Iodine in PDB 3wb4: Crystal Structure of Beta Secetase in Complex with 2-Amino-3,6- Dimethyl-6-(2-Phenylethyl)-3,4,5,6-Tetrahydropyrimidin-4-One

All present enzymatic activity of Crystal Structure of Beta Secetase in Complex with 2-Amino-3,6- Dimethyl-6-(2-Phenylethyl)-3,4,5,6-Tetrahydropyrimidin-4-One:
3.4.23.46;

The structure of Crystal Structure of Beta Secetase in Complex with 2-Amino-3,6- Dimethyl-6-(2-Phenylethyl)-3,4,5,6-Tetrahydropyrimidin-4-One, PDB code: 3wb4 was solved by S.Yonezawa, K.Fujiwara, T.Yamamoto, K.Hattori, H.Yamakawa, C.Muto, M.Hosono, 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)	33.45 / 2.25
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.208, 102.208, 169.984, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 25.4

The binding sites of Iodine atom in the Crystal Structure of Beta Secetase in Complex with 2-Amino-3,6- Dimethyl-6-(2-Phenylethyl)-3,4,5,6-Tetrahydropyrimidin-4-One (pdb code 3wb4). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of Beta Secetase in Complex with 2-Amino-3,6- Dimethyl-6-(2-Phenylethyl)-3,4,5,6-Tetrahydropyrimidin-4-One, PDB code: 3wb4:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-3,6- Dimethyl-6-(2-Phenylethyl)-3,4,5,6-Tetrahydropyrimidin-4-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-3,6- Dimethyl-6-(2-Phenylethyl)-3,4,5,6-Tetrahydropyrimidin-4-One within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:0.0 occ:1.00 O A:ARG96 3.7 43.1 1.0 OE1 A:GLU134 4.0 51.6 1.0 NE2 A:GLN143 4.1 49.9 1.0 O A:HOH1032 4.2 34.9 1.0 OG A:SER139 4.3 44.0 1.0 C A:ARG96 4.4 37.8 1.0 O A:HOH1081 4.4 41.9 1.0 CG A:ARG96 4.5 48.9 1.0 O A:HOH1066 4.6 41.9 1.0 CA A:ALA97 4.7 35.2 1.0 CG2 A:THR82 4.7 40.6 1.0 ND2 A:ASN98 4.8 39.5 1.0 OD1 A:ASN98 4.8 36.8 1.0 N A:ASN98 4.8 32.6 1.0 N A:ALA97 4.8 37.2 1.0 C A:ALA97 4.9 34.4 1.0 O A:HOH1015 4.9 34.3 1.0 CB A:ARG96 4.9 48.0 1.0 CG A:ASN98 5.0 39.2 1.0

Iodine binding site 2 out of 2 in the Crystal Structure of Beta Secetase in Complex with 2-Amino-3,6- Dimethyl-6-(2-Phenylethyl)-3,4,5,6-Tetrahydropyrimidin-4-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-3,6- Dimethyl-6-(2-Phenylethyl)-3,4,5,6-Tetrahydropyrimidin-4-One within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:0.3 occ:1.00 CE A:LYS75 3.6 62.6 1.0 CG A:GLU104 3.8 42.6 1.0 CD A:LYS75 4.1 59.2 1.0 CG A:LYS75 4.2 54.1 1.0 CB A:GLU104 4.3 39.2 1.0 O A:GLU104 4.3 33.2 1.0 C A:GLU104 4.4 32.8 1.0 N A:SER105 4.5 30.5 1.0 CE2 A:TYR68 4.5 75.2 1.0 CB A:GLU77 4.5 46.7 1.0 NZ A:LYS75 4.6 65.4 1.0 CA A:SER105 4.6 36.0 1.0 N A:GLU77 4.7 41.4 1.0 C A:SER105 4.8 41.0 1.0 C A:TRP76 5.0 41.2 1.0

S.Yonezawa, K.Fujiwara, T.Yamamoto, K.Hattori, H.Yamakawa, C.Muto, M.Hosono, Y.Tanaka, T.Nakano, H.Takemoto, M.Arisawa, S.Shuto. Conformational Restriction Approach to Beta-Secretase (BACE1) Inhibitors III: Effective Investigation of the Binding Mode By Combinational Use of X-Ray Analysis, Isothermal Titration Calorimetry and Theoretical Calculations Bioorg.Med.Chem. V. 21 6506 2013.
ISSN: ISSN 0968-0896
PubMed: 24051074
DOI: 10.1016/J.BMC.2013.08.036