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Iodine in PDB 5ygx: Structure of BACE1 in Complex with N-(3-((4R,5R,6S)-2-Amino-6-(1,1- Difluoroethyl)-5-Fluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-4- Fluorophenyl)-5-(Fluoromethoxy)Pyrazine-2-Carboxamide

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

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

Protein crystallography data

The structure of Structure of BACE1 in Complex with N-(3-((4R,5R,6S)-2-Amino-6-(1,1- Difluoroethyl)-5-Fluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-4- Fluorophenyl)-5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 5ygx was solved by K.Nakahara, K.Fuchino, K.Komano, N.Asada, G.Tadano, T.Hasegawa, T.Yamamoto, Y.Sako, M.Ogawa, C.Unemura, M.Hosono, G.Sakaguchi, S.Ando, S.Ohnishi, Y.Kido, T.Fukushima, 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 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.550, 101.550, 170.811, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 20.7

Other elements in 5ygx:

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

Fluorine (F) 5 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of BACE1 in Complex with N-(3-((4R,5R,6S)-2-Amino-6-(1,1- Difluoroethyl)-5-Fluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-4- Fluorophenyl)-5-(Fluoromethoxy)Pyrazine-2-Carboxamide (pdb code 5ygx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Structure of BACE1 in Complex with N-(3-((4R,5R,6S)-2-Amino-6-(1,1- Difluoroethyl)-5-Fluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-4- Fluorophenyl)-5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 5ygx:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 5ygx

Go back to Iodine Binding Sites List in 5ygx
Iodine binding site 1 out of 2 in the Structure of BACE1 in Complex with N-(3-((4R,5R,6S)-2-Amino-6-(1,1- Difluoroethyl)-5-Fluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-4- Fluorophenyl)-5-(Fluoromethoxy)Pyrazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of BACE1 in Complex with N-(3-((4R,5R,6S)-2-Amino-6-(1,1- Difluoroethyl)-5-Fluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-4- Fluorophenyl)-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:43.4
occ:0.44
 O A:HOH801 2.8 30.8 1.0
O A:HOH650 3.0 51.0 1.0
OG A:SER105 3.5 26.6 1.0
N A:SER105 3.5 29.1 1.0
CA A:GLU104 3.6 33.6 1.0
C A:GLU104 3.7 30.7 1.0
N A:GLU104 3.7 34.2 1.0
CD2 A:HIS45 4.0 28.9 1.0
C A:THR103 4.0 35.6 1.0
CB A:SER105 4.1 27.7 1.0
CB A:HIS45 4.1 27.0 1.0
CG2 A:ILE102 4.2 24.3 1.0
O A:THR103 4.2 40.9 1.0
CE2 A:PHE109 4.3 25.1 1.0
CG A:HIS45 4.4 28.9 1.0
CA A:SER105 4.4 30.2 1.0
O A:GLU104 4.5 30.9 1.0
O A:ILE102 4.7 25.6 1.0
CA A:THR103 4.8 33.0 1.0
N A:THR103 4.8 29.6 1.0
CD2 A:PHE109 4.8 25.1 1.0
C A:ILE102 4.9 27.4 1.0

Iodine binding site 2 out of 2 in 5ygx

Go back to Iodine Binding Sites List in 5ygx
Iodine binding site 2 out of 2 in the Structure of BACE1 in Complex with N-(3-((4R,5R,6S)-2-Amino-6-(1,1- Difluoroethyl)-5-Fluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-4- Fluorophenyl)-5-(Fluoromethoxy)Pyrazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of BACE1 in Complex with N-(3-((4R,5R,6S)-2-Amino-6-(1,1- Difluoroethyl)-5-Fluoro-4-Methyl-5,6-Dihydro-4H-1,3-Oxazin-4-Yl)-4- Fluorophenyl)-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:54.8
occ:0.59
 N A:LYS107 3.5 29.8 1.0
O A:HOH643 3.7 21.6 1.0
NE2 A:HIS45 3.8 29.7 1.0
CA A:ASP106 4.0 32.8 1.0
OD1 A:ASP106 4.2 42.9 1.0
C A:ASP106 4.2 31.0 1.0
CE2 A:PHE47 4.3 50.2 1.0
O A:SER105 4.3 31.3 1.0
CA A:LYS107 4.4 30.6 1.0
CE1 A:HIS45 4.5 29.2 1.0
N A:ASP106 4.8 31.9 1.0
CG A:ASP106 4.9 38.7 1.0
CZ A:PHE47 4.9 51.5 1.0
C A:SER105 4.9 30.7 1.0
CD2 A:HIS45 4.9 28.9 1.0
CB A:ASP106 4.9 35.2 1.0

Reference:

K.Nakahara, K.Fuchino, K.Komano, N.Asada, G.Tadano, T.Hasegawa, T.Yamamoto, Y.Sako, M.Ogawa, C.Unemura, M.Hosono, H.Ito, G.Sakaguchi, S.Ando, S.Ohnishi, Y.Kido, T.Fukushima, D.Dhuyvetter, H.Borghys, H.J.M.Gijsen, Y.Yamano, Y.Iso, K.I.Kusakabe. Discovery of Potent and Centrally Active 6-Substituted 5-Fluoro-1,3-Dihydro-Oxazine Beta-Secretase (BACE1) Inhibitors Via Active Conformation Stabilization J. Med. Chem. V. 61 5525 2018.
ISSN: ISSN 1520-4804
PubMed: 29775538
DOI: 10.1021/ACS.JMEDCHEM.8B00011
Page generated: Sun Aug 11 22:21:39 2024

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