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Iodine in PDB 6jt3: Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-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-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-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-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-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-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jt3 was solved by G.Tadano, K.Komano, S.Yoshida, S.Suzuki, K.Nakahara, K.Fuchino, K.Fujimoto, E.Matsuoka, T.Yamamoto, N.Asada, H.Ito, G.Sakaguchi, N.Kanegawa, Y.Kido, S.Ando, T.Fukushima, A.Teisman, V.Urmaliya, D.Dhuyvetter, H.Borghys, A.V.D.Bergh, N.Austin, H.J.M.Gijsen, Y.Yamano, Y.Iso, K.I.Kusakabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.210, 101.210, 171.351, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 24.3

Other elements in 6jt3:

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

Fluorine (F) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 5-(Fluoromethoxy)Pyrazine-2-Carboxamide (pdb code 6jt3). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jt3:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 6jt3

Go back to Iodine Binding Sites List in 6jt3
Iodine binding site 1 out of 2 in the Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-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 Iodine with other atoms in the I binding site number 1 of Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-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:I501

b:48.6
occ:0.49
 O A:HOH751 2.9 33.4 1.0
OG A:SER105 3.4 34.1 1.0
N A:SER105 3.5 35.6 1.0
CA A:GLU104 3.8 36.3 1.0
C A:GLU104 3.8 35.5 1.0
CD2 A:HIS45 3.9 33.2 1.0
CB A:SER105 4.0 34.5 1.0
N A:GLU104 4.0 36.8 1.0
O A:THR103 4.0 41.8 1.0
CB A:HIS45 4.0 32.9 1.0
C A:THR103 4.0 36.9 1.0
OE2 A:GLU104 4.1 42.5 1.0
CG2 A:ILE102 4.1 27.6 1.0
CE2 A:PHE109 4.2 28.4 1.0
CG A:HIS45 4.3 33.4 1.0
CA A:SER105 4.3 35.9 1.0
O A:ILE102 4.5 27.6 1.0
O A:GLU104 4.7 35.5 1.0
C A:ILE102 4.8 29.9 1.0
CD2 A:PHE109 4.8 29.6 1.0
CD A:GLU104 4.8 41.3 1.0
CA A:THR103 4.8 34.7 1.0
N A:THR103 4.8 31.7 1.0
CB A:ALA43 5.0 27.1 1.0

Iodine binding site 2 out of 2 in 6jt3

Go back to Iodine Binding Sites List in 6jt3
Iodine binding site 2 out of 2 in the Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-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 Iodine with other atoms in the I binding site number 2 of Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-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:I502

b:60.9
occ:0.60
 N A:LYS107 3.5 34.5 1.0
O A:HOH636 3.6 22.0 1.0
NE2 A:HIS45 3.7 33.1 1.0
CA A:ASP106 4.0 36.0 1.0
C A:ASP106 4.2 35.7 1.0
CE1 A:HIS45 4.3 33.4 1.0
OD1 A:ASP106 4.3 41.7 1.0
CA A:LYS107 4.3 34.2 1.0
CE2 A:PHE47 4.4 54.4 1.0
O A:SER105 4.5 35.8 1.0
N A:ASP106 4.7 36.1 1.0
CD2 A:HIS45 4.8 33.2 1.0
C A:SER105 4.9 36.0 1.0
CG A:ASP106 5.0 40.0 1.0
CB A:ASP106 5.0 37.6 1.0

Reference:

G.Tadano, K.Komano, S.Yoshida, S.Suzuki, K.Nakahara, K.Fuchino, K.Fujimoto, E.Matsuoka, T.Yamamoto, N.Asada, H.Ito, G.Sakaguchi, N.Kanegawa, Y.Kido, S.Ando, T.Fukushima, A.Teisman, V.Urmaliya, D.Dhuyvetter, H.Borghys, A.Van Den Bergh, N.Austin, H.J.M.Gijsen, Y.Yamano, Y.Iso, K.I.Kusakabe. Discovery of An Extremely Potent Thiazine-Based Beta-Secretase Inhibitor with Reduced Cardiovascular and Liver Toxicity at A Low Projected Human Dose. J.Med.Chem. V. 62 9331 2019.
ISSN: ISSN 0022-2623
PubMed: 31549838
DOI: 10.1021/ACS.JMEDCHEM.9B01140
Page generated: Sun Aug 11 23:18:54 2024

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