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Fluorine in PDB 7d2v: Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in 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: 7d2v 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 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.72, 102.72, 170.591, 90, 90, 120
R / Rfree (%) 20.6 / 24.5

Other elements in 7d2v:

The structure of Crystal Structure of BACE1 in 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:

Iodine (I) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of BACE1 in 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 7d2v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of BACE1 in 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: 7d2v:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7d2v

Go back to Fluorine Binding Sites List in 7d2v
Fluorine binding site 1 out of 2 in the Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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:F506

b:37.5
occ:1.00
 F18 A:66F506 0.0 37.5 1.0
C17 A:66F506 1.4 35.0 1.0
C16 A:66F506 2.4 33.2 1.0
C1 A:66F506 2.5 34.6 1.0
C3 A:66F506 2.9 34.3 1.0
C2 A:66F506 2.9 35.3 1.0
C4 A:66F506 3.0 35.9 1.0
CE2 A:TYR71 3.0 51.5 1.0
CE1 A:PHE108 3.3 29.5 1.0
CZ A:TYR71 3.5 50.7 1.0
CD1 A:PHE108 3.5 28.6 1.0
CD2 A:TYR71 3.5 51.0 1.0
C15 A:66F506 3.7 32.6 1.0
C13 A:66F506 3.7 33.6 1.0
OH A:TYR71 3.8 55.5 1.0
CD1 A:ILE118 4.0 26.4 1.0
O12 A:66F506 4.0 33.8 1.0
S5 A:66F506 4.1 40.3 1.0
C14 A:66F506 4.2 33.8 1.0
CE1 A:TYR71 4.3 50.3 1.0
CG A:TYR71 4.4 50.8 1.0
N8 A:66F506 4.4 33.4 1.0
CZ A:PHE108 4.6 27.9 1.0
CD1 A:TYR71 4.7 50.4 1.0
CG A:PHE108 4.9 30.1 1.0

Fluorine binding site 2 out of 2 in 7d2v

Go back to Fluorine Binding Sites List in 7d2v
Fluorine binding site 2 out of 2 in the Crystal Structure of BACE1 in 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 Crystal Structure of BACE1 in 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:F506

b:34.0
occ:1.00
 F28 A:66F506 0.0 34.0 1.0
C21 A:66F506 1.4 34.7 1.0
C22 A:66F506 2.4 33.5 1.0
C20 A:66F506 2.4 35.3 1.0
OG1 A:THR232 3.4 31.6 1.0
CB A:ALA335 3.5 33.4 1.0
N23 A:66F506 3.6 33.7 1.0
C25 A:66F506 3.7 35.1 1.0
CA A:THR232 3.7 31.8 1.0
CA A:GLY13 3.9 30.9 1.0
N A:THR232 4.0 30.0 1.0
O A:THR231 4.0 30.1 1.0
CB A:THR232 4.0 32.2 1.0
N A:GLY13 4.1 32.0 1.0
C24 A:66F506 4.1 34.2 1.0
C A:THR231 4.2 30.4 1.0
O A:SER229 4.4 22.8 1.0
CG2 A:THR232 4.6 31.5 1.0
CE2 A:TYR14 4.6 28.4 1.0
CD2 A:TYR14 4.8 28.2 1.0
CA A:ALA335 4.9 33.6 1.0
C A:THR232 5.0 33.0 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 19:02:14 2025

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