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Iodine in PDB 6jt4: Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-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-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-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-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-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-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jt4 was solved by K.Anan, Y.Iso, T.Oguma, K.Nakahara, S.Suzuki, T.Yamamoto, E.Matsuoka, H.Ito, G.Sakaguchi, S.Ando, K.Morimoto, N.Kanegawa, Y.Kido, T.Kawachi, T.Fukushima, A.Teisman, V.Urmaliya, D.Dhuyvetter, H.Borghys, N.Austin, A.V.D.Bergh, P.Verboven, F.Bischoff, H.J.M.Gijsen, Y.Yamano, K.I.Kusakabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.590, 101.590, 170.351, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 23.4

Other elements in 6jt4:

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-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 Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide (pdb code 6jt4). 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,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jt4:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 6jt4

Go back to Iodine Binding Sites List in 6jt4
Iodine binding site 1 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-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-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-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:55.1
occ:0.95
 O A:HOH765 3.0 28.9 1.0
OG A:SER105 3.4 27.6 1.0
CA A:GLU104 3.5 28.9 1.0
N A:SER105 3.6 26.9 1.0
C A:GLU104 3.7 27.0 1.0
N A:GLU104 3.7 28.7 1.0
OE2 A:GLU104 3.8 41.2 1.0
CD2 A:HIS45 3.9 31.1 1.0
C A:THR103 3.9 26.6 1.0
O A:THR103 4.1 30.8 1.0
CB A:SER105 4.1 27.4 1.0
CB A:HIS45 4.2 26.3 1.0
CG2 A:ILE102 4.3 22.7 1.0
CE2 A:PHE109 4.3 24.3 1.0
CG A:HIS45 4.4 28.3 1.0
CA A:SER105 4.5 27.7 1.0
O A:GLU104 4.5 25.9 1.0
O A:ILE102 4.6 21.1 1.0
CD A:GLU104 4.6 39.0 1.0
CA A:THR103 4.7 26.0 1.0
CD2 A:PHE109 4.9 22.7 1.0
N A:THR103 4.9 23.7 1.0
C A:ILE102 4.9 21.9 1.0
CB A:GLU104 4.9 31.6 1.0

Iodine binding site 2 out of 3 in 6jt4

Go back to Iodine Binding Sites List in 6jt4
Iodine binding site 2 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-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-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-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:85.4
occ:0.84
 O A:HOH642 3.5 21.7 1.0
O A:HOH694 3.6 32.4 1.0
NH2 A:ARG349 4.1 54.3 1.0
CD2 A:LEU149 4.6 31.2 1.0
CD1 A:ILE179 4.6 34.4 1.0
NE A:ARG349 4.6 45.1 1.0
OD2 A:ASP346 4.7 25.4 1.0
CZ A:ARG349 4.9 50.7 1.0
NH2 A:ARG351 5.0 21.5 1.0

Iodine binding site 3 out of 3 in 6jt4

Go back to Iodine Binding Sites List in 6jt4
Iodine binding site 3 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-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 3 of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-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:I503

b:63.8
occ:0.84
 N A:LYS107 3.5 27.3 1.0
O A:HOH696 3.7 22.6 1.0
NE2 A:HIS45 4.0 30.0 1.0
CA A:ASP106 4.0 28.9 1.0
OD1 A:ASP106 4.0 39.6 1.0
C A:ASP106 4.3 29.2 1.0
CA A:LYS107 4.4 28.3 1.0
O A:SER105 4.5 28.2 1.0
CE2 A:PHE47 4.5 51.0 1.0
CE1 A:HIS45 4.6 31.0 1.0
CG A:ASP106 4.7 35.9 1.0
CB A:ASP106 4.9 32.4 1.0
N A:ASP106 4.9 28.5 1.0
CZ A:PHE47 5.0 51.1 1.0
C A:SER105 5.0 27.7 1.0

Reference:

K.Anan, Y.Iso, T.Oguma, K.Nakahara, S.Suzuki, T.Yamamoto, E.Matsuoka, H.Ito, G.Sakaguchi, S.Ando, K.Morimoto, N.Kanegawa, Y.Kido, T.Kawachi, T.Fukushima, A.Teisman, V.Urmaliya, D.Dhuyvetter, H.Borghys, N.Austin, A.Van Den Bergh, P.Verboven, F.Bischoff, H.J.M.Gijsen, Y.Yamano, K.Kusakabe. Trifluoromethyl Dihydrothiazine-Based Beta-Secretase (BACE1) Inhibitors with Robust Central Beta-Amyloid Reduction and Minimal Covalent Binding Burden. Chemmedchem V. 14 1894 2019.
ISSN: ESSN 1860-7187
PubMed: 31657130
DOI: 10.1002/CMDC.201900478
Page generated: Sun Aug 11 23:19:01 2024

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