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Fluorine in PDB 6jsn: Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in 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: 6jsn 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) 20.00 / 2.60
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.705, 101.705, 170.422, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 25.9

Other elements in 6jsn:

The structure of Crystal Structure of BACE1 in 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:

Iodine (I) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of BACE1 in 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 6jsn). 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-[(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: 6jsn:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6jsn

Go back to Fluorine Binding Sites List in 6jsn
Fluorine binding site 1 out of 2 in the Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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:F508

b:35.6
occ:1.00
 F2 A:C7O508 0.0 35.6 1.0
C21 A:C7O508 1.4 35.3 1.0
C20 A:C7O508 2.3 36.1 1.0
C10 A:C7O508 2.4 36.2 1.0
C1 A:C7O508 2.8 35.6 1.0
C2 A:C7O508 3.0 36.3 1.0
C9 A:C7O508 3.0 39.9 1.0
CE1 A:PHE132 3.1 35.1 1.0
CD1 A:PHE132 3.4 38.4 1.0
C5 A:C7O508 3.5 37.5 1.0
C19 A:C7O508 3.6 34.7 1.0
C11 A:C7O508 3.7 35.0 1.0
C12 A:C7O508 4.1 34.0 1.0
CD1 A:ILE142 4.2 49.5 1.0
CZ A:PHE132 4.2 36.4 1.0
N1 A:C7O508 4.3 35.2 1.0
C8 A:C7O508 4.4 42.0 1.0
C4 A:C7O508 4.6 35.4 1.0
CG A:PHE132 4.7 37.4 1.0
O A:HOH677 4.7 24.6 1.0
C6 A:C7O508 4.8 39.8 1.0

Fluorine binding site 2 out of 2 in 6jsn

Go back to Fluorine Binding Sites List in 6jsn
Fluorine binding site 2 out of 2 in the Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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:F508

b:43.6
occ:1.00
 F1 A:C7O508 0.0 43.6 1.0
C17 A:C7O508 1.4 41.0 1.0
O4 A:C7O508 2.3 40.5 1.0
C16 A:C7O508 2.9 37.0 1.0
N A:GLY37 2.9 41.0 1.0
N5 A:C7O508 3.0 38.0 1.0
CA A:GLY37 3.2 36.0 1.0
N A:GLY35 3.6 45.7 1.0
N A:GLN36 3.7 42.1 1.0
CA A:GLY35 3.8 42.9 1.0
CE1 A:TYR38 3.9 30.0 1.0
C A:GLY35 3.9 43.0 1.0
C A:GLY37 4.0 34.5 1.0
C15 A:C7O508 4.1 36.1 1.0
C18 A:C7O508 4.1 37.1 1.0
C A:GLN36 4.2 40.6 1.0
O A:LYS33 4.2 43.6 1.0
NH2 A:ARG331 4.2 52.5 1.0
CD1 A:TYR38 4.3 27.9 1.0
O A:GLY37 4.3 34.3 1.0
CA A:GLN36 4.5 39.3 1.0
OG1 A:THR256 4.6 34.7 1.0
CZ A:TYR38 4.6 30.6 1.0
C A:SER34 4.7 47.2 1.0
O A:GLY35 4.7 47.3 1.0
N A:TYR38 4.8 33.7 1.0
OE1 A:GLU363 4.9 42.1 1.0
CB A:ALA359 4.9 35.9 1.0
OH A:TYR38 4.9 27.6 1.0
N4 A:C7O508 5.0 35.5 1.0
CA A:SER34 5.0 49.6 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 12:42:28 2025

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