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Iodine in PDB 3rsv: Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide

Enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide

All present enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide:
3.4.23.46;

Protein crystallography data

The structure of Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide, PDB code: 3rsv was solved by E.A.Sickmier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.420, 103.420, 169.535, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 25

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide (pdb code 3rsv). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide, PDB code: 3rsv:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 3rsv

Go back to Iodine Binding Sites List in 3rsv
Iodine binding site 1 out of 4 in the Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I393

b:28.0
occ:0.75
 O A:HOH424 3.3 24.1 1.0
OG A:SER105 3.5 27.6 1.0
N A:SER105 3.7 27.5 1.0
N A:GLU104 3.8 26.9 1.0
CA A:GLU104 3.8 27.8 1.0
C A:THR103 3.9 26.0 1.0
C A:GLU104 3.9 27.7 1.0
CD2 A:HIS45 4.0 23.2 1.0
CG2 A:ILE102 4.0 19.6 1.0
O A:THR103 4.1 26.4 1.0
CB A:SER105 4.2 27.4 1.0
CE2 A:PHE109 4.3 21.8 1.0
CB A:HIS45 4.3 22.1 1.0
CG A:HIS45 4.5 22.4 1.0
O A:ILE102 4.5 22.3 1.0
CA A:SER105 4.5 27.5 1.0
CA A:THR103 4.6 25.1 1.0
O A:GLU104 4.7 28.1 1.0
N A:THR103 4.8 23.8 1.0
C A:ILE102 4.8 22.6 1.0
CD2 A:PHE109 4.8 23.1 1.0

Iodine binding site 2 out of 4 in 3rsv

Go back to Iodine Binding Sites List in 3rsv
Iodine binding site 2 out of 4 in the Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I394

b:31.2
occ:0.50
 N A:LYS107 3.6 26.0 1.0
O A:HOH418 3.6 14.8 1.0
NE2 A:HIS45 3.9 22.8 1.0
CA A:ASP106 4.2 27.1 1.0
CE2 A:PHE47 4.3 33.4 1.0
C A:ASP106 4.4 26.9 1.0
CA A:LYS107 4.4 25.9 1.0
O A:SER105 4.5 27.6 1.0
CE1 A:HIS45 4.5 22.9 1.0
OD2 A:ASP106 4.6 27.5 0.5
CZ A:PHE47 4.9 34.5 1.0
N A:ASP106 4.9 27.3 1.0
C A:SER105 5.0 27.6 1.0

Iodine binding site 3 out of 4 in 3rsv

Go back to Iodine Binding Sites List in 3rsv
Iodine binding site 3 out of 4 in the Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I395

b:48.0
occ:0.50
 NH2 A:ARG349 2.6 36.0 1.0
NE A:ARG349 3.3 33.3 1.0
CZ A:ARG349 3.4 35.3 1.0
O A:HOH422 3.8 26.3 1.0
NH2 A:ARG351 3.8 23.6 1.0
OD2 A:ASP346 4.3 21.0 1.0
CD A:ARG349 4.6 30.0 1.0
NH1 A:ARG349 4.7 35.1 1.0

Iodine binding site 4 out of 4 in 3rsv

Go back to Iodine Binding Sites List in 3rsv
Iodine binding site 4 out of 4 in the Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Bace-1 (Beta-Secretase) in Complex with (R)-3-(2-Amino-6- O-Tolylquinolin-3-Yl)-N-((R)-2,2-Dimethyltetrahydro-2H-Pyran-4-Yl)-2- Methylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I396

b:65.1
occ:0.25
 O A:HOH493 4.1 34.9 1.0
O A:ARG96 4.1 26.7 1.0
OE1 A:GLU134 4.2 31.2 1.0
O A:HOH459 4.2 22.9 1.0
OG A:SER139 4.4 23.8 1.0
NE2 A:GLN143 4.5 24.6 1.0
OD1 A:ASN98 4.5 25.0 1.0
ND2 A:ASN98 4.7 24.3 1.0
C A:ARG96 4.8 26.8 1.0
CG A:ASN98 4.8 25.0 1.0
CD A:GLU134 5.0 30.9 1.0
O A:HOH519 5.0 22.3 1.0
CG2 A:THR82 5.0 21.7 1.0

Reference:

Y.Cheng, T.C.Judd, M.D.Bartberger, J.Brown, K.Chen, R.T.Fremeau, D.Hickman, S.A.Hitchcock, B.Jordan, V.Li, P.Lopez, S.W.Louie, Y.Luo, K.Michelsen, T.Nixey, T.S.Powers, C.Rattan, E.A.Sickmier, D.J.St Jean, R.C.Wahl, P.H.Wen, S.Wood. From Fragment Screening to in Vivo Efficacy: Optimization of A Series of 2-Aminoquinolines As Potent Inhibitors of Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1). J.Med.Chem. V. 54 5836 2011.
ISSN: ISSN 0022-2623
PubMed: 21707077
DOI: 10.1021/JM200544Q
Page generated: Sun Aug 11 16:27:50 2024

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