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Iodine in PDB 7f1d: Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-Carboxamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-Carboxamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-Carboxamide, PDB code: 7f1d was solved by T.Ueno, E.Matsuoka, N.Asada, S.Yamamoto, N.Kanegawa, M.Ito, 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 / 2.05
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.057, 102.057, 170.262, 90, 90, 120
R / Rfree (%) 19.8 / 22.2

Other elements in 7f1d:

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-Carboxamide also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-Carboxamide (pdb code 7f1d). 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-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-Carboxamide, PDB code: 7f1d:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 7f1d

Go back to Iodine Binding Sites List in 7f1d
Iodine binding site 1 out of 4 in the Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-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,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:32.1
occ:0.59
 O A:HOH817 3.2 30.4 1.0
O A:HOH768 3.2 44.1 1.0
OG A:SER105 3.5 32.1 1.0
N A:SER105 3.7 32.2 1.0
CA A:GLU104 3.8 36.1 1.0
N A:GLU104 3.8 35.8 1.0
C A:GLU104 3.8 34.1 1.0
C A:THR103 3.9 35.4 1.0
CD2 A:HIS45 3.9 29.6 1.0
O A:THR103 4.0 38.9 1.0
CB A:SER105 4.2 31.7 1.0
CB A:HIS45 4.2 29.2 1.0
CG2 A:ILE102 4.2 27.0 1.0
CE2 A:PHE109 4.3 32.9 1.0
CG A:HIS45 4.4 30.1 1.0
O A:ILE102 4.4 27.8 1.0
CA A:SER105 4.5 32.8 1.0
O A:GLU104 4.6 32.1 1.0
CA A:THR103 4.6 33.9 1.0
C A:ILE102 4.7 28.7 1.0
N A:THR103 4.8 30.1 1.0
CB A:ALA43 4.8 29.1 1.0
CD2 A:PHE109 4.9 32.8 1.0

Iodine binding site 2 out of 4 in 7f1d

Go back to Iodine Binding Sites List in 7f1d
Iodine binding site 2 out of 4 in the Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-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,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:54.1
occ:0.56
 O A:HOH759 3.3 37.1 1.0
NH2 A:ARG349 3.5 44.5 1.0
NE A:ARG349 3.5 41.0 1.0
O A:HOH715 3.6 30.7 1.0
NH2 A:ARG351 3.9 26.7 1.0
CZ A:ARG349 4.0 43.1 1.0
OD2 A:ASP346 4.4 26.4 1.0
CD A:ARG349 4.6 38.4 1.0

Iodine binding site 3 out of 4 in 7f1d

Go back to Iodine Binding Sites List in 7f1d
Iodine binding site 3 out of 4 in the Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-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-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:40.7
occ:0.49
 N A:LYS107 3.4 33.6 1.0
O A:HOH722 3.5 24.7 1.0
NE2 A:HIS45 3.9 30.7 1.0
CA A:ASP106 4.0 35.9 1.0
OD1 A:ASP106 4.1 43.5 1.0
C A:ASP106 4.2 34.5 1.0
CA A:LYS107 4.3 35.3 1.0
CE1 A:HIS45 4.4 30.4 1.0
CE2 A:PHE47 4.4 44.5 1.0
O A:SER105 4.4 33.0 1.0
CG A:ASP106 4.7 40.9 1.0
N A:ASP106 4.8 33.8 1.0
CB A:ASP106 4.9 38.3 1.0
C A:SER105 4.9 34.0 1.0
N A:PHE108 5.0 32.1 1.0

Iodine binding site 4 out of 4 in 7f1d

Go back to Iodine Binding Sites List in 7f1d
Iodine binding site 4 out of 4 in the Crystal Structure of BACE1 in Complex with N-{3-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-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-[(4R,5R,6R)-2-Amino-5- Fluoro-4,6-Dimethyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4-Fluorophenyl}- 2H,3H-[1,4]Dioxino[2,3-C]Pyridine-7-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:60.0
occ:0.40
 CD1 A:TYR222 4.1 31.8 1.0
CB A:LYS218 4.1 36.5 1.0
CG A:TYR222 4.1 31.4 1.0
CD1 A:TYR384 4.1 46.5 1.0
CE1 A:TYR384 4.2 48.6 1.0
CB A:TYR222 4.3 30.5 1.0
O A:LYS218 4.5 34.0 1.0
C A:LYS218 4.5 34.1 1.0
CD A:LYS218 4.5 39.9 1.0
OE1 A:GLU219 4.5 36.5 1.0
OE2 A:GLU219 4.6 35.9 1.0
CD A:GLU219 4.6 36.3 1.0
CE1 A:TYR222 4.6 32.8 1.0
CD2 A:TYR222 4.7 31.7 1.0
N A:GLU219 4.7 34.0 1.0
CG A:LYS218 4.8 38.4 1.0
CA A:LYS218 5.0 35.1 1.0

Reference:

T.Ueno, E.Matsuoka, N.Asada, S.Yamamoto, N.Kanegawa, M.Ito, H.Ito, D.Moechars, F.J.R.Rombouts, H.J.M.Gijsen, K.I.Kusakabe. Discovery of Extremely Selective Fused Pyridine-Derived Beta-Site Amyloid Precursor Protein-Cleaving Enzyme (BACE1) Inhibitors with High in Vivo Efficacy Through 10S Loop Interactions. J.Med.Chem. V. 64 14165 2021.
ISSN: ISSN 0022-2623
PubMed: 34553947
DOI: 10.1021/ACS.JMEDCHEM.1C00359
Page generated: Mon Aug 12 01:03:52 2024

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