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Fluorine in PDB 5ygy: Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide, PDB code: 5ygy was solved by K.Fuchino, Y.Mitsuoka, M.Masui, N.Kurose, S.Yoshida, K.Komano, T.Yamamoto, M.Ogawa, C.Unemura, M.Hosono, H.Ito, G.Sakaguchi, S.Ando, S.Ohnishi, Y.Kido, T.Fukushima, H.Miyajima, S.Hiroyama, K.Koyabu, D.Dhuyvetter, H.Borghys, H.Gijsen, Y.Yamano, Y.Iso, K.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 (°) 102.149, 102.149, 171.125, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 23.5

Other elements in 5ygy:

The structure of Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide also contains other interesting chemical elements:

Iodine (I) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide (pdb code 5ygy). 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 (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide, PDB code: 5ygy:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5ygy

Go back to Fluorine Binding Sites List in 5ygy
Fluorine binding site 1 out of 2 in the Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide


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 (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F509

b:45.8
occ:1.00
 F2 A:0B6509 0.0 45.8 1.0
C19 A:0B6509 1.3 48.0 1.0
C18 A:0B6509 2.3 45.8 1.0
C7 A:0B6509 2.5 48.4 1.0
C1 A:0B6509 3.0 48.8 1.0
C2 A:0B6509 3.1 50.2 1.0
CE2 A:TYR71 3.1 63.7 1.0
CZ A:TYR71 3.2 63.9 1.0
CE1 A:PHE108 3.3 30.1 1.0
C3 A:0B6509 3.4 53.5 1.0
OH A:TYR71 3.4 68.3 1.0
CD1 A:PHE108 3.6 30.6 1.0
C17 A:0B6509 3.6 45.0 1.0
C8 A:0B6509 3.7 48.0 1.0
CD2 A:TYR71 3.7 61.2 1.0
CE1 A:TYR71 4.0 64.0 1.0
C9 A:0B6509 4.2 47.0 1.0
CG A:TYR71 4.4 62.2 1.0
CD1 A:ILE118 4.5 32.1 1.0
N2 A:0B6509 4.5 48.5 1.0
CD1 A:TYR71 4.5 62.5 1.0
CZ A:PHE108 4.5 29.8 1.0
C4 A:0B6509 4.6 57.2 1.0
CG A:PHE108 4.9 31.7 1.0

Fluorine binding site 2 out of 2 in 5ygy

Go back to Fluorine Binding Sites List in 5ygy
Fluorine binding site 2 out of 2 in the Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide


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 (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F509

b:64.1
occ:1.00
 F1 A:0B6509 0.0 64.1 1.0
C5 A:0B6509 1.4 58.7 1.0
C4 A:0B6509 2.4 57.2 1.0
C3 A:0B6509 3.1 53.5 1.0
O1 A:0B6509 3.4 53.6 1.0
CD1 A:TYR71 4.0 62.5 1.0
O A:HOH744 4.3 53.9 1.0
CB A:TYR71 4.5 58.4 1.0
CG A:TYR71 4.5 62.2 1.0
C2 A:0B6509 4.5 50.2 1.0
C6 A:0B6509 4.6 49.7 1.0
CE1 A:TYR71 4.8 64.0 1.0
N2 A:0B6509 5.0 48.5 1.0

Reference:

K.Fuchino, Y.Mitsuoka, M.Masui, N.Kurose, S.Yoshida, K.Komano, T.Yamamoto, M.Ogawa, C.Unemura, M.Hosono, H.Ito, G.Sakaguchi, S.Ando, S.Ohnishi, Y.Kido, T.Fukushima, H.Miyajima, S.Hiroyama, K.Koyabu, D.Dhuyvetter, H.Borghys, H.J.M.Gijsen, Y.Yamano, Y.Iso, K.I.Kusakabe. Rational Design of Novel 1,3-Oxazine Based Beta-Secretase (BACE1) Inhibitors: Incorporation of A Double Bond to Reduce P-Gp Efflux Leading to Robust A Beta Reduction in the Brain J. Med. Chem. V. 61 5122 2018.
ISSN: ISSN 1520-4804
PubMed: 29733614
DOI: 10.1021/ACS.JMEDCHEM.8B00002
Page generated: Tue Jul 15 09:30:15 2025

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