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Iodine in PDB 3wb5: Crystal Structure of Beta Secetase in Complex with (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-3,4,5,6-Tetrahydropyrimidin- 4-One

Enzymatic activity of Crystal Structure of Beta Secetase in Complex with (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-3,4,5,6-Tetrahydropyrimidin- 4-One

All present enzymatic activity of Crystal Structure of Beta Secetase in Complex with (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-3,4,5,6-Tetrahydropyrimidin- 4-One:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Beta Secetase in Complex with (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-3,4,5,6-Tetrahydropyrimidin- 4-One, PDB code: 3wb5 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) 19.69 / 2.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.926, 101.926, 168.936, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 26.1

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Beta Secetase in Complex with (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-3,4,5,6-Tetrahydropyrimidin- 4-One (pdb code 3wb5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Crystal Structure of Beta Secetase in Complex with (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-3,4,5,6-Tetrahydropyrimidin- 4-One, PDB code: 3wb5:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 3wb5

Go back to Iodine Binding Sites List in 3wb5
Iodine binding site 1 out of 3 in the Crystal Structure of Beta Secetase in Complex with (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-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 (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-3,4,5,6-Tetrahydropyrimidin- 4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:0.3
occ:1.00
 O A:ARG96 3.5 38.4 1.0
OE1 A:GLU134 3.9 41.2 1.0
NE2 A:GLN143 4.0 38.6 1.0
OG A:SER139 4.3 34.8 1.0
CG A:ARG96 4.3 43.0 1.0
C A:ARG96 4.3 37.0 1.0
O A:HOH1049 4.7 33.5 1.0
ND2 A:ASN98 4.7 41.3 1.0
CA A:ALA97 4.7 30.6 1.0
O A:HOH1052 4.8 33.2 1.0
CB A:ARG96 4.9 42.2 1.0
CD A:GLU134 4.9 40.8 1.0
N A:ALA97 4.9 31.7 1.0
O A:HOH1042 4.9 30.1 1.0
N A:ASN98 4.9 34.1 1.0
C A:ALA97 4.9 36.2 1.0
CD A:ARG96 4.9 41.5 1.0
OD1 A:ASN98 5.0 52.4 1.0
CG2 A:THR82 5.0 38.1 1.0

Iodine binding site 2 out of 3 in 3wb5

Go back to Iodine Binding Sites List in 3wb5
Iodine binding site 2 out of 3 in the Crystal Structure of Beta Secetase in Complex with (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-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 (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-3,4,5,6-Tetrahydropyrimidin- 4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:0.5
occ:1.00
 CA A:GLU104 3.6 49.1 1.0
N A:GLU104 3.7 44.0 1.0
N A:SER105 3.7 56.5 1.0
OG A:SER105 3.8 46.8 1.0
C A:GLU104 3.8 52.8 1.0
CD2 A:HIS45 3.9 51.9 1.0
C A:THR103 4.0 45.6 1.0
CG2 A:ILE102 4.1 29.4 1.0
CB A:HIS45 4.1 42.2 1.0
CB A:SER105 4.2 51.4 1.0
CE2 A:PHE109 4.2 48.5 1.0
O A:ILE102 4.3 29.6 1.0
CG A:HIS45 4.3 48.4 1.0
O A:THR103 4.4 53.8 1.0
OE2 A:GLU104 4.4 60.7 1.0
O A:GLU104 4.5 50.9 1.0
CA A:SER105 4.6 57.3 1.0
C A:ILE102 4.7 37.3 1.0
CD2 A:PHE109 4.7 48.1 1.0
CA A:THR103 4.8 42.9 1.0
N A:THR103 4.8 41.1 1.0

Iodine binding site 3 out of 3 in 3wb5

Go back to Iodine Binding Sites List in 3wb5
Iodine binding site 3 out of 3 in the Crystal Structure of Beta Secetase in Complex with (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-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 3 of Crystal Structure of Beta Secetase in Complex with (6S)-2-Amino-3,6- Dimethyl-6-[(1R,2R)-2-Phenylcyclopropyl]-3,4,5,6-Tetrahydropyrimidin- 4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:0.8
occ:1.00
 NH2 A:ARG349 3.0 39.1 1.0
O A:HOH1032 4.0 29.3 1.0
O A:HOH1046 4.1 30.4 1.0
CD1 A:ILE179 4.2 26.2 1.0
CZ A:ARG349 4.2 51.3 1.0
CD1 A:LEU149 4.7 35.6 1.0
NH1 A:ARG349 4.8 57.2 1.0

Reference:

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
Page generated: Fri Aug 8 15:50:57 2025

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