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Fluorine in PDB 6jsf: Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jsf was solved by K.Fujimoto, E.Matsuoka, N.Asada, G.Tadano, T.Yamamoto, K.Nakahara, K.Fuchino, H.Ito, N.Kanegawa, D.Moechars, 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 / 2.30
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.535, 102.535, 170.350, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21.3

Other elements in 6jsf:

The structure of Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide also contains other interesting chemical elements:

Iodine (I) 7 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide (pdb code 6jsf). 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-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jsf:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6jsf

Go back to Fluorine Binding Sites List in 6jsf
Fluorine binding site 1 out of 2 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-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-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F510

b:36.2
occ:1.00
 F1 A:C7X510 0.0 36.2 1.0
C17 A:C7X510 1.4 34.5 1.0
O1 A:C7X510 2.3 34.0 1.0
C13 A:C7X510 2.9 32.8 1.0
O A:HOH746 2.9 47.0 1.0
N4 A:C7X510 3.0 32.5 1.0
N A:GLY37 3.2 33.4 1.0
CA A:GLY37 3.5 32.3 1.0
N A:GLY35 3.5 39.5 1.0
CA A:GLY35 3.8 37.7 1.0
CE1 A:TYR38 3.8 29.1 1.0
N A:GLN36 3.8 36.3 1.0
C A:GLY35 4.0 37.5 1.0
C12 A:C7X510 4.1 32.1 1.0
C A:GLY37 4.2 32.3 1.0
CD1 A:TYR38 4.2 29.3 1.0
C14 A:C7X510 4.2 31.7 1.0
O A:LYS33 4.3 40.8 1.0
C A:GLN36 4.3 35.6 1.0
O A:GLY37 4.4 32.1 1.0
OG1 A:THR256 4.5 31.6 1.0
C A:SER34 4.5 42.1 1.0
CZ A:TYR38 4.6 30.0 1.0
CA A:GLN36 4.7 35.8 1.0
NH1 A:ARG331 4.8 48.3 1.0
O A:GLY35 4.8 37.3 1.0
CB A:ALA359 4.8 28.7 1.0
OE2 A:GLU363 4.8 37.3 1.0
CA A:SER34 4.9 43.9 1.0
OH A:TYR38 4.9 31.5 1.0
N A:TYR38 5.0 30.6 1.0

Fluorine binding site 2 out of 2 in 6jsf

Go back to Fluorine Binding Sites List in 6jsf
Fluorine binding site 2 out of 2 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-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-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F510

b:33.1
occ:1.00
 F A:C7X510 0.0 33.1 1.0
C3 A:C7X510 1.3 32.5 1.0
C2 A:C7X510 2.4 32.5 1.0
C4 A:C7X510 2.5 32.2 1.0
C15 A:C7X510 2.9 31.5 1.0
C6 A:C7X510 3.0 33.0 1.0
CE1 A:PHE132 3.0 32.8 1.0
C16 A:C7X510 3.1 36.0 1.0
C22 A:C7X510 3.2 35.9 1.0
CD1 A:PHE132 3.3 33.1 1.0
C18 A:C7X510 3.4 37.2 1.0
C21 A:C7X510 3.6 36.8 1.0
C7 A:C7X510 3.6 34.5 1.0
CD1 A:ILE142 3.6 37.8 1.0
C1 A:C7X510 3.6 31.6 1.0
C5 A:C7X510 3.7 31.7 1.0
C19 A:C7X510 3.8 38.2 1.0
C20 A:C7X510 3.9 36.6 1.0
C A:C7X510 4.1 31.8 1.0
CZ A:PHE132 4.2 33.0 1.0
N A:C7X510 4.4 32.8 1.0
CG A:PHE132 4.5 32.9 1.0
C8 A:C7X510 4.9 33.8 1.0
O A:HOH710 4.9 48.0 1.0
CG1 A:ILE142 5.0 34.7 1.0
CD1 A:TRP100 5.0 33.4 1.0

Reference:

K.Fujimoto, E.Matsuoka, N.Asada, G.Tadano, T.Yamamoto, K.Nakahara, K.Fuchino, H.Ito, N.Kanegawa, D.Moechars, H.J.M.Gijsen, K.I.Kusakabe. Structure-Based Design of Selective Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitors: Targeting the Flap to Gain Selectivity Over BACE2. J.Med.Chem. V. 62 5080 2019.
ISSN: ISSN 0022-2623
PubMed: 31021626
DOI: 10.1021/ACS.JMEDCHEM.9B00309
Page generated: Tue Jul 15 12:41:55 2025

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