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Iodine in PDB 4dh6: Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide

Enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide

All present enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide:
3.4.23.46;

Protein crystallography data

The structure of Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide, PDB code: 4dh6 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 (°) 103.694, 103.694, 168.866, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 27.1

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide (pdb code 4dh6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide, PDB code: 4dh6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 4dh6

Go back to Iodine Binding Sites List in 4dh6
Iodine binding site 1 out of 8 in the Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide


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 (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:30.6
occ:0.75
 O A:HOH536 3.2 27.4 1.0
OG A:SER105 3.6 36.0 1.0
N A:SER105 3.6 38.3 1.0
CA A:GLU104 3.6 39.3 1.0
C A:GLU104 3.8 39.2 1.0
N A:GLU104 3.9 38.5 1.0
CD2 A:HIS45 4.0 26.8 1.0
C A:THR103 4.0 36.0 1.0
O A:THR103 4.1 37.5 1.0
CB A:SER105 4.2 37.6 1.0
CG2 A:ILE102 4.2 26.4 1.0
CE2 A:PHE109 4.3 30.7 1.0
CB A:HIS45 4.4 26.7 1.0
O A:ILE102 4.5 28.6 1.0
CA A:SER105 4.5 38.2 1.0
CG A:HIS45 4.6 27.1 1.0
CD2 A:PHE109 4.7 30.7 1.0
O A:GLU104 4.7 39.4 1.0
CA A:THR103 4.8 32.9 1.0
C A:ILE102 4.9 28.7 1.0
CB A:ALA43 4.9 23.9 1.0
CB A:GLU104 5.0 43.3 1.0
N A:THR103 5.0 30.6 1.0

Iodine binding site 2 out of 8 in 4dh6

Go back to Iodine Binding Sites List in 4dh6
Iodine binding site 2 out of 8 in the Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide


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 (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:47.0
occ:0.50
 N A:LYS107 3.7 39.5 1.0
CA A:LYS107 4.1 40.5 1.0
CG A:LYS107 4.6 46.0 1.0
OD1 A:ASP106 4.8 44.0 1.0
C A:ASP106 4.8 39.5 1.0
CB A:LYS107 5.0 43.6 1.0
CA A:ASP106 5.0 39.6 1.0

Iodine binding site 3 out of 8 in 4dh6

Go back to Iodine Binding Sites List in 4dh6
Iodine binding site 3 out of 8 in the Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide


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 (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:62.6
occ:0.25
 O A:HOH523 3.7 34.0 1.0
OE1 A:GLU134 4.0 36.4 1.0
OG A:SER139 4.2 30.8 1.0
ND2 A:ASN98 4.4 32.9 1.0
O A:ARG96 4.5 34.9 1.0
NE2 A:GLN143 4.6 32.6 1.0
OD1 A:ASN98 4.7 34.4 1.0
CG A:ASN98 4.8 32.9 1.0
CD A:GLU134 4.8 36.4 1.0
O A:HOH526 4.9 25.5 1.0
O A:HOH564 4.9 44.1 1.0
CB A:GLU134 4.9 32.7 1.0

Iodine binding site 4 out of 8 in 4dh6

Go back to Iodine Binding Sites List in 4dh6
Iodine binding site 4 out of 8 in the Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide


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 (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:53.8
occ:0.50
 O A:HOH547 3.6 39.9 1.0
NE A:ARG349 3.8 40.4 1.0
NH2 A:ARG351 3.9 25.2 1.0
OD2 A:ASP346 4.3 27.3 1.0
NH2 A:ARG349 4.4 43.1 1.0
CZ A:ARG349 4.6 41.8 1.0
CD A:ARG349 4.7 37.5 1.0

Iodine binding site 5 out of 8 in 4dh6

Go back to Iodine Binding Sites List in 4dh6
Iodine binding site 5 out of 8 in the Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide


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 (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:67.5
occ:0.50
 CE2 A:TYR222 3.2 48.4 1.0
CD2 A:TYR222 3.6 45.9 1.0
CD A:LYS239 4.2 52.0 1.0
CZ A:TYR222 4.4 49.1 1.0
OH A:TYR222 4.7 49.7 1.0
CE A:LYS239 4.9 51.8 1.0
CB A:LYS238 4.9 50.2 1.0
OE2 A:GLU219 5.0 52.0 1.0
CG A:TYR222 5.0 45.5 1.0

