Atomistry » Fluorine » PDB 7cky-7db4 » 7d5u
Atomistry »
  Fluorine »
    PDB 7cky-7db4 »
      7d5u »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy