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Fluorine in PDB 7d5u: BACE2 Xaperone 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 BACE2 Xaperone 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 BACE2 Xaperone 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:
3.4.23.45;

Protein crystallography data

The structure of BACE2 Xaperone 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: 7d5u 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) 61.31 / 2.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.926, 74.339, 108.389, 90, 90, 90
R / Rfree (%) 20.7 / 25.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the BACE2 Xaperone 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 7d5u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the BACE2 Xaperone 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: 7d5u:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7d5u

Go back to Fluorine Binding Sites List in 7d5u
Fluorine binding site 1 out of 3 in the BACE2 Xaperone 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 BACE2 Xaperone 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:F401

b:63.0
occ:1.00
 F1 A:GX6401 0.0 63.0 1.0
C1 A:GX6401 1.3 64.5 1.0
C2 A:GX6401 2.3 60.5 1.0
C13 A:GX6401 2.4 64.3 1.0
C15 A:GX6401 2.8 53.4 1.0
C14 A:GX6401 2.9 55.1 1.0
C21 A:GX6401 2.9 61.4 1.0
C16 A:GX6401 3.3 63.1 1.0
C18 A:GX6401 3.3 67.4 1.0
CD1 A:PHE124 3.3 79.6 1.0
CE1 A:PHE124 3.4 81.4 1.0
C3 A:GX6401 3.6 57.2 1.0
OH A:TYR87 3.6 79.8 1.0
C12 A:GX6401 3.6 55.5 1.0
CZ A:TYR87 3.8 90.5 1.0
CE2 A:TYR87 3.9 81.0 1.0
C4 A:GX6401 4.1 49.3 1.0
C22 A:GX6401 4.2 55.4 1.0
C17 A:GX6401 4.2 53.0 1.0
C20 A:GX6401 4.3 72.2 1.0
N5 A:GX6401 4.3 45.6 1.0
CD1 A:ILE134 4.4 69.0 1.0
C19 A:GX6401 4.4 69.2 1.0
CG A:PHE124 4.4 63.7 1.0
CE1 A:TYR87 4.6 73.2 1.0
CZ A:PHE124 4.6 70.6 1.0
F3 A:GX6401 4.6 86.8 1.0
CD2 A:TYR87 4.8 76.6 1.0
CD1 A:TRP92 4.9 81.3 1.0

Fluorine binding site 2 out of 3 in 7d5u

Go back to Fluorine Binding Sites List in 7d5u
Fluorine binding site 2 out of 3 in the BACE2 Xaperone 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 BACE2 Xaperone 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:F401

b:82.1
occ:1.00
 F2 A:GX6401 0.0 82.1 1.0
C20 A:GX6401 1.4 72.2 1.0
F3 A:GX6401 2.3 86.8 1.0
C19 A:GX6401 2.4 69.2 1.0
C21 A:GX6401 2.6 61.4 1.0
C18 A:GX6401 3.1 67.4 1.0
CB A:TYR87 3.2 68.3 1.0
CG A:TYR87 3.4 79.4 1.0
C22 A:GX6401 3.6 55.4 1.0
CD1 A:TYR87 4.0 84.5 1.0
CD2 A:TYR87 4.0 76.6 1.0
O2 A:GX6401 4.3 64.3 1.0
C14 A:GX6401 4.5 55.1 1.0
O A:HOH560 4.7 74.7 1.0
CA A:TYR87 4.7 80.7 1.0
O A:HOH578 4.9 84.8 1.0
CE2 A:TYR87 4.9 81.0 1.0
CE1 A:TYR87 4.9 73.2 1.0

Fluorine binding site 3 out of 3 in 7d5u

Go back to Fluorine Binding Sites List in 7d5u
Fluorine binding site 3 out of 3 in the BACE2 Xaperone 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 BACE2 Xaperone 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:F401

b:86.8
occ:1.00
 F3 A:GX6401 0.0 86.8 1.0
C20 A:GX6401 1.4 72.2 1.0
F2 A:GX6401 2.3 82.1 1.0
C21 A:GX6401 2.4 61.4 1.0
C19 A:GX6401 2.5 69.2 1.0
CD2 A:TYR87 3.0 76.6 1.0
CG A:TYR87 3.3 79.4 1.0
C18 A:GX6401 3.3 67.4 1.0
CB A:TYR87 3.5 68.3 1.0
CE2 A:TYR87 3.8 81.0 1.0
CG1 A:VAL85 3.9 79.6 1.0
O A:HOH584 4.0 73.2 1.0
C15 A:GX6401 4.1 53.4 1.0
C16 A:GX6401 4.3 63.1 1.0
C14 A:GX6401 4.3 55.1 1.0
O A:HOH560 4.3 74.7 1.0
CD1 A:TYR87 4.3 84.5 1.0
C22 A:GX6401 4.6 55.4 1.0
F1 A:GX6401 4.6 63.0 1.0
CZ A:TYR87 4.7 90.5 1.0
CA A:TYR87 4.9 80.7 1.0
NE1 A:TRP92 4.9 72.4 1.0
C17 A:GX6401 4.9 53.0 1.0
CE1 A:TYR87 5.0 73.2 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: Fri Aug 2 06:21:10 2024

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