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Fluorine in PDB 6jsz: BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-5-Methyl-9,9-Dioxo-2, 9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4-Fluorophenyl}-5- (Fluoromethoxy)Pyrazine-2-Carboxamide

Enzymatic activity of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-5-Methyl-9,9-Dioxo-2, 9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4-Fluorophenyl}-5- (Fluoromethoxy)Pyrazine-2-Carboxamide

All present enzymatic activity of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-5-Methyl-9,9-Dioxo-2, 9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4-Fluorophenyl}-5- (Fluoromethoxy)Pyrazine-2-Carboxamide:
3.4.23.45;

Protein crystallography data

The structure of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-5-Methyl-9,9-Dioxo-2, 9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4-Fluorophenyl}-5- (Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jsz was solved by K.Fujimoto, E.Matsuoka, N.Asada, G.Tadano, T.Yamamoto, K.Nakahara, K.Fuchino, H.Ito, N.Kanegawa, D.Moechars, 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) 61.51 / 1.53
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.542, 74.467, 109.135, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 23.7

Other elements in 6jsz:

The structure of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-5-Methyl-9,9-Dioxo-2, 9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4-Fluorophenyl}-5- (Fluoromethoxy)Pyrazine-2-Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-5-Methyl-9,9-Dioxo-2, 9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4-Fluorophenyl}-5- (Fluoromethoxy)Pyrazine-2-Carboxamide (pdb code 6jsz). 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-[(5R)-3-Amino-5-Methyl-9,9-Dioxo-2, 9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4-Fluorophenyl}-5- (Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jsz:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6jsz

Go back to Fluorine Binding Sites List in 6jsz
Fluorine binding site 1 out of 2 in the BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-5-Methyl-9,9-Dioxo-2, 9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-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 BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-5-Methyl-9,9-Dioxo-2, 9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4-Fluorophenyl}-5- (Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:33.5
occ:1.00
 F2 A:C7O401 0.0 33.5 1.0
C21 A:C7O401 1.3 31.4 1.0
C20 A:C7O401 2.3 31.0 1.0
C10 A:C7O401 2.4 29.2 1.0
C1 A:C7O401 3.0 27.9 1.0
C9 A:C7O401 3.0 34.4 1.0
C2 A:C7O401 3.0 28.7 1.0
CE1 A:PHE124 3.3 52.3 1.0
CD1 A:ILE134 3.4 25.2 1.0
C5 A:C7O401 3.6 31.2 1.0
C19 A:C7O401 3.6 31.1 1.0
C11 A:C7O401 3.7 29.0 1.0
CD1 A:PHE124 3.9 52.3 1.0
CZ A:PHE124 4.0 50.9 1.0
C12 A:C7O401 4.1 29.2 1.0
C8 A:C7O401 4.3 36.7 1.0
N1 A:C7O401 4.4 25.6 1.0
C4 A:C7O401 4.5 28.8 1.0
OH A:TYR87 4.6 55.2 1.0
C6 A:C7O401 4.7 33.7 1.0
CG1 A:ILE134 5.0 23.6 1.0

Fluorine binding site 2 out of 2 in 6jsz

Go back to Fluorine Binding Sites List in 6jsz
Fluorine binding site 2 out of 2 in the BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-5-Methyl-9,9-Dioxo-2, 9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-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 BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-5-Methyl-9,9-Dioxo-2, 9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4-Fluorophenyl}-5- (Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.6
occ:1.00
 F1 A:C7O401 0.0 35.6 1.0
C17 A:C7O401 1.4 32.7 1.0
O4 A:C7O401 2.3 30.6 1.0
N A:GLY29 2.7 33.9 1.0
C16 A:C7O401 3.1 29.8 1.0
CA A:GLY29 3.1 30.3 1.0
N5 A:C7O401 3.3 28.9 1.0
C A:GLY27 3.6 45.0 1.0
N A:ARG28 3.6 42.0 1.0
CE2 A:TYR30 3.6 25.6 1.0
O A:HOH577 3.7 42.9 1.0
C A:GLY29 3.7 27.4 1.0
CA A:GLY27 3.8 45.9 1.0
CD2 A:TYR30 3.8 24.7 1.0
C A:ARG28 3.9 38.1 1.0
O A:GLY27 4.0 47.1 1.0
CA A:ARG28 4.2 40.1 1.0
N A:TYR30 4.2 25.0 1.0
O A:GLY29 4.3 27.9 1.0
C15 A:C7O401 4.3 29.5 1.0
C18 A:C7O401 4.5 28.8 1.0
N A:GLY27 4.6 47.2 1.0
CB A:ALA347 4.6 22.0 1.0
CZ A:TYR30 4.6 26.5 1.0
CG A:TYR30 4.9 24.7 1.0
O A:ARG28 4.9 40.3 1.0

Reference:

K.Fujimoto, E.Matsuoka, N.Asada, G.Tadano, T.Yamamoto, K.Nakahara, K.Fuchino, H.Ito, N.Kanegawa, D.Moechars, H.J.M.Gijsen, K.I.Kusakabe. Structure-Based Design of Selective Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitors: Targeting the Flap to Gain Selectivity Over BACE2. J.Med.Chem. V. 62 5080 2019.
ISSN: ISSN 0022-2623
PubMed: 31021626
DOI: 10.1021/ACS.JMEDCHEM.9B00309
Page generated: Tue Jul 15 12:42:27 2025

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