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Fluorine in PDB 7d5b: BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide

Enzymatic activity of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide

All present enzymatic activity of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide:
3.4.23.45;

Protein crystallography data

The structure of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide, PDB code: 7d5b 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) 61.70 / 1.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.807, 74.396, 110.408, 90, 90, 90
R / Rfree (%) 19.5 / 22.2

Other elements in 7d5b:

The structure of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide (pdb code 7d5b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide, PDB code: 7d5b:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7d5b

Go back to Fluorine Binding Sites List in 7d5b
Fluorine binding site 1 out of 2 in the BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-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-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:23.4
occ:1.00
 F18 A:66F401 0.0 23.4 1.0
C17 A:66F401 1.3 21.1 1.0
C16 A:66F401 2.3 19.8 1.0
C1 A:66F401 2.4 17.3 1.0
C2 A:66F401 2.9 17.8 1.0
CE2 A:TYR87 3.0 32.9 1.0
C4 A:66F401 3.0 17.2 1.0
C3 A:66F401 3.1 20.8 1.0
CD2 A:TYR87 3.3 36.2 1.0
CD1 A:PHE124 3.4 34.1 1.0
CE1 A:PHE124 3.4 36.1 1.0
CZ A:TYR87 3.5 29.2 1.0
C15 A:66F401 3.6 20.5 1.0
C13 A:66F401 3.6 17.2 1.0
O A:HOH727 3.7 35.3 1.0
O11 A:66F401 3.7 20.1 1.0
OH A:TYR87 3.9 29.7 1.0
S5 A:66F401 4.0 19.6 1.0
C14 A:66F401 4.1 18.5 1.0
CG A:TYR87 4.2 28.9 1.0
CD1 A:ILE134 4.2 16.6 0.5
CE1 A:TYR87 4.3 27.9 1.0
N8 A:66F401 4.3 15.9 1.0
CD1 A:TYR87 4.6 28.4 1.0
CG A:PHE124 4.6 32.3 1.0
CZ A:PHE124 4.6 36.4 1.0

Fluorine binding site 2 out of 2 in 7d5b

Go back to Fluorine Binding Sites List in 7d5b
Fluorine binding site 2 out of 2 in the BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-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-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:21.2
occ:1.00
 F28 A:66F401 0.0 21.2 1.0
C21 A:66F401 1.3 19.7 1.0
C22 A:66F401 2.3 21.2 1.0
C20 A:66F401 2.4 20.7 1.0
CB A:ALA347 3.1 24.7 1.0
O A:SER26 3.2 32.8 1.0
CA A:SER26 3.4 27.0 1.0
N23 A:66F401 3.5 19.1 1.0
C25 A:66F401 3.6 20.3 1.0
C A:SER26 3.6 26.6 1.0
O A:ASP25 3.9 24.2 1.0
CA A:GLY29 4.0 23.5 1.0
CA A:THR245 4.1 19.1 0.5
CB A:SER26 4.1 26.4 1.0
C24 A:66F401 4.1 20.6 1.0
CA A:THR245 4.1 18.9 0.5
CG2 A:THR245 4.1 23.7 0.5
O A:THR244 4.2 16.6 1.0
N A:GLY29 4.2 23.5 1.0
OG1 A:THR245 4.3 24.6 0.5
O A:SER242 4.3 15.5 1.0
N A:SER26 4.5 24.3 1.0
O A:HOH648 4.5 18.9 1.0
CA A:ALA347 4.5 25.3 1.0
CD1 A:TYR30 4.6 19.3 1.0
N A:THR245 4.6 16.9 0.5
CB A:THR245 4.6 21.2 0.5
N A:THR245 4.6 16.8 0.5
C A:THR244 4.6 16.1 1.0
C A:ASP25 4.6 23.9 1.0
CB A:THR245 4.6 20.2 0.5
CE1 A:TYR30 4.7 18.3 1.0
CG2 A:THR245 4.8 18.6 0.5
N A:GLY27 4.8 24.8 1.0
C A:GLY29 4.9 18.8 1.0
O A:THR245 5.0 22.8 0.5
N A:TYR30 5.0 17.1 1.0
O A:THR245 5.0 22.4 0.5

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 06:20:54 2024

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