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Iodine in PDB 4dus: Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide

Enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide

All present enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide:
3.4.23.46;

Protein crystallography data

The structure of Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide, PDB code: 4dus 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 (°) 102.309, 102.309, 169.758, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 28.9

Other elements in 4dus:

The structure of Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide also contains other interesting chemical elements:

Fluorine (F) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide (pdb code 4dus). 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 N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide, PDB code: 4dus:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 4dus

Go back to Iodine Binding Sites List in 4dus
Iodine binding site 1 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide


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 N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:21.3
occ:0.75
 O A:HOH513 3.4 26.8 1.0
O A:HOH521 3.4 21.7 1.0
OG A:SER105 3.5 23.4 1.0
N A:SER105 3.7 24.8 1.0
CA A:GLU104 3.9 30.1 1.0
CD2 A:HIS45 3.9 18.9 1.0
C A:GLU104 3.9 27.9 1.0
N A:GLU104 4.0 31.8 1.0
C A:THR103 4.0 29.2 1.0
CB A:SER105 4.0 23.5 1.0
CE2 A:PHE109 4.1 15.1 1.0
O A:THR103 4.1 32.0 1.0
CB A:HIS45 4.2 19.3 1.0
CG2 A:ILE102 4.3 16.1 1.0
CG A:HIS45 4.4 19.6 1.0
CA A:SER105 4.5 24.4 1.0
O A:ILE102 4.6 19.1 1.0
O A:GLU104 4.6 28.7 1.0
CA A:THR103 4.7 26.4 1.0
CD2 A:PHE109 4.8 15.5 1.0
C A:ILE102 4.9 20.1 1.0
N A:THR103 5.0 21.3 1.0

Iodine binding site 2 out of 7 in 4dus

Go back to Iodine Binding Sites List in 4dus
Iodine binding site 2 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide


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 N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:34.4
occ:0.50
 N A:LYS107 3.4 22.3 1.0
O A:HOH510 3.6 14.1 1.0
NE2 A:HIS45 4.0 18.9 1.0
CA A:LYS107 4.0 21.9 1.0
C A:ASP106 4.5 25.9 1.0
CA A:ASP106 4.5 28.3 1.0
CE1 A:HIS45 4.6 20.8 1.0
CG A:LYS107 4.7 22.2 1.0
O A:SER105 4.7 24.4 1.0
CE2 A:PHE47 4.7 36.0 1.0
N A:PHE108 4.9 20.2 1.0
CB A:LYS107 5.0 22.2 1.0

Iodine binding site 3 out of 7 in 4dus

Go back to Iodine Binding Sites List in 4dus
Iodine binding site 3 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide


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 N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:45.3
occ:0.25
 OE1 A:GLU134 4.0 33.9 1.0
O A:ARG96 4.0 26.0 1.0
OG A:SER139 4.3 27.9 1.0
NE2 A:GLN143 4.4 27.6 1.0
ND2 A:ASN98 4.4 27.4 1.0
CG A:ARG96 4.6 25.7 1.0
C A:ARG96 4.7 25.1 1.0
OD1 A:ASN98 4.8 29.6 1.0
CG A:ASN98 4.8 28.0 1.0
CD A:GLU134 4.9 35.5 1.0
N A:ASN98 4.9 25.4 1.0
O A:HOH507 4.9 15.0 1.0
CA A:ALA97 4.9 24.7 1.0
CG2 A:THR82 4.9 19.8 1.0

Iodine binding site 4 out of 7 in 4dus

Go back to Iodine Binding Sites List in 4dus
Iodine binding site 4 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide


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 N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:52.9
occ:0.50
 NH2 A:ARG349 2.2 39.5 1.0
CZ A:ARG349 3.4 42.8 1.0
O A:HOH537 3.5 22.8 1.0
NE A:ARG349 3.8 43.3 1.0
OD2 A:ASP346 4.2 22.3 1.0
NH2 A:ARG351 4.3 18.0 1.0
NH1 A:ARG349 4.5 42.6 1.0
CD1 A:LEU149 4.8 22.2 1.0

Iodine binding site 5 out of 7 in 4dus

Go back to Iodine Binding Sites List in 4dus
Iodine binding site 5 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide


