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Iodine in PDB 3rtm: Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-Methylpropanamide

Enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-Methylpropanamide

All present enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-Methylpropanamide:
3.4.23.46;

Protein crystallography data

The structure of Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-Methylpropanamide, PDB code: 3rtm 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 / 2.76
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.875, 101.875, 169.165, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 28.8

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-Methylpropanamide (pdb code 3rtm). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-Methylpropanamide, PDB code: 3rtm:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 3rtm

Go back to Iodine Binding Sites List in 3rtm
Iodine binding site 1 out of 3 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-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 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-Methylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1502

b:49.7
occ:1.00
 OG A:SER105 3.4 38.0 1.0
CA A:GLU104 3.7 41.1 1.0
N A:SER105 3.8 40.0 1.0
N A:GLU104 3.8 40.2 1.0
C A:THR103 3.9 39.3 1.0
C A:GLU104 4.0 40.5 1.0
CD2 A:HIS45 4.0 40.7 1.0
O A:THR103 4.1 40.6 1.0
CB A:SER105 4.2 39.3 1.0
CE2 A:PHE109 4.3 35.4 1.0
CG2 A:ILE102 4.4 35.0 1.0
CB A:HIS45 4.4 37.1 1.0
CG A:HIS45 4.5 40.1 1.0
CA A:THR103 4.6 38.1 1.0
CA A:SER105 4.6 39.6 1.0
O A:ILE102 4.7 36.2 1.0
O A:GLU104 4.8 41.0 1.0
CB A:ALA43 4.8 36.6 1.0
CD2 A:PHE109 4.8 36.1 1.0
N A:THR103 4.9 36.5 1.0
C A:ILE102 4.9 36.1 1.0

Iodine binding site 2 out of 3 in 3rtm

Go back to Iodine Binding Sites List in 3rtm
Iodine binding site 2 out of 3 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-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 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-Methylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1503

b:46.3
occ:0.50
 N A:LYS107 3.5 40.1 1.0
O A:HOH444 3.8 30.3 1.0
NE2 A:HIS45 4.1 39.0 1.0
CA A:LYS107 4.2 40.6 1.0
CA A:ASP106 4.2 39.4 1.0
OD1 A:ASP106 4.3 39.6 0.5
C A:ASP106 4.4 39.8 1.0
O A:SER105 4.5 39.7 1.0
CE1 A:HIS45 4.5 40.8 1.0
CE2 A:PHE47 4.6 46.2 1.0
CG A:ASP106 4.9 39.8 0.5
CG A:LYS107 4.9 42.6 1.0
N A:PHE108 5.0 40.0 1.0

Iodine binding site 3 out of 3 in 3rtm

Go back to Iodine Binding Sites List in 3rtm
Iodine binding site 3 out of 3 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-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 3-(2- Aminoquinolin-3-Yl)-N-Cyclohexyl-N-Methylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1505

b:57.6
occ:0.50
 NE A:ARG349 3.6 54.7 1.0
O A:HOH421 3.7 47.6 1.0
NH2 A:ARG351 3.8 44.7 1.0
OD2 A:ASP346 4.1 43.1 1.0
CD A:ARG349 4.3 49.9 1.0
NH2 A:ARG349 4.4 57.6 1.0
CZ A:ARG349 4.4 57.2 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 16:29:54 2024

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