Iodine binding site 6 out of 8 in 4dh6

Go back to Iodine Binding Sites List in 4dh6
Iodine binding site 6 out of 8 in the Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide


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 (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:51.7
occ:0.50
 N A:TYR68 3.4 41.4 1.0
O A:TYR68 3.7 43.5 1.0
CB A:PRO129 3.8 35.8 1.0
CA A:PRO129 3.9 36.6 1.0
CB A:TYR68 4.0 44.1 1.0
CA A:TYR68 4.1 42.3 1.0
CA A:VAL67 4.2 41.8 1.0
C A:VAL67 4.3 40.9 1.0
C A:TYR68 4.3 42.5 1.0
CG A:ARG128 4.4 37.7 1.0
CG A:PRO129 4.5 35.2 1.0
CB A:ARG128 4.6 36.6 1.0
N A:PRO129 4.6 35.7 1.0
CG2 A:VAL67 4.6 41.4 1.0
O A:GLY66 4.8 44.0 1.0
CB A:VAL67 5.0 42.2 1.0

Iodine binding site 7 out of 8 in 4dh6

Go back to Iodine Binding Sites List in 4dh6
Iodine binding site 7 out of 8 in the Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide


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 (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:50.5
occ:0.50
 CE2 A:TYR68 2.7 48.6 1.0
OH A:TYR68 3.4 54.6 1.0
CZ A:TYR68 3.5 51.4 1.0
CG A:PRO70 3.6 35.0 1.0
CD2 A:TYR68 3.6 47.5 1.0
CB A:PRO70 4.2 34.8 1.0
CD A:PRO70 4.5 35.5 1.0
CE1 A:TYR68 4.8 49.7 1.0
CG A:TYR68 4.9 46.9 1.0

Iodine binding site 8 out of 8 in 4dh6

Go back to Iodine Binding Sites List in 4dh6
Iodine binding site 8 out of 8 in the Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)- 1-(Benzo[D][1,3]Dioxol-5-Yl)-3-Hydroxy-4-((S)-6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridine]-4'-Ylamino) Butan-2-Yl)-2-Methoxypropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I408

b:0.0
occ:0.50
 OH A:TYR184 2.3 32.5 1.0
ND1 A:HIS181 3.1 50.2 1.0
CE1 A:HIS181 3.2 50.5 1.0
CZ A:TYR184 3.3 32.1 1.0
CD1 A:LEU188 3.5 25.0 1.0
CG2 A:ILE179 3.6 38.4 1.0
O A:HOH551 3.6 39.4 1.0
CE1 A:TYR184 3.7 32.4 1.0
CG A:HIS181 4.4 49.0 1.0
NE2 A:HIS181 4.5 49.6 1.0
CE2 A:TYR184 4.5 31.0 1.0
CB A:ILE179 4.5 36.5 1.0
CD1 A:ILE179 4.5 38.8 1.0
CG A:LEU188 4.6 24.6 1.0
CG1 A:ILE179 4.9 37.2 1.0
CD1 A:TYR184 5.0 31.8 1.0

Reference:

M.M.Weiss, T.Williamson, S.Babu-Khan, M.D.Bartberger, J.Brown, K.Chen, Y.Cheng, M.Citron, M.D.Croghan, T.A.Dineen, J.Esmay, R.F.Graceffa, S.S.Harried, D.Hickman, S.A.Hitchcock, D.B.Horne, H.Huang, R.Imbeah-Ampiah, T.Judd, M.R.Kaller, C.R.Kreiman, D.S.La, V.Li, P.Lopez, S.Louie, H.Monenschein, T.T.Nguyen, L.D.Pennington, C.Rattan, T.San Miguel, E.A.Sickmier, R.C.Wahl, P.H.Wen, S.Wood, Q.Xue, B.H.Yang, V.F.Patel, W.Zhong. Design and Preparation of A Potent Series of Hydroxyethylamine Containing Beta-Secretase Inhibitors That Demonstrate Robust Reduction of Central Beta-Amyloid. J.Med.Chem. V. 55 9009 2012.
ISSN: ISSN 0022-2623
PubMed: 22468639
DOI: 10.1021/JM300119P
Page generated: Sun Aug 11 17:32:54 2024

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