Atomistry » Iodine » PDB 3usl-3zzz » 3vv7
Atomistry »
  Iodine »
    PDB 3usl-3zzz »
      3vv7 »

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: Sun Aug 11 17:07:01 2024

Last articles

Cl in 8UFH
Cl in 8UEI
Cl in 8UF4
Cl in 8UEC
Cl in 8UEH
Cl in 8UEG
Cl in 8UEF
Cl in 8UEA
Cl in 8UE2
Cl in 8UE9
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy