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Fluorine in PDB 6jt4: Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jt4 was solved by K.Anan, Y.Iso, T.Oguma, K.Nakahara, S.Suzuki, T.Yamamoto, E.Matsuoka, H.Ito, G.Sakaguchi, S.Ando, K.Morimoto, N.Kanegawa, Y.Kido, T.Kawachi, T.Fukushima, A.Teisman, V.Urmaliya, D.Dhuyvetter, H.Borghys, N.Austin, A.V.D.Bergh, P.Verboven, F.Bischoff, H.J.M.Gijsen, Y.Yamano, K.I.Kusakabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.590, 101.590, 170.351, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 23.4

Other elements in 6jt4:

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide also contains other interesting chemical elements:

Iodine (I) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide (pdb code 6jt4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jt4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 6jt4

Go back to Fluorine Binding Sites List in 6jt4
Fluorine binding site 1 out of 5 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-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-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:26.8
occ:1.00
 F1 A:C86506 0.0 26.8 1.0
C10 A:C86506 1.3 27.1 1.0
O2 A:C86506 2.2 26.7 1.0
O A:HOH752 2.9 35.0 1.0
C9 A:C86506 3.0 26.8 1.0
N5 A:C86506 3.1 27.3 1.0
N A:GLY13 3.1 21.9 1.0
CA A:GLY13 3.4 22.6 1.0
N A:GLY11 3.6 31.4 1.0
N A:GLN12 3.9 25.4 1.0
CE1 A:TYR14 3.9 22.5 1.0
CA A:GLY11 3.9 29.0 1.0
C A:GLY11 4.0 28.1 1.0
C8 A:C86506 4.2 26.2 1.0
C A:GLY13 4.2 21.5 1.0
O A:LYS9 4.3 31.9 1.0
C A:GLN12 4.3 24.1 1.0
C11 A:C86506 4.3 26.3 1.0
CD1 A:TYR14 4.4 21.8 1.0
NH2 A:ARG307 4.5 37.2 1.0
O A:GLY13 4.6 22.2 1.0
C A:SER10 4.6 33.8 1.0
OG1 A:THR232 4.7 24.5 1.0
CZ A:TYR14 4.7 23.4 1.0
CA A:GLN12 4.7 25.7 1.0
OE2 A:GLU339 4.7 29.6 1.0
O A:GLY11 4.7 27.3 1.0
CB A:ALA335 4.7 22.2 1.0
CA A:SER10 4.8 36.0 1.0
OH A:TYR14 4.9 24.9 1.0

Fluorine binding site 2 out of 5 in 6jt4

Go back to Fluorine Binding Sites List in 6jt4
Fluorine binding site 2 out of 5 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-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-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:22.6
occ:1.00
 F2 A:C86506 0.0 22.6 1.0
C14 A:C86506 1.3 23.8 1.0
C13 A:C86506 2.3 22.6 1.0
C3 A:C86506 2.4 23.0 1.0
C15 A:C86506 2.8 23.4 1.0
C2 A:C86506 2.9 23.6 1.0
C16 A:C86506 3.1 23.3 1.0
CE1 A:PHE108 3.2 23.9 1.0
CD1 A:PHE108 3.3 24.1 1.0
CE2 A:TYR71 3.5 45.6 1.0
CZ A:TYR71 3.6 42.7 1.0
C12 A:C86506 3.6 23.8 1.0
C4 A:C86506 3.6 23.2 1.0
OH A:TYR71 3.7 44.5 1.0
C17 A:C86506 4.0 24.5 1.0
CD1 A:ILE118 4.0 19.6 0.5
C5 A:C86506 4.1 24.0 1.0
CD2 A:TYR71 4.1 47.4 1.0
CE1 A:TYR71 4.3 43.0 1.0
N2 A:C86506 4.3 23.0 1.0
CZ A:PHE108 4.4 23.7 1.0
F4 A:C86506 4.5 30.0 1.0
CG A:PHE108 4.6 23.7 1.0
CG A:TYR71 4.7 46.0 1.0
CD1 A:TYR71 4.8 43.8 1.0
C18 A:C86506 4.9 27.1 1.0

