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Iodine in PDB 3rtn: Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide

Enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide

All present enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide:
3.4.23.46;

Protein crystallography data

The structure of Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide, PDB code: 3rtn 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 / 2.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.365, 103.365, 170.197, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 27.1

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide (pdb code 3rtn). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide, PDB code: 3rtn:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 3rtn

Go back to Iodine Binding Sites List in 3rtn
Iodine binding site 1 out of 5 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide


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-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I393

b:32.2
occ:0.75
 O A:HOH449 3.3 28.7 1.0
OG A:SER105 3.7 38.9 1.0
N A:GLU104 3.7 38.8 1.0
N A:SER105 3.8 39.0 1.0
CA A:GLU104 3.8 39.3 1.0
C A:THR103 3.9 38.3 1.0
C A:GLU104 4.0 39.2 1.0
CE2 A:PHE109 4.1 29.3 1.0
CD2 A:HIS45 4.1 35.9 1.0
CB A:HIS45 4.1 34.7 1.0
O A:THR103 4.2 38.6 1.0
CB A:SER105 4.3 39.0 1.0
O A:ILE102 4.4 36.1 1.0
CG A:HIS45 4.5 35.3 1.0
CG2 A:ILE102 4.5 34.7 1.0
CA A:THR103 4.6 37.4 1.0
CA A:SER105 4.6 39.1 1.0
CD2 A:PHE109 4.7 29.4 1.0
C A:ILE102 4.8 36.0 1.0
CB A:ALA43 4.8 33.1 1.0
N A:THR103 4.9 36.5 1.0
O A:GLU104 4.9 39.0 1.0

Iodine binding site 2 out of 5 in 3rtn

Go back to Iodine Binding Sites List in 3rtn
Iodine binding site 2 out of 5 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide


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-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I394

b:45.4
occ:0.50
 O A:HOH409 3.6 20.1 1.0
N A:LYS107 3.6 37.4 1.0
NE2 A:HIS45 3.8 36.8 1.0
CA A:ASP106 4.0 39.1 1.0
C A:ASP106 4.3 38.5 1.0
O A:SER105 4.5 39.5 1.0
CA A:LYS107 4.5 36.9 1.0
CE1 A:HIS45 4.6 37.0 1.0
CE2 A:PHE47 4.6 38.0 1.0
N A:ASP106 4.7 39.3 1.0
CD2 A:HIS45 4.9 35.9 1.0
C A:SER105 4.9 39.3 1.0

Iodine binding site 3 out of 5 in 3rtn

Go back to Iodine Binding Sites List in 3rtn
Iodine binding site 3 out of 5 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide


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-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I395

b:64.4
occ:0.25
 O A:ARG96 4.0 45.6 1.0
CG A:ARG96 4.2 46.5 1.0
NE2 A:GLN143 4.3 45.7 1.0
O A:HOH453 4.4 59.6 1.0
OE1 A:GLU134 4.5 48.2 1.0
C A:ARG96 4.7 45.1 1.0
CD A:ARG96 4.7 49.1 1.0
CG2 A:THR82 4.8 40.6 1.0
CA A:ALA97 4.9 43.1 1.0
OG A:SER139 4.9 42.3 1.0
ND2 A:ASN98 5.0 46.5 1.0

Iodine binding site 4 out of 5 in 3rtn

Go back to Iodine Binding Sites List in 3rtn
Iodine binding site 4 out of 5 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide


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 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I396

b:64.2
occ:0.50
 NE A:ARG349 3.8 49.2 1.0
NH2 A:ARG351 4.1 34.2 1.0
OD2 A:ASP346 4.2 35.4 1.0
NH2 A:ARG349 4.3 52.0 1.0
CZ A:ARG349 4.5 51.1 1.0
CD A:ARG349 4.6 44.1 1.0

Iodine binding site 5 out of 5 in 3rtn

Go back to Iodine Binding Sites List in 3rtn
Iodine binding site 5 out of 5 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-O- Tolylquinolin-3-Yl)-N-Cyclohexylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I397

b:53.7
occ:0.25
 NE2 A:GLN12 2.8 53.9 1.0
N A:ASN114 3.2 31.9 1.0
CE2 A:TYR15 3.6 31.8 1.0
CG A:LYS9 3.7 51.5 1.0
CA A:SER113 3.7 32.8 1.0
CB A:LYS9 3.9 49.8 1.0
C A:SER113 3.9 32.2 1.0
N A:LYS9 3.9 48.0 1.0
CB A:SER113 4.0 33.0 1.0
CD A:GLN12 4.0 53.1 1.0
CA A:ASN114 4.1 31.5 1.0
CB A:ASN114 4.1 31.6 1.0
CB A:GLN12 4.2 48.9 1.0
CD1 A:TRP115 4.2 32.1 1.0
CD2 A:TYR15 4.3 30.9 1.0
C A:GLY8 4.4 47.0 1.0
CA A:GLY8 4.4 46.3 1.0
CD A:LYS9 4.5 56.2 1.0
CA A:LYS9 4.6 49.7 1.0
OH A:TYR15 4.6 36.3 1.0
CZ A:TYR15 4.6 33.8 1.0
CG A:GLN12 4.6 51.2 1.0
C A:ASN114 4.6 31.1 1.0
O A:GLN12 4.6 47.1 1.0
OG A:SER113 4.8 33.3 1.0
N A:TRP115 4.8 30.8 1.0
NE1 A:TRP115 4.8 32.6 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 16:30:50 2024

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