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Iodine in PDB 7d5a: Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-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-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide, PDB code: 7d5a 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 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.1, 102.1, 170.041, 90, 90, 120
R / Rfree (%) 20.7 / 24.2

Other elements in 7d5a:

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-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-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide (pdb code 7d5a). 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-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide, PDB code: 7d5a:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 7d5a

Go back to Iodine Binding Sites List in 7d5a
Iodine binding site 1 out of 2 in the Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-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-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:25.6
occ:0.72
 O A:HOH788 3.4 25.3 1.0
OG A:SER105 3.5 27.8 1.0
O A:HOH780 3.5 32.9 1.0
CA A:GLU104 3.8 29.9 1.0
N A:SER105 3.8 26.2 1.0
N A:GLU104 3.8 30.2 1.0
C A:THR103 3.9 29.6 1.0
C A:GLU104 3.9 27.5 1.0
CD2 A:HIS45 4.0 24.9 1.0
O A:THR103 4.1 31.1 1.0
CE2 A:PHE109 4.1 26.0 1.0
CB A:SER105 4.3 25.7 1.0
CG2 A:ILE102 4.3 24.1 1.0
CB A:HIS45 4.3 25.4 1.0
CG A:HIS45 4.5 26.6 1.0
CA A:THR103 4.6 28.3 1.0
O A:ILE102 4.6 25.4 1.0
CA A:SER105 4.6 28.5 1.0
O A:GLU104 4.6 27.4 1.0
CD2 A:PHE109 4.7 25.6 1.0
N A:THR103 4.7 26.0 1.0
C A:ILE102 4.8 25.2 1.0
CB A:ALA43 5.0 26.1 1.0

Iodine binding site 2 out of 2 in 7d5a

Go back to Iodine Binding Sites List in 7d5a
Iodine binding site 2 out of 2 in the Crystal Structure of BACE1 in Complex with N-{3-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-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-[(9S)-7-Amino-2,2- Difluoro-9-(Prop-1-Yn-1-Yl)-6-Oxa-8-Azaspiro[3.5]Non-7-En-9-Yl]-4- Fluorophenyl}-5-Cyanopyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:36.5
occ:0.55
 O A:HOH729 3.4 43.5 1.0
N A:LYS107 3.5 30.4 1.0
O A:HOH751 3.5 24.5 1.0
NE2 A:HIS45 3.9 26.8 1.0
CA A:ASP106 4.1 33.5 1.0
C A:ASP106 4.3 31.4 1.0
CA A:LYS107 4.3 30.8 1.0
CE2 A:PHE47 4.4 43.4 1.0
CE1 A:HIS45 4.5 26.7 1.0
OD1 A:ASP106 4.5 47.6 1.0
O A:SER105 4.5 30.7 1.0
CZ A:PHE47 4.8 45.1 1.0
N A:ASP106 4.9 29.7 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: Mon Aug 12 00:58:11 2024

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