Iodine in PDB 7d2x: Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-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-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide, PDB code: 7d2x was solved by K.Fujimoto, S.Yoshida, G.Tadano, N.Asada, K.Fuchino, S.Suzuki, E.Matsuoka, T.Yamamoto, S.Yamamoto, S.Ando, N.Kanegawa, Y.Tonomura, H.Ito, D.Moechars, F.J.R.Rombouts, 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 / 2.45
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.719, 101.719, 169.35, 90, 90, 120
R / Rfree (%) 18.5 / 22.9

Other elements in 7d2x:

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-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-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide (pdb code 7d2x). 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)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide, PDB code: 7d2x:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 7d2x

Go back to Iodine Binding Sites List in 7d2x
Iodine binding site 1 out of 2 in the Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-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-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:59.2
occ:0.43
 O A:HOH733 2.6 36.8 1.0
OG A:SER105 3.5 37.4 1.0
N A:SER105 3.7 37.6 1.0
CA A:GLU104 3.7 39.1 1.0
CD2 A:HIS45 3.8 41.0 1.0
N A:GLU104 3.8 39.6 1.0
C A:GLU104 3.9 37.8 1.0
CB A:HIS45 4.1 39.0 1.0
C A:THR103 4.1 39.2 1.0
CB A:SER105 4.1 37.5 1.0
CE2 A:PHE109 4.2 36.6 1.0
CG2 A:ILE102 4.2 33.5 1.0
CG A:HIS45 4.3 40.6 1.0
O A:THR103 4.3 44.6 1.0
CA A:SER105 4.5 38.8 1.0
O A:ILE102 4.6 33.3 1.0
O A:GLU104 4.7 36.0 1.0
OE2 A:GLU104 4.8 52.0 1.0
CD2 A:PHE109 4.8 37.0 1.0
CA A:THR103 4.8 37.9 1.0
C A:ILE102 4.9 33.5 1.0
N A:THR103 4.9 35.9 1.0
NE2 A:HIS45 5.0 41.7 1.0

Iodine binding site 2 out of 2 in 7d2x

Go back to Iodine Binding Sites List in 7d2x
Iodine binding site 2 out of 2 in the Crystal Structure of BACE1 in Complex with N-{3-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-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-[(4R)-2-Amino-4-(Prop- 1-Yn-1-Yl)-5,6-Dihydro-4H-1,3-Oxazin-4-Yl]-4-Fluorophenyl}-5- Cyanopyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:79.2
occ:0.55
 O A:HOH772 3.5 36.5 0.5
N A:LYS107 3.5 39.4 1.0
O A:HOH613 3.6 33.4 1.0
NE2 A:HIS45 3.9 41.7 1.0
CA A:ASP106 4.1 43.7 1.0
OD1 A:ASP106 4.2 55.8 1.0
O A:SER105 4.3 42.7 1.0
C A:ASP106 4.3 40.9 1.0
CA A:LYS107 4.3 40.8 1.0
CE2 A:PHE47 4.4 63.2 1.0
CE1 A:HIS45 4.5 40.8 1.0
CG A:ASP106 4.9 53.1 1.0
N A:ASP106 4.9 42.7 1.0
C A:SER105 4.9 40.5 1.0
CD2 A:PHE47 5.0 59.9 1.0

Reference:

K.Fujimoto, S.Yoshida, G.Tadano, N.Asada, K.Fuchino, S.Suzuki, E.Matsuoka, T.Yamamoto, S.Yamamoto, S.Ando, N.Kanegawa, Y.Tonomura, H.Ito, D.Moechars, F.J.R.Rombouts, H.J.M.Gijsen, K.I.Kusakabe. Structure-Based Approaches to Improving Selectivity Through Utilizing Explicit Water Molecules: Discovery of Selective Beta-Secretase (BACE1) Inhibitors Over BACE2. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 33719429
DOI: 10.1021/ACS.JMEDCHEM.0C01858
Page generated: Sat Apr 3 16:03:00 2021

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