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Fluorine in PDB 6jse: Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-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,5R)-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,5R)-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,5R)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jse 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 / 2.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.788, 101.788, 170.425, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 20.8

Other elements in 6jse:

The structure of Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-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) 6 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 2 in 6jse

Go back to Fluorine Binding Sites List in 6jse
Fluorine binding site 1 out of 2 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-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,5R)-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:F508

b:35.8
occ:1.00
 F1 A:C6R508 0.0 35.8 1.0
C17 A:C6R508 1.4 35.0 1.0
O1 A:C6R508 2.3 33.4 1.0
C13 A:C6R508 3.1 31.8 1.0
N A:GLY37 3.1 29.8 1.0
N4 A:C6R508 3.3 32.2 1.0
CA A:GLY37 3.4 29.0 1.0
N A:GLY35 3.4 39.1 1.0
N A:GLN36 3.7 33.2 1.0
CA A:GLY35 3.9 36.7 1.0
NH1 A:ARG331 3.9 56.9 1.0
O A:LYS33 3.9 39.3 1.0
CE1 A:TYR38 3.9 28.8 1.0
C A:GLY35 4.0 35.2 1.0
C A:GLY37 4.1 28.4 1.0
C12 A:C6R508 4.2 31.2 1.0
C A:GLN36 4.2 32.1 1.0
CD1 A:TYR38 4.3 27.7 1.0
C A:SER34 4.4 42.8 1.0
O A:GLY37 4.5 29.5 1.0
C14 A:C6R508 4.5 31.5 1.0
CA A:GLN36 4.6 32.7 1.0
NH2 A:ARG331 4.6 57.0 1.0
OG1 A:THR256 4.6 28.4 1.0
CZ A:ARG331 4.6 56.5 1.0
CA A:SER34 4.7 44.0 1.0
CZ A:TYR38 4.7 28.9 1.0
OE2 A:GLU363 4.7 37.3 1.0
CB A:ALA359 4.7 29.7 1.0
O A:GLY35 4.8 35.7 1.0
C A:LYS33 4.9 41.3 1.0
OH A:TYR38 4.9 31.3 1.0
N A:TYR38 4.9 27.2 1.0

Fluorine binding site 2 out of 2 in 6jse

Go back to Fluorine Binding Sites List in 6jse
Fluorine binding site 2 out of 2 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-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,5R)-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:F508

b:29.9
occ:1.00
 F A:C6R508 0.0 29.9 1.0
C3 A:C6R508 1.3 29.7 1.0
C2 A:C6R508 2.4 29.1 1.0
C4 A:C6R508 2.5 29.2 1.0
C6 A:C6R508 3.0 29.0 1.0
C15 A:C6R508 3.1 28.4 1.0
OH A:TYR95 3.1 30.1 1.0
CZ A:TYR95 3.1 30.4 1.0
C7 A:C6R508 3.2 29.6 1.0
CE1 A:PHE132 3.2 27.3 1.0
CD1 A:PHE132 3.3 27.1 1.0
CE2 A:TYR95 3.5 31.6 1.0
CE1 A:TYR95 3.6 30.1 1.0
C1 A:C6R508 3.6 29.5 1.0
C5 A:C6R508 3.7 29.5 1.0
CD1 A:ILE142 3.9 26.5 1.0
C8 A:C6R508 4.1 29.5 1.0
C A:C6R508 4.2 30.0 1.0
C16 A:C6R508 4.2 30.9 1.0
C22 A:C6R508 4.2 31.4 1.0
CD2 A:TYR95 4.3 30.8 1.0
O A:HOH628 4.3 31.4 1.0
CD1 A:TYR95 4.4 30.4 1.0
N A:C6R508 4.5 28.3 1.0
CZ A:PHE132 4.5 27.0 1.0
CG A:PHE132 4.6 26.9 1.0
CG A:TYR95 4.7 31.3 1.0
CD1 A:TRP100 4.9 31.9 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 12:41:49 2025

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