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Iodine in PDB 6jsg: Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-5- Chloropyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-5- Chloropyridine-2-Carboxamide

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

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-5- Chloropyridine-2-Carboxamide, PDB code: 6jsg 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 (°) 101.972, 101.972, 169.792, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 22.9

Other elements in 6jsg:

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

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Iodine Binding Sites:

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

Iodine binding site 1 out of 3 in 6jsg

Go back to Iodine Binding Sites List in 6jsg
Iodine binding site 1 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-5- Chloropyridine-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-[(4S)-2-Amino-4- Methyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-5- Chloropyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:40.7
occ:0.73
 O A:HOH747 3.1 39.0 1.0
O A:HOH729 3.4 40.8 1.0
OG A:SER129 3.5 35.5 1.0
N A:GLU128 3.8 39.5 1.0
CA A:GLU128 3.8 38.4 1.0
N A:SER129 3.9 35.7 1.0
C A:THR127 3.9 37.6 1.0
C A:GLU128 3.9 37.6 1.0
CD2 A:HIS69 4.0 34.4 1.0
O A:THR127 4.1 40.6 1.0
CB A:HIS69 4.2 33.1 1.0
CG2 A:ILE126 4.2 32.5 1.0
CE2 A:PHE133 4.2 36.5 1.0
CB A:SER129 4.3 35.2 1.0
CG A:HIS69 4.4 34.9 1.0
O A:ILE126 4.5 32.0 1.0
CA A:THR127 4.6 37.9 1.0
O A:GLU128 4.7 37.6 1.0
CA A:SER129 4.7 37.5 1.0
N A:THR127 4.7 35.2 1.0
C A:ILE126 4.7 33.1 1.0
CB A:ALA67 4.7 36.1 1.0
CD2 A:PHE133 4.8 37.4 1.0

Iodine binding site 2 out of 3 in 6jsg

Go back to Iodine Binding Sites List in 6jsg
Iodine binding site 2 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-5- Chloropyridine-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-[(4S)-2-Amino-4- Methyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-5- Chloropyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:72.2
occ:0.66
 NH1 A:ARG373 3.2 53.2 1.0
NE A:ARG373 3.5 46.4 1.0
O A:HOH612 3.7 33.0 1.0
CZ A:ARG373 3.8 50.2 1.0
NH2 A:ARG375 4.0 31.7 1.0
OD2 A:ASP370 4.4 37.3 1.0
CD A:ARG373 4.7 43.2 1.0

Iodine binding site 3 out of 3 in 6jsg

Go back to Iodine Binding Sites List in 6jsg
Iodine binding site 3 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-5- Chloropyridine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}-5- Chloropyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:55.5
occ:0.65
 N A:LYS131 3.4 38.5 1.0
O A:HOH658 3.6 27.9 1.0
NE2 A:HIS69 3.9 35.0 1.0
CA A:ASP130 4.0 41.2 1.0
C A:ASP130 4.2 39.1 1.0
CA A:LYS131 4.3 38.5 1.0
CE2 A:PHE71 4.3 56.3 1.0
OD1 A:ASP130 4.4 52.9 1.0
CE1 A:HIS69 4.4 34.7 1.0
O A:SER129 4.4 39.3 1.0
N A:ASP130 4.9 39.3 1.0
CZ A:PHE71 4.9 57.4 1.0
CG A:ASP130 4.9 49.9 1.0
C A:SER129 4.9 37.9 1.0
N A:PHE132 5.0 37.9 1.0
CD2 A:PHE71 5.0 52.4 1.0
CB A:ASP130 5.0 44.1 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: Sun Aug 11 23:16:49 2024

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