1d

Go back to Fluorine Binding Sites List in 7f1d
Fluorine binding site 1 out of 2 in the Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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:F505

b:28.3
occ:1.00
 F24 A:0QQ505 0.0 28.3 1.0
C23 A:0QQ505 1.3 27.7 1.0
C22 A:0QQ505 2.3 27.8 1.0
C05 A:0QQ505 2.4 27.8 1.0
C04 A:0QQ505 3.0 27.8 1.0
C25 A:0QQ505 3.1 27.4 1.0
C26 A:0QQ505 3.2 28.6 1.0
CE2 A:TYR71 3.2 36.5 1.0
CE1 A:PHE108 3.3 29.5 1.0
CD1 A:PHE108 3.4 29.7 1.0
CZ A:TYR71 3.5 36.3 1.0
C21 A:0QQ505 3.6 27.7 1.0
C06 A:0QQ505 3.6 27.1 1.0
OH A:TYR71 3.8 36.8 1.0
CD2 A:TYR71 3.8 36.5 1.0
CD1 A:ILE118 3.9 27.9 1.0
C28 A:0QQ505 4.1 29.2 1.0
C07 A:0QQ505 4.2 28.4 1.0
CE1 A:TYR71 4.3 36.0 1.0
F27 A:0QQ505 4.3 29.2 1.0
N03 A:0QQ505 4.5 27.6 1.0
CG A:TYR71 4.5 37.1 1.0
CZ A:PHE108 4.5 29.1 1.0
CG A:PHE108 4.7 29.7 1.0
CD1 A:TYR71 4.7 36.6 1.0
C30 A:0QQ505 4.8 29.7 1.0
O A:HOH602 4.9 37.6 1.0

Fluorine binding site 2 out of 2 in 7f1d

Go back to Fluorine Binding Sites List in 7f1d
Fluorine binding site 2 out of 2 in the Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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:F505

b:29.2
occ:1.00
 F27 A:0QQ505 0.0 29.2 1.0
C26 A:0QQ505 1.4 28.6 1.0
C28 A:0QQ505 2.4 29.2 1.0
C04 A:0QQ505 2.5 27.8 1.0
C30 A:0QQ505 2.8 29.7 1.0
N03 A:0QQ505 3.0 27.6 1.0
C25 A:0QQ505 3.0 27.4 1.0
S29 A:0QQ505 3.1 28.9 1.0
CE1 A:TYR71 3.2 36.0 1.0
C02 A:0QQ505 3.2 27.4 1.0
CD1 A:TYR71 3.3 36.6 1.0
C05 A:0QQ505 3.8 27.8 1.0
CZ A:TYR71 3.9 36.3 1.0
CG A:TYR71 4.2 37.1 1.0
F24 A:0QQ505 4.3 28.3 1.0
N01 A:0QQ505 4.3 26.3 1.0
C23 A:0QQ505 4.5 27.7 1.0
OH A:TYR71 4.5 36.8 1.0
O A:HOH800 4.6 41.6 1.0
CE2 A:TYR71 4.7 36.5 1.0
C06 A:0QQ505 4.8 27.1 1.0
CD2 A:TYR71 4.8 36.5 1.0
CB A:SER35 5.0 23.9 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 19:22:33 2025

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