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 N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:45.5
occ:0.30
 CE1 A:TYR68 3.8 34.5 1.0
CG A:LYS75 4.0 37.6 1.0
C A:TRP76 4.2 25.4 1.0
N A:GLU77 4.3 28.2 1.0
CA A:TRP76 4.3 24.9 1.0
CB A:GLU77 4.3 37.3 1.0
O A:LYS75 4.3 26.0 1.0
C A:LYS75 4.3 26.9 1.0
CD1 A:TYR68 4.3 34.4 1.0
CB A:LYS75 4.4 32.2 1.0
N A:TRP76 4.4 24.8 1.0
CB A:ASP106 4.5 32.0 1.0
CD A:LYS75 4.5 44.5 1.0
O A:GLU104 4.5 28.7 1.0
CA A:SER105 4.5 24.4 1.0
O A:TRP76 4.5 22.8 1.0
C A:SER105 4.6 24.7 1.0
N A:ASP106 4.6 26.9 1.0
CG A:GLU104 4.6 36.2 1.0
OE1 A:GLU77 4.7 60.8 1.0
C A:GLU104 4.7 27.9 1.0
N A:SER105 4.8 24.8 1.0
CA A:GLU77 4.9 29.2 1.0
CZ A:TYR68 5.0 36.0 1.0
CA A:LYS75 5.0 29.3 1.0

Iodine binding site 6 out of 7 in 4dus

Go back to Iodine Binding Sites List in 4dus
Iodine binding site 6 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide


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 N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:34.9
occ:0.25
 N A:TYR68 3.4 29.1 1.0
O A:TYR68 3.8 35.8 1.0
CA A:PRO129 3.9 30.4 1.0
CB A:PRO129 4.0 28.4 1.0
CA A:VAL67 4.0 31.8 1.0
CB A:TYR68 4.1 28.5 1.0
C A:VAL67 4.2 28.7 1.0
CA A:TYR68 4.2 29.4 1.0
CG A:PRO129 4.4 27.1 1.0
C A:TYR68 4.5 32.2 1.0
N A:PRO129 4.5 29.4 1.0
CG A:ARG128 4.5 38.4 1.0
CB A:ARG128 4.6 30.9 1.0
CG2 A:VAL67 4.7 28.5 1.0
O A:GLY66 4.8 35.8 1.0
CB A:VAL67 4.9 31.3 1.0
N A:VAL67 5.0 33.4 1.0

Iodine binding site 7 out of 7 in 4dus

Go back to Iodine Binding Sites List in 4dus
Iodine binding site 7 out of 7 in the Structure of Bace-1 (Beta-Secretase) in Complex with N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide


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 N-((2S,3R)-1-(4- Fluorophenyl)-3-Hydroxy-4-((6'-Neopentyl-3',4'- Dihydrospiro[Cyclobutane-1,2'-Pyrano[2,3-B]Pyridin]-4'-Yl)Amino) Butan-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:29.6
occ:0.25
 CE2 A:TYR68 2.6 34.3 1.0
OH A:TYR68 2.9 42.5 1.0
CZ A:TYR68 3.2 36.0 1.0
CG A:PRO70 3.6 23.9 1.0
CD2 A:TYR68 3.8 33.7 1.0
CB A:PRO70 4.1 23.9 1.0
CD A:PRO70 4.4 25.0 1.0
CE1 A:TYR68 4.6 34.5 1.0
NZ A:LYS75 4.6 53.1 1.0

Reference:

M.R.Kaller, S.S.Harried, B.Albrecht, P.Amarante, S.Babu-Khan, M.D.Bartberger, J.Brown, R.Brown, K.Chen, Y.Cheng, M.Citron, M.D.Croghan, R.Graceffa, D.Hickman, T.Judd, C.Kriemen, D.La, V.Li, P.Lopez, Y.Luo, C.Masse, H.Monenschein, T.Nguyen, L.D.Pennington, T.S.Miguel, E.A.Sickmier, R.C.Wahl, M.M.Weiss, P.H.Wen, T.Williamson, S.Wood, M.Xue, B.Yang, J.Zhang, V.Patel, W.Zhong, S.Hitchcock. A Potent and Orally Efficacious, Hydroxyethylamine-Based Inhibitor of Beta-Secretase. Acs Med Chem Lett V. 3 886 2012.
ISSN: ISSN 1948-5875
PubMed: 24900403
DOI: 10.1021/ML3000148
Page generated: Sun Aug 11 17:32:54 2024

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