Atomistry » Fluorine » PDB 7cl1-7db8 » 7d5u
Atomistry »
  Fluorine »
    PDB 7cl1-7db8 »
      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: Tue Jul 15 19:03:55 2025

Last articles

Mg in 6RCW
Mg in 6RCZ
Mg in 6RB7
Mg in 6RCN
Mg in 6RCR
Mg in 6RCL
Mg in 6RCA
Mg in 6RBM
Mg in 6RBL
Mg in 6RAM
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy