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Iodine in PDB 7d2v: Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-2-Carboxamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-2-Carboxamide, PDB code: 7d2v 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 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.72, 102.72, 170.591, 90, 90, 120
R / Rfree (%) 20.6 / 24.5

Other elements in 7d2v:

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-2-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-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-2-Carboxamide (pdb code 7d2v). 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-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-2-Carboxamide, PDB code: 7d2v:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 7d2v

Go back to Iodine Binding Sites List in 7d2v
Iodine binding site 1 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-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-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:33.6
occ:1.00
 O A:HOH776 3.3 25.6 1.0
O A:HOH775 3.3 40.7 1.0
OG A:SER105 3.6 27.8 1.0
CA A:GLU104 3.8 33.2 1.0
N A:GLU104 3.8 34.0 1.0
N A:SER105 3.8 29.7 1.0
C A:THR103 4.0 34.5 1.0
C A:GLU104 4.0 30.4 1.0
CD2 A:HIS45 4.1 23.6 1.0
CE2 A:PHE109 4.2 25.9 1.0
O A:THR103 4.2 34.0 1.0
CB A:HIS45 4.3 23.7 1.0
CB A:SER105 4.3 28.0 1.0
CG2 A:ILE102 4.4 25.9 1.0
O A:ILE102 4.4 26.2 1.0
CG A:HIS45 4.5 24.3 1.0
CA A:THR103 4.6 32.6 1.0
CA A:SER105 4.7 29.7 1.0
O A:GLU104 4.7 29.3 1.0
CD2 A:PHE109 4.8 25.3 1.0
C A:ILE102 4.8 27.8 1.0
N A:THR103 4.8 29.7 1.0
CB A:ALA43 4.9 24.7 1.0

Iodine binding site 2 out of 3 in 7d2v

Go back to Iodine Binding Sites List in 7d2v
Iodine binding site 2 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-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-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:52.8
occ:1.00
 O A:HOH802 2.2 16.6 1.0
NH1 A:ARG349 2.6 46.3 1.0
O A:HOH738 3.4 36.1 1.0
CZ A:ARG349 3.7 45.9 1.0
O A:HOH677 3.8 32.8 1.0
NH2 A:ARG351 3.9 23.0 1.0
NE A:ARG349 4.0 44.1 1.0
OD2 A:ASP346 4.4 24.4 1.0
NH1 A:ARG-4 4.8 52.0 1.0
NH2 A:ARG-4 4.8 57.1 1.0
NH2 A:ARG349 4.9 42.2 1.0

Iodine binding site 3 out of 3 in 7d2v

Go back to Iodine Binding Sites List in 7d2v
Iodine binding site 3 out of 3 in the Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-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-[(5R)-3-Amino-2,5- Dimethyl-1,1-Dioxo-5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4- Fluorophenyl}-5-Fluoropyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:59.1
occ:1.00
 O A:HOH812 2.7 28.9 1.0
O A:HOH720 3.5 26.1 1.0
N A:LYS107 3.5 31.2 1.0
O A:HOH725 3.7 43.4 1.0
NE2 A:HIS45 3.9 25.6 1.0
CA A:ASP106 4.0 34.3 1.0
C A:ASP106 4.3 32.8 1.0
OD1 A:ASP106 4.3 47.9 1.0
CA A:LYS107 4.4 33.3 1.0
CE2 A:PHE47 4.4 44.4 1.0
O A:SER105 4.6 31.9 1.0
CE1 A:HIS45 4.6 25.3 1.0
N A:ASP106 4.9 30.8 1.0
CG A:ASP106 4.9 43.3 1.0
CB A:ASP106 5.0 37.8 1.0
N A:PHE108 5.0 30.8 1.0
CD2 A:HIS45 5.0 23.6 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 00:57:01 2024

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