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Iodine in PDB 7dcz: Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2- Carboxamide

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

All present enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-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-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2- Carboxamide, PDB code: 7dcz was solved by Y.Koriyama, A.Hori, H.Ito, S.Yonezawa, Y.Baba, N.Tanimoto, T.Ueno, S.Yamamoto, T.Yamamoto, N.Asada, K.Morimoto, S.Einaru, K.Sakai, T.Kanazu, A.Matsuda, Y.Yamaguchi, T.Oguma, M.Timmers, L.Tritsmans, K.I.Kusakabe, A.Kato, G.Sakaguchi, 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 (°) 101.958, 101.958, 171.653, 90, 90, 120
R / Rfree (%) 21.3 / 25.5

Other elements in 7dcz:

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

Fluorine (F) 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-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2- Carboxamide (pdb code 7dcz). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2- Carboxamide, PDB code: 7dcz:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 7dcz

Go back to Iodine Binding Sites List in 7dcz
Iodine binding site 1 out of 4 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-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-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:28.3
occ:1.00
 O A:HOH579 3.2 17.3 1.0
OG A:SER105 3.5 14.9 1.0
O A:HOH623 3.6 20.7 1.0
CA A:GLU104 3.8 17.0 1.0
N A:SER105 3.8 16.6 1.0
N A:GLU104 3.8 15.9 1.0
C A:GLU104 3.9 16.6 1.0
C A:THR103 4.0 15.7 1.0
CD2 A:HIS45 4.1 10.5 1.0
CB A:HIS45 4.1 12.7 1.0
CE2 A:PHE109 4.2 15.7 1.0
O A:THR103 4.2 16.4 1.0
CG2 A:ILE102 4.3 12.0 1.0
CB A:SER105 4.4 16.1 1.0
CG A:HIS45 4.4 12.3 1.0
O A:ILE102 4.6 12.7 1.0
O A:GLU104 4.6 16.4 1.0
CA A:SER105 4.7 16.7 1.0
CD2 A:PHE109 4.7 15.5 1.0
CA A:THR103 4.7 14.8 1.0
C A:ILE102 4.9 13.0 1.0
N A:THR103 4.9 13.7 1.0

Iodine binding site 2 out of 4 in 7dcz

Go back to Iodine Binding Sites List in 7dcz
Iodine binding site 2 out of 4 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-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-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:44.4
occ:1.00
 NH2 A:ARG349 3.2 26.7 1.0
NE A:ARG349 3.6 24.2 1.0
O A:HOH530 3.6 5.7 1.0
CZ A:ARG349 3.9 26.1 1.0
NH2 A:ARG351 4.1 12.3 1.0
OD2 A:ASP346 4.3 12.4 1.0
CD A:ARG349 4.9 21.2 1.0

Iodine binding site 3 out of 4 in 7dcz

Go back to Iodine Binding Sites List in 7dcz
Iodine binding site 3 out of 4 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-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-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:67.3
occ:1.00
 N A:LYS107 3.4 18.1 1.0
O A:HOH551 3.7 23.2 1.0
NE2 A:HIS45 3.9 10.6 1.0
CA A:ASP106 4.0 18.5 1.0
O A:HOH656 4.1 24.2 1.0
C A:ASP106 4.2 18.2 1.0
CA A:LYS107 4.2 17.9 1.0
OD1 A:ASP106 4.3 23.6 1.0
CE1 A:HIS45 4.6 11.0 1.0
O A:SER105 4.6 17.2 1.0
CE2 A:PHE47 4.6 23.3 1.0
CG A:ASP106 4.8 21.3 1.0
N A:ASP106 4.9 17.8 1.0
CD2 A:HIS45 4.9 10.5 1.0
N A:PHE108 5.0 17.2 1.0
O A:PHE109 5.0 17.9 1.0
C A:SER105 5.0 17.2 1.0

Iodine binding site 4 out of 4 in 7dcz

Go back to Iodine Binding Sites List in 7dcz
Iodine binding site 4 out of 4 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of BACE1 in Complex with N-{3-[(4S)-2-Amino-4- Methyl-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:69.2
occ:0.50
 CE A:LYS238 3.5 26.0 1.0
CE2 A:TYR222 4.2 24.9 1.0
NZ A:LYS238 4.3 25.4 1.0
CG A:LYS238 4.3 26.2 1.0
CG A:LYS239 4.4 28.8 1.0
CD A:LYS238 4.5 27.3 1.0
CE A:LYS239 4.6 32.7 1.0
NZ A:LYS239 4.6 34.1 1.0
CD2 A:TYR222 4.7 23.6 1.0
CD A:LYS239 4.9 30.5 1.0

Reference:

Y.Koriyama, A.Hori, H.Ito, S.Yonezawa, Y.Baba, N.Tanimoto, T.Ueno, S.Yamamoto, T.Yamamoto, N.Asada, K.Morimoto, S.Einaru, K.Sakai, T.Kanazu, A.Matsuda, Y.Yamaguchi, T.Oguma, M.Timmers, L.Tritsmans, K.I.Kusakabe, A.Kato, G.Sakaguchi. Discovery of Atabecestat (Jnj-54861911): A Thiazine-Based Beta-Amyloid Precursor Protein Cleaving Enzyme 1 Inhibitor Advanced to the Phase 2B/3 Early Clinical Trial. J.Med.Chem. V. 64 1873 2021.
ISSN: ISSN 0022-2623
PubMed: 33588527
DOI: 10.1021/ACS.JMEDCHEM.0C01917
Page generated: Mon Aug 12 00:58:13 2024

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