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Fluorine in PDB 7d5a: Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide, PDB code: 7d5a was solved by K.Fujimoto, S.Yoshida, G.Tadano, N.Asada, K.Fuchino, S.Suzuki, E.Matsuoka, T.Yamamoto, S.Yamamoto, S.Ando, N.Kanegawa, Y.Tonomura, 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 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.1, 102.1, 170.041, 90, 90, 120
R / Rfree (%) 20.7 / 24.2

Other elements in 7d5a:

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide also contains other interesting chemical elements:

Iodine (I) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide (pdb code 7d5a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide, PDB code: 7d5a:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7d5a

Go back to Fluorine Binding Sites List in 7d5a
Fluorine binding site 1 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-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-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:38.6
occ:1.00
 F1 A:GX6504 0.0 38.6 1.0
C1 A:GX6504 1.3 39.2 1.0
C2 A:GX6504 2.3 39.5 1.0
C13 A:GX6504 2.4 42.5 1.0
C15 A:GX6504 2.7 38.6 1.0
C14 A:GX6504 2.9 41.7 1.0
C19 A:GX6504 3.0 47.0 1.0
CE1 A:PHE108 3.2 28.3 1.0
C16 A:GX6504 3.2 38.0 1.0
C18 A:GX6504 3.4 45.3 1.0
CD1 A:PHE108 3.4 26.6 1.0
C3 A:GX6504 3.6 40.6 1.0
C12 A:GX6504 3.6 39.9 1.0
OH A:TYR71 3.9 47.2 1.0
CZ A:TYR71 3.9 44.6 1.0
CD1 A:ILE118 3.9 27.3 1.0
C4 A:GX6504 4.1 41.7 1.0
CE2 A:TYR71 4.1 42.8 1.0
C17 A:GX6504 4.2 33.4 1.0
N5 A:GX6504 4.3 38.8 1.0
C20 A:GX6504 4.3 49.1 1.0
CE1 A:TYR71 4.4 46.3 1.0
C21 A:GX6504 4.4 46.7 1.0
CZ A:PHE108 4.4 26.7 1.0
C22 A:GX6504 4.5 44.7 1.0
F2 A:GX6504 4.6 50.8 1.0
CG A:PHE108 4.7 27.4 1.0
CD2 A:TYR71 4.8 44.5 1.0
CD1 A:TRP76 4.9 35.2 1.0

Fluorine binding site 2 out of 3 in 7d5a

Go back to Fluorine Binding Sites List in 7d5a
Fluorine binding site 2 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-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-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:50.8
occ:1.00
 F2 A:GX6504 0.0 50.8 1.0
C20 A:GX6504 1.4 49.1 1.0
F3 A:GX6504 2.2 47.2 1.0
C21 A:GX6504 2.4 46.7 1.0
C19 A:GX6504 2.4 47.0 1.0
C18 A:GX6504 3.3 45.3 1.0
CB A:TYR71 3.4 47.9 1.0
O A:HOH765 3.5 46.8 1.0
CG A:TYR71 3.5 46.5 1.0
CD2 A:TYR71 3.5 44.5 1.0
O A:HOH764 3.6 47.7 1.0
O A:HOH803 3.9 49.9 1.0
C15 A:GX6504 4.1 38.6 1.0
CD1 A:TYR71 4.3 45.3 1.0
C14 A:GX6504 4.3 41.7 1.0
CE2 A:TYR71 4.3 42.8 1.0
C16 A:GX6504 4.4 38.0 1.0
C22 A:GX6504 4.4 44.7 1.0
O A:HOH795 4.5 50.9 1.0
F1 A:GX6504 4.6 38.6 1.0
O A:HOH699 4.8 38.7 1.0
CA A:TYR71 4.8 46.9 1.0
CG1 A:VAL69 4.9 39.1 1.0
CE1 A:TYR71 5.0 46.3 1.0

Fluorine binding site 3 out of 3 in 7d5a

Go back to Fluorine Binding Sites List in 7d5a
Fluorine binding site 3 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-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-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:47.2
occ:1.00
 F3 A:GX6504 0.0 47.2 1.0
C20 A:GX6504 1.4 49.1 1.0
F2 A:GX6504 2.2 50.8 1.0
C19 A:GX6504 2.4 47.0 1.0
C21 A:GX6504 2.4 46.7 1.0
C18 A:GX6504 3.0 45.3 1.0
C22 A:GX6504 3.4 44.7 1.0
CB A:TYR71 3.5 47.9 1.0
CG A:TYR71 3.9 46.5 1.0
O A:HOH699 4.0 38.7 1.0
CD1 A:TYR71 4.2 45.3 1.0
O2 A:GX6504 4.4 45.2 1.0
C14 A:GX6504 4.6 41.7 1.0
O A:HOH769 4.6 48.4 1.0
CD2 A:TYR71 4.6 44.5 1.0
O A:HOH764 4.7 47.7 1.0
CA A:TYR71 4.9 46.9 1.0

Reference:

K.Fujimoto, S.Yoshida, G.Tadano, N.Asada, K.Fuchino, S.Suzuki, E.Matsuoka, T.Yamamoto, S.Yamamoto, S.Ando, N.Kanegawa, Y.Tonomura, H.Ito, D.Moechars, F.J.R.Rombouts, H.J.M.Gijsen, K.I.Kusakabe. Structure-Based Approaches to Improving Selectivity Through Utilizing Explicit Water Molecules: Discovery of Selective Beta-Secretase (BACE1) Inhibitors Over BACE2. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 33719429
DOI: 10.1021/ACS.JMEDCHEM.0C01858
Page generated: Tue Jul 15 19:03:21 2025

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