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Iodine in PDB 3vv7: Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One

Enzymatic activity of Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One

All present enzymatic activity of Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One, PDB code: 3vv7 was solved by S.Yonezawa, T.Yamamoto, H.Yamakawa, C.Muto, M.Hosono, K.Hattori, K.Higashino, M.Sakagami, H.Togame, Y.Tanaka, T.Nakano, H.Takemoto, M.Arisawa, S.Shuto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.681, 103.681, 169.006, 90.00, 90.00, 120.00
R / Rfree (%) 24.2 / 28

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One (pdb code 3vv7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One, PDB code: 3vv7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 3vv7

Go back to Iodine Binding Sites List in 3vv7
Iodine binding site 1 out of 6 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:28.1
occ:1.00
 O A:HOH1013 3.4 21.1 1.0
O A:HOH1083 3.4 40.4 1.0
OG A:SER105 3.5 29.1 1.0
CA A:GLU104 3.9 28.5 1.0
N A:SER105 3.9 27.9 1.0
N A:GLU104 3.9 28.1 1.0
C A:THR103 4.0 27.6 1.0
C A:GLU104 4.0 27.4 1.0
CE2 A:PHE109 4.0 25.0 1.0
CD2 A:HIS45 4.1 21.2 1.0
O A:THR103 4.1 27.4 1.0
CB A:SER105 4.2 28.3 1.0
CB A:HIS45 4.3 22.4 1.0
CG2 A:ILE102 4.4 23.0 1.0
O A:ILE102 4.5 23.9 1.0
CG A:HIS45 4.6 21.9 1.0
CD2 A:PHE109 4.6 23.6 1.0
CA A:THR103 4.7 26.7 1.0
CA A:SER105 4.7 29.3 1.0
O A:GLU104 4.7 26.5 1.0
N A:THR103 4.8 25.3 1.0
C A:ILE102 4.8 24.5 1.0

Iodine binding site 2 out of 6 in 3vv7

Go back to Iodine Binding Sites List in 3vv7
Iodine binding site 2 out of 6 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:54.6
occ:1.00
 NH2 A:ARG349 3.3 39.7 1.0
O A:HOH1060 3.4 34.0 1.0
NH2 A:ARG351 3.9 16.9 1.0
O A:HOH1039 3.9 27.3 1.0
OD2 A:ASP346 4.4 22.2 1.0
CD A:ARG349 4.4 33.7 1.0
CZ A:ARG349 4.5 40.0 1.0
NE A:ARG349 4.9 38.0 1.0
CG A:ARG349 5.0 28.1 1.0

Iodine binding site 3 out of 6 in 3vv7

Go back to Iodine Binding Sites List in 3vv7
Iodine binding site 3 out of 6 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:79.5
occ:1.00
 O A:HOH1001 2.2 9.0 1.0
N A:LYS107 3.7 32.6 1.0
CA A:LYS107 4.0 34.1 1.0
CG A:LYS107 4.5 38.0 1.0
OD1 A:ASP106 4.8 45.8 1.0
CB A:LYS107 4.8 33.9 1.0
CE2 A:PHE47 4.9 44.2 1.0
C A:ASP106 4.9 32.9 1.0

Iodine binding site 4 out of 6 in 3vv7

Go back to Iodine Binding Sites List in 3vv7
Iodine binding site 4 out of 6 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:0.2
occ:1.00
 O A:LEU56 3.7 25.3 1.0
O A:GLN55 3.8 25.2 1.0
C A:LEU56 3.9 26.5 1.0
N A:SER58 3.9 29.9 1.0
C A:SER57 4.2 28.0 1.0
CA A:SER58 4.2 31.8 1.0
N A:SER57 4.3 26.9 1.0
CA A:LEU56 4.4 25.6 1.0
CB A:SER58 4.4 32.2 1.0
O A:SER57 4.5 27.3 1.0
CA A:SER57 4.7 27.6 1.0
C A:GLN55 4.8 24.5 1.0

Iodine binding site 5 out of 6 in 3vv7

Go back to Iodine Binding Sites List in 3vv7
Iodine binding site 5 out of 6 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:0.9
occ:1.00
 O A:ARG96 3.4 29.4 1.0
OE2 A:GLU134 3.7 37.4 1.0
OG A:SER139 4.0 25.4 1.0
OE1 A:GLN143 4.1 33.7 1.0
O A:HOH1049 4.1 34.9 1.0
C A:ARG96 4.2 29.5 1.0
CA A:ALA97 4.6 26.1 1.0
OD1 A:ASN98 4.6 29.9 1.0
CG A:ARG96 4.7 31.1 1.0
N A:ASN98 4.7 25.4 1.0
CB A:SER139 4.7 26.9 1.0
O A:HOH1027 4.7 28.4 1.0
N A:ALA97 4.8 26.8 1.0
CD A:GLU134 4.8 37.0 1.0
C A:ALA97 4.8 24.9 1.0
ND2 A:ASN98 4.9 24.9 1.0
CG A:ASN98 4.9 28.7 1.0
O A:HOH1131 4.9 32.1 1.0
CG2 A:THR82 4.9 23.5 1.0
CB A:ARG96 5.0 30.5 1.0
O A:HOH1056 5.0 30.3 1.0

Iodine binding site 6 out of 6 in 3vv7

Go back to Iodine Binding Sites List in 3vv7
Iodine binding site 6 out of 6 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Beta Secetase in Complex with 2-Amino-6-((1S,2R)- 2-(3'-Methoxybiphenyl-3-Yl)Cyclopropyl)-3-Methylpyrimidin-4(3H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I506

b:75.5
occ:1.00
 CB A:LYS238 3.0 42.5 1.0
CA A:LYS238 4.2 42.2 1.0
N A:LYS238 4.3 42.9 1.0
O A:HOH1085 4.7 25.6 1.0
N A:LYS239 4.8 41.3 1.0
C A:LYS238 4.9 40.9 1.0

Reference:

S.Yonezawa, T.Yamamoto, H.Yamakawa, C.Muto, M.Hosono, K.Hattori, K.Higashino, T.Yutsudo, H.Iwamoto, Y.Kondo, M.Sakagami, H.Togame, Y.Tanaka, T.Nakano, H.Takemoto, M.Arisawa, S.Shuto. Conformational Restriction Approach to Beta-Secretase (BACE1) Inhibitors: Effect of A Cyclopropane Ring to Induce An Alternative Binding Mode. J.Med.Chem. V. 55 8838 2012.
ISSN: ISSN 0022-2623
PubMed: 22998419
DOI: 10.1021/JM3011405
Page generated: Fri Aug 8 15:48:44 2025

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