Fluorine binding site 3 out of 5 in 6jt4

Go back to Fluorine Binding Sites List in 6jt4
Fluorine binding site 3 out of 5 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:28.3
occ:1.00
 F3 A:C86506 0.0 28.3 1.0
C18 A:C86506 1.3 27.1 1.0
F4 A:C86506 2.1 30.0 1.0
F5 A:C86506 2.1 25.1 1.0
C17 A:C86506 2.4 24.5 1.0
C16 A:C86506 2.9 23.3 1.0
S1 A:C86506 3.1 22.5 1.0
O A:HOH804 3.3 45.6 1.0
O A:HOH625 3.5 57.2 1.0
CD1 A:TYR71 3.8 43.8 1.0
O A:HOH790 3.9 48.4 1.0
C1 A:C86506 4.1 21.4 1.0
C2 A:C86506 4.3 23.6 1.0
CE1 A:TYR71 4.4 43.0 1.0
CG A:TYR71 4.5 46.0 1.0
O A:HOH757 4.6 44.6 1.0
CB A:TYR71 4.6 48.9 1.0
N2 A:C86506 4.6 23.0 1.0
O A:HOH720 4.9 41.8 1.0

Fluorine binding site 4 out of 5 in 6jt4

Go back to Fluorine Binding Sites List in 6jt4
Fluorine binding site 4 out of 5 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:30.0
occ:1.00
 F4 A:C86506 0.0 30.0 1.0
C18 A:C86506 1.3 27.1 1.0
F3 A:C86506 2.1 28.3 1.0
F5 A:C86506 2.1 25.1 1.0
C17 A:C86506 2.4 24.5 1.0
C16 A:C86506 3.0 23.3 1.0
O A:HOH625 3.4 57.2 1.0
CB A:TYR71 3.4 48.9 1.0
CG A:TYR71 3.5 46.0 1.0
CD1 A:TYR71 3.5 43.8 1.0
S1 A:C86506 3.9 22.5 1.0
CD2 A:TYR71 4.3 47.4 1.0
CE1 A:TYR71 4.3 43.0 1.0
O A:HOH804 4.4 45.6 1.0
C2 A:C86506 4.4 23.6 1.0
F2 A:C86506 4.5 22.6 1.0
O A:HOH786 4.7 46.5 1.0
C3 A:C86506 4.7 23.0 1.0
O A:THR72 4.8 69.2 1.0
C14 A:C86506 4.8 23.8 1.0
OG1 A:THR72 4.8 68.5 1.0
CA A:TYR71 4.8 49.7 1.0
N A:THR72 4.8 63.6 1.0
CE2 A:TYR71 4.9 45.6 1.0
CZ A:TYR71 4.9 42.7 1.0

Fluorine binding site 5 out of 5 in 6jt4

Go back to Fluorine Binding Sites List in 6jt4
Fluorine binding site 5 out of 5 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:25.1
occ:1.00
 F5 A:C86506 0.0 25.1 1.0
C18 A:C86506 1.3 27.1 1.0
F4 A:C86506 2.1 30.0 1.0
F3 A:C86506 2.1 28.3 1.0
C17 A:C86506 2.4 24.5 1.0
S1 A:C86506 2.9 22.5 1.0
O A:HOH786 3.4 46.5 1.0
C16 A:C86506 3.7 23.3 1.0
O A:HOH720 3.7 41.8 1.0
O A:HOH790 3.9 48.4 1.0
O A:HOH625 4.1 57.2 1.0
C1 A:C86506 4.5 21.4 1.0
OG1 A:THR72 4.9 68.5 1.0
C2 A:C86506 4.9 23.6 1.0
O A:HOH804 5.0 45.6 1.0

Reference:

K.Anan, Y.Iso, T.Oguma, K.Nakahara, S.Suzuki, T.Yamamoto, E.Matsuoka, H.Ito, G.Sakaguchi, S.Ando, K.Morimoto, N.Kanegawa, Y.Kido, T.Kawachi, T.Fukushima, A.Teisman, V.Urmaliya, D.Dhuyvetter, H.Borghys, N.Austin, A.Van Den Bergh, P.Verboven, F.Bischoff, H.J.M.Gijsen, Y.Yamano, K.Kusakabe. Trifluoromethyl Dihydrothiazine-Based Beta-Secretase (BACE1) Inhibitors with Robust Central Beta-Amyloid Reduction and Minimal Covalent Binding Burden. Chemmedchem V. 14 1894 2019.
ISSN: ESSN 1860-7187
PubMed: 31657130
DOI: 10.1002/CMDC.201900478
Page generated: Tue Jul 15 12:42:38 2025

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