Fluorine in PDB 7d2x: Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide, PDB code: 7d2x 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 / 2.45
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.719, 101.719, 169.35, 90, 90, 120
R / Rfree (%) 18.5 / 22.9

Other elements in 7d2x:

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide also contains other interesting chemical elements:

Iodine (I) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide (pdb code 7d2x). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide, PDB code: 7d2x:

Fluorine binding site 1 out of 1 in 7d2x

Go back to Fluorine Binding Sites List in 7d2x
Fluorine binding site 1 out of 1 in the Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-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 Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F505

b:32.1
occ:1.00
 F A:GTU505 0.0 32.1 1.0
C19 A:GTU505 1.3 30.9 1.0
C18 A:GTU505 2.4 30.6 1.0
C7 A:GTU505 2.4 31.3 1.0
C2 A:GTU505 2.9 29.6 1.0
C3 A:GTU505 2.9 30.5 1.0
C4 A:GTU505 3.1 29.2 1.0
CE1 A:PHE108 3.3 30.4 1.0
C1 A:GTU505 3.3 29.6 1.0
CD1 A:PHE108 3.4 31.8 1.0
C17 A:GTU505 3.6 31.2 1.0
C8 A:GTU505 3.7 31.1 1.0
O A:HOH766 4.0 36.9 1.0
CD1 A:ILE118 4.1 28.4 1.0
C9 A:GTU505 4.1 32.2 1.0
C5 A:GTU505 4.2 29.5 1.0
C A:GTU505 4.2 30.1 1.0
CZ A:PHE108 4.4 31.1 1.0
N1 A:GTU505 4.4 29.6 1.0
CG A:PHE108 4.6 31.8 1.0
OH A:TYR71 4.7 82.6 1.0
CE2 A:TYR71 4.8 78.8 1.0
CZ A:TYR71 4.9 80.7 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: Sat Apr 3 15:09:01 2021

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