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Iodine in PDB 3vv6: Crystal Structure of Beta Secetase in Complex with 2-Amino-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-4(3H)-One

Enzymatic activity of Crystal Structure of Beta Secetase in Complex with 2-Amino-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-4(3H)-One

All present enzymatic activity of Crystal Structure of Beta Secetase in Complex with 2-Amino-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-4(3H)-One:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Beta Secetase in Complex with 2-Amino-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-4(3H)-One, PDB code: 3vv6 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 / 2.05
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.491, 102.491, 170.156, 90.00, 90.00, 120.00
R / Rfree (%) 24.9 / 28

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Beta Secetase in Complex with 2-Amino-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-4(3H)-One (pdb code 3vv6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Crystal Structure of Beta Secetase in Complex with 2-Amino-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-4(3H)-One, PDB code: 3vv6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 3vv6

Go back to Iodine Binding Sites List in 3vv6
Iodine binding site 1 out of 5 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-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-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-4(3H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:25.6
occ:1.00
 O A:HOH1019 3.2 37.7 1.0
O A:HOH1014 3.4 20.3 1.0
OG A:SER105 3.4 23.6 1.0
CA A:GLU104 3.9 25.1 1.0
N A:GLU104 3.9 24.6 1.0
N A:SER105 3.9 24.0 1.0
C A:THR103 4.0 24.1 1.0
C A:GLU104 4.0 24.3 1.0
CE2 A:PHE109 4.1 23.8 1.0
CD2 A:HIS45 4.1 18.1 1.0
O A:THR103 4.1 24.8 1.0
CB A:SER105 4.2 24.4 1.0
CG2 A:ILE102 4.3 20.3 1.0
CB A:HIS45 4.4 19.1 1.0
O A:ILE102 4.6 22.8 1.0
CG A:HIS45 4.6 19.5 1.0
CD2 A:PHE109 4.6 23.0 1.0
CA A:SER105 4.7 24.7 1.0
CA A:THR103 4.7 23.7 1.0
O A:GLU104 4.8 23.8 1.0
C A:ILE102 4.9 21.6 1.0
N A:THR103 4.9 22.5 1.0

Iodine binding site 2 out of 5 in 3vv6

Go back to Iodine Binding Sites List in 3vv6
Iodine binding site 2 out of 5 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-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-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-4(3H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:50.2
occ:1.00
 O A:HOH1203 2.3 21.9 1.0
O A:HOH1144 3.3 32.2 1.0
NH2 A:ARG349 3.5 41.0 1.0
NE A:ARG349 3.6 35.1 1.0
O A:HOH1184 3.7 26.4 1.0
NH2 A:ARG351 3.8 15.4 1.0
CZ A:ARG349 4.0 38.4 1.0
OD1 A:ASP346 4.4 19.2 1.0
CD A:ARG349 4.7 28.9 1.0

Iodine binding site 3 out of 5 in 3vv6

Go back to Iodine Binding Sites List in 3vv6
Iodine binding site 3 out of 5 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-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-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-4(3H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:61.4
occ:1.00
 N A:LYS107 3.4 27.6 1.0
O A:HOH1018 3.5 27.2 1.0
O A:HOH1208 3.6 43.2 1.0
NE2 A:HIS45 4.1 20.9 1.0
CA A:ASP106 4.2 28.5 1.0
CA A:LYS107 4.2 27.8 1.0
C A:ASP106 4.3 28.0 1.0
OD2 A:ASP106 4.4 37.6 1.0
CE2 A:PHE47 4.6 40.1 1.0
O A:SER105 4.6 25.9 1.0
CE1 A:HIS45 4.7 20.2 1.0
N A:ASP106 5.0 26.4 1.0
N A:PHE108 5.0 26.7 1.0

Iodine binding site 4 out of 5 in 3vv6

Go back to Iodine Binding Sites List in 3vv6
Iodine binding site 4 out of 5 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-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-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-4(3H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:54.1
occ:1.00
 CB A:LYS238 3.1 41.3 1.0
CA A:LYS238 4.4 41.4 1.0
N A:LYS238 4.6 42.7 1.0
N A:LYS239 4.7 39.9 1.0

Iodine binding site 5 out of 5 in 3vv6

Go back to Iodine Binding Sites List in 3vv6
Iodine binding site 5 out of 5 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-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-3-Methyl-6- ((1S, 2R)-2-Phenylcyclopropyl)Pyrimidin-4(3H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:0.7
occ:1.00
 O A:ARG96 3.3 24.7 1.0
O A:HOH1178 4.0 32.3 1.0
OE2 A:GLU134 4.0 35.3 1.0
NE2 A:GLN143 4.0 26.6 1.0
C A:ARG96 4.3 24.5 1.0
OG A:SER139 4.5 22.9 1.0
CG A:ARG96 4.5 24.3 1.0
O A:HOH1189 4.6 53.5 1.0
O A:HOH1188 4.8 31.6 1.0
CA A:ALA97 4.8 21.9 1.0
OD1 A:ASN98 4.9 25.7 1.0
CB A:ARG96 4.9 25.3 1.0
CB A:SER139 4.9 21.8 1.0
N A:ALA97 4.9 22.6 1.0
O A:HOH1035 5.0 25.1 1.0
CD A:GLU134 5.0 33.2 1.0
ND2 A:ASN98 5.0 23.2 1.0
CG2 A:THR82 5.0 21.7 1.0
N A:ASN98 5.0 21.0 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 15:48:35 2025

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