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Iodine in PDB 3rvi: Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide

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

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

Protein crystallography data

The structure of Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide, PDB code: 3rvi 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 / 2.65
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.124, 103.124, 170.326, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 26.1

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide (pdb code 3rvi). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide, PDB code: 3rvi:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 3rvi

Go back to Iodine Binding Sites List in 3rvi
Iodine binding site 1 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide


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 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I393

b:18.3
occ:0.75
 O A:HOH408 3.1 16.1 1.0
OG A:SER105 3.5 23.5 1.0
N A:SER105 3.8 24.5 1.0
N A:GLU104 3.9 24.6 1.0
CA A:GLU104 3.9 24.9 1.0
C A:THR103 4.0 24.2 1.0
CD2 A:HIS45 4.0 23.3 1.0
C A:GLU104 4.0 24.7 1.0
O A:THR103 4.1 24.2 1.0
CE2 A:PHE109 4.1 22.2 1.0
CB A:SER105 4.2 24.2 1.0
CG2 A:ILE102 4.3 22.5 1.0
CB A:HIS45 4.3 22.6 1.0
O A:ILE102 4.4 23.1 1.0
CG A:HIS45 4.5 23.3 1.0
CA A:SER105 4.6 24.4 1.0
CD2 A:PHE109 4.7 22.9 1.0
CA A:THR103 4.7 23.9 1.0
C A:ILE102 4.8 23.2 1.0
O A:GLU104 4.8 24.6 1.0
N A:THR103 4.9 23.4 1.0
CB A:ALA43 4.9 21.3 1.0

Iodine binding site 2 out of 7 in 3rvi

Go back to Iodine Binding Sites List in 3rvi
Iodine binding site 2 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide


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 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I394

b:27.1
occ:0.50
 N A:LYS107 3.5 24.9 1.0
O A:HOH409 3.6 20.8 1.0
NE2 A:HIS45 3.9 23.6 1.0
CA A:ASP106 4.1 25.1 1.0
OD1 A:ASP106 4.2 26.0 0.5
C A:ASP106 4.3 25.1 1.0
CA A:LYS107 4.4 24.9 1.0
CE1 A:HIS45 4.5 23.6 1.0
O A:SER105 4.5 24.5 1.0
CE2 A:PHE47 4.7 27.0 1.0
N A:ASP106 4.8 24.8 1.0
C A:SER105 5.0 24.6 1.0

Iodine binding site 3 out of 7 in 3rvi

Go back to Iodine Binding Sites List in 3rvi
Iodine binding site 3 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide


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 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I395

b:47.4
occ:0.25
 O A:ARG96 3.6 26.2 1.0
OE1 A:GLU134 3.9 28.5 1.0
OG A:SER139 3.9 26.7 1.0
NE2 A:GLN143 4.2 29.1 1.0
O A:HOH445 4.3 21.8 1.0
C A:ARG96 4.5 26.0 1.0
OD1 A:ASN98 4.7 25.9 1.0
ND2 A:ASN98 4.7 26.5 1.0
CG A:ARG96 4.9 26.1 1.0
CA A:ALA97 4.9 25.4 1.0
CG A:ASN98 4.9 25.8 1.0
N A:ASN98 4.9 25.3 1.0
CG2 A:THR82 4.9 21.6 1.0

Iodine binding site 4 out of 7 in 3rvi

Go back to Iodine Binding Sites List in 3rvi
Iodine binding site 4 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide


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

b:37.1
occ:0.50
 NH2 A:ARG349 2.6 27.2 1.0
NE A:ARG349 3.3 27.1 1.0
CZ A:ARG349 3.4 27.8 1.0
NH2 A:ARG351 3.7 23.9 1.0
O A:HOH442 3.8 29.7 1.0
OD2 A:ASP346 4.3 22.3 1.0
CD A:ARG349 4.6 24.9 1.0
NH1 A:ARG349 4.7 27.1 1.0
CZ A:ARG351 5.0 23.4 1.0

Iodine binding site 5 out of 7 in 3rvi

Go back to Iodine Binding Sites List in 3rvi
Iodine binding site 5 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide


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 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I397

b:39.8
occ:0.50
 CE2 A:TYR222 2.6 34.9 1.0
CD2 A:TYR222 3.5 34.0 1.0
CZ A:TYR222 3.6 35.5 1.0
OH A:TYR222 3.6 36.4 1.0
CG A:TYR222 4.8 33.6 1.0
CE1 A:TYR222 4.8 34.8 1.0
OE1 A:GLU219 5.0 40.5 1.0

Iodine binding site 6 out of 7 in 3rvi

Go back to Iodine Binding Sites List in 3rvi
Iodine binding site 6 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I398

b:36.1
occ:0.25
 NE2 A:GLN12 2.3 35.7 1.0
N A:ASN114 3.1 22.9 1.0
CD A:GLN12 3.5 35.1 1.0
CE2 A:TYR15 3.6 24.4 1.0
CG A:LYS9 3.7 37.6 1.0
CA A:SER113 3.8 24.0 1.0
N A:LYS9 3.9 36.1 1.0
CB A:ASN114 3.9 22.5 1.0
C A:SER113 3.9 23.5 1.0
CA A:ASN114 4.0 22.3 1.0
CD1 A:TRP115 4.1 21.1 1.0
CB A:SER113 4.1 24.2 1.0
CB A:LYS9 4.2 36.6 1.0
CD2 A:TYR15 4.3 24.1 1.0
CG A:GLN12 4.3 34.1 1.0
OE1 A:GLN12 4.4 34.7 1.0
CA A:GLY8 4.5 35.3 1.0
C A:GLY8 4.6 35.7 1.0
C A:ASN114 4.6 21.8 1.0
CZ A:TYR15 4.6 24.9 1.0
CB A:GLN12 4.6 33.4 1.0
OH A:TYR15 4.6 25.6 1.0
N A:TRP115 4.6 21.3 1.0
O A:GLN12 4.7 32.0 1.0
CA A:LYS9 4.7 36.5 1.0
NE1 A:TRP115 4.7 21.8 1.0
NZ A:LYS9 4.8 39.9 1.0

Iodine binding site 7 out of 7 in 3rvi

Go back to Iodine Binding Sites List in 3rvi
Iodine binding site 7 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Bace-1 (Beta-Secretase) in Complex with 2-((2-Amino-6-O- Tolylquinolin-3-Yl)Methyl)-N-(Cyclohexylmethyl)Pentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I399

b:48.6
occ:0.50
 CE1 A:TYR68 3.0 34.8 1.0
CD1 A:TYR68 3.3 34.7 1.0
CG A:PRO70 4.1 32.4 1.0
CZ A:TYR68 4.1 35.3 1.0
OH A:TYR68 4.5 34.7 1.0
CG A:TYR68 4.5 34.2 1.0
CD A:PRO70 4.6 32.4 1.0
CB A:PRO70 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 16:35:02 2024

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