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Iodine in PDB 3ru1: Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-(Cyclohexylmethyl)Propanamide

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

All present enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-(Cyclohexylmethyl)Propanamide:
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-(Cyclohexylmethyl)Propanamide, PDB code: 3ru1 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) 30.00 / 2.30
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.237, 102.237, 170.741, 90.00, 90.00, 120.00
R / Rfree (%) 22.4 / 27.9

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-(Cyclohexylmethyl)Propanamide (pdb code 3ru1). 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 3-(2- Aminoquinolin-3-Yl)-N-(Cyclohexylmethyl)Propanamide, PDB code: 3ru1:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 3ru1

Go back to Iodine Binding Sites List in 3ru1
Iodine binding site 1 out of 4 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-(Cyclohexylmethyl)Propanamide


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-(Cyclohexylmethyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1502

b:13.0
occ:0.75
 O A:HOH425 3.3 19.1 1.0
O A:HOH412 3.4 14.6 1.0
CB A:SER105 3.5 20.6 1.0
N A:SER105 3.8 20.0 1.0
CA A:GLU104 3.9 20.1 1.0
CD2 A:HIS45 3.9 15.4 1.0
C A:GLU104 3.9 19.9 1.0
N A:GLU104 4.0 19.8 1.0
C A:THR103 4.0 18.9 1.0
O A:THR103 4.1 19.5 1.0
CE2 A:PHE109 4.2 16.3 1.0
CA A:SER105 4.3 20.8 1.0
CG2 A:ILE102 4.4 14.7 1.0
CB A:HIS45 4.4 16.5 1.0
O A:ILE102 4.5 16.1 1.0
CG A:HIS45 4.5 16.5 1.0
OG A:SER105 4.6 23.0 1.0
O A:GLU104 4.6 19.4 1.0
CA A:THR103 4.7 18.5 1.0
C A:ILE102 4.8 16.4 1.0
CD2 A:PHE109 4.8 16.9 1.0
N A:THR103 4.9 17.4 1.0

Iodine binding site 2 out of 4 in 3ru1

Go back to Iodine Binding Sites List in 3ru1
Iodine binding site 2 out of 4 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-(Cyclohexylmethyl)Propanamide


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-(Cyclohexylmethyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1503

b:21.9
occ:0.50
 N A:LYS107 3.5 20.3 1.0
O A:HOH408 3.6 12.5 1.0
O A:HOH573 3.9 30.6 1.0
NE2 A:HIS45 4.0 15.8 1.0
CA A:LYS107 4.3 20.0 1.0
CA A:ASP106 4.3 21.6 1.0
C A:ASP106 4.4 21.0 1.0
CE1 A:HIS45 4.5 16.4 1.0
OD1 A:ASP106 4.5 28.0 1.0
CE2 A:PHE47 4.6 25.2 1.0
O A:SER105 4.7 20.8 1.0
CZ A:PHE47 4.8 25.0 1.0
CG A:LYS107 4.9 20.9 1.0
N A:ASP106 5.0 21.1 1.0

Iodine binding site 3 out of 4 in 3ru1

Go back to Iodine Binding Sites List in 3ru1
Iodine binding site 3 out of 4 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-(Cyclohexylmethyl)Propanamide


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-(Cyclohexylmethyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1504

b:50.9
occ:0.25
 O A:HOH551 2.3 54.1 1.0
O A:ARG96 3.5 18.3 1.0
OG A:SER139 4.1 17.2 1.0
OE1 A:GLU134 4.2 24.5 1.0
ND2 A:ASN98 4.2 15.3 1.0
C A:ARG96 4.2 18.7 1.0
O A:HOH436 4.3 18.8 1.0
NE2 A:GLN143 4.3 20.2 1.0
CA A:ALA97 4.3 17.0 1.0
N A:ASN98 4.4 16.3 1.0
C A:ALA97 4.5 16.4 1.0
CG A:ASN98 4.5 16.0 1.0
O A:HOH535 4.5 15.1 1.0
OD1 A:ASN98 4.5 16.3 1.0
CG2 A:THR82 4.6 16.1 1.0
CG A:ARG96 4.6 18.8 1.0
N A:ALA97 4.6 17.6 1.0
O A:HOH503 4.7 24.0 1.0
O A:HOH458 4.7 16.4 1.0
CB A:SER139 4.8 17.3 1.0

Iodine binding site 4 out of 4 in 3ru1

Go back to Iodine Binding Sites List in 3ru1
Iodine binding site 4 out of 4 in the Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2- Aminoquinolin-3-Yl)-N-(Cyclohexylmethyl)Propanamide


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- Aminoquinolin-3-Yl)-N-(Cyclohexylmethyl)Propanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1505

b:41.0
occ:0.75
 O A:HOH440 3.4 17.8 1.0
NE A:ARG349 3.5 24.3 1.0
NH2 A:ARG349 3.5 27.6 1.0
O A:HOH420 3.7 15.7 1.0
NH2 A:ARG351 3.9 12.0 1.0
CZ A:ARG349 4.0 26.6 1.0
OD2 A:ASP346 4.2 16.9 1.0
CD A:ARG349 4.6 20.8 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 16:35:02 2024

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