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Iodine in PDB 5uyu: Crystal Structure of BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12

Enzymatic activity of Crystal Structure of BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12

All present enzymatic activity of Crystal Structure of BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12, PDB code: 5uyu was solved by D.A.Whittington, A.M.Long, E.A.Sickmier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.287, 102.287, 170.374, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 22.8

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12 (pdb code 5uyu). 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 BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12, PDB code: 5uyu:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 5uyu

Go back to Iodine Binding Sites List in 5uyu
Iodine binding site 1 out of 5 in the Crystal Structure of BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12


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 BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:24.7
occ:1.00
 O A:HOH763 3.4 30.3 1.0
O A:HOH759 3.4 24.9 1.0
OG A:SER105 3.5 20.3 1.0
CA A:GLU104 3.8 25.1 1.0
N A:GLU104 3.9 23.8 1.0
CD2 A:HIS45 3.9 23.6 1.0
C A:GLU104 4.0 24.0 1.0
N A:SER105 4.0 23.0 1.0
C A:THR103 4.0 23.7 1.0
CB A:SER105 4.1 19.9 1.0
O A:THR103 4.2 24.9 1.0
CE2 A:PHE109 4.3 18.9 1.0
CB A:HIS45 4.3 21.6 1.0
CG2 A:ILE102 4.4 20.5 1.0
CG A:HIS45 4.5 22.6 1.0
O A:ILE102 4.6 21.9 1.0
O A:GLU104 4.6 22.2 1.0
CA A:SER105 4.7 22.6 1.0
CA A:THR103 4.7 22.4 1.0
CD2 A:PHE109 4.8 19.4 1.0
C A:ILE102 4.9 20.9 1.0
N A:THR103 4.9 21.4 1.0
CB A:ALA43 4.9 21.5 1.0

Iodine binding site 2 out of 5 in 5uyu

Go back to Iodine Binding Sites List in 5uyu
Iodine binding site 2 out of 5 in the Crystal Structure of BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12


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 BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:38.8
occ:1.00
 O A:HOH509 3.1 22.6 1.0
O A:HOH835 3.4 26.5 0.5
O A:HOH618 3.6 18.7 1.0
N A:LYS107 3.6 23.3 1.0
NE2 A:HIS45 3.9 25.1 1.0
CA A:ASP106 4.2 23.9 1.0
CE1 A:HIS45 4.4 24.8 1.0
C A:ASP106 4.4 23.6 1.0
CE2 A:PHE47 4.4 36.3 1.0
CA A:LYS107 4.4 24.0 1.0
O A:SER105 4.4 23.6 1.0
OD1 A:ASP106 4.5 27.7 0.5
N A:ASP106 4.9 22.5 1.0
C A:SER105 4.9 22.9 1.0
CZ A:PHE47 5.0 37.7 1.0

Iodine binding site 3 out of 5 in 5uyu

Go back to Iodine Binding Sites List in 5uyu
Iodine binding site 3 out of 5 in the Crystal Structure of BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12


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 BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:50.6
occ:0.50
 O A:HOH781 2.7 27.1 1.0
O A:HOH848 3.2 20.0 1.0
O A:HOH563 3.8 35.5 1.0
CE2 A:TYR222 4.2 40.1 1.0
CE A:LYS239 4.4 61.3 1.0
NZ A:LYS239 4.5 63.2 1.0
CD A:LYS239 4.6 56.9 1.0
CD2 A:TYR222 4.6 37.5 1.0
CB A:LYS239 4.7 50.3 1.0
CB A:LYS238 4.7 48.7 1.0
N A:LYS239 4.7 46.8 1.0
CG A:LYS239 4.9 55.1 1.0
O A:HOH508 5.0 23.7 1.0

Iodine binding site 4 out of 5 in 5uyu

Go back to Iodine Binding Sites List in 5uyu
Iodine binding site 4 out of 5 in the Crystal Structure of BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12


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 BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:42.1
occ:1.00
 N A:GLN55 3.9 25.1 1.0
CA A:GLN55 4.0 27.0 1.0
CB A:GLN55 4.1 27.1 1.0
CB A:ARG54 4.2 24.1 1.0
C A:ARG54 4.3 25.5 1.0
CA A:ARG54 4.8 24.1 1.0
O A:ARG54 4.8 26.6 1.0
O A:HOH658 4.9 31.6 1.0
OE1 A:GLN55 4.9 22.3 1.0

Iodine binding site 5 out of 5 in 5uyu

Go back to Iodine Binding Sites List in 5uyu
Iodine binding site 5 out of 5 in the Crystal Structure of BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12


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 BACE1 in Complex with 2-Aminooxazoline-3- Azaxanthene Compound 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:69.1
occ:1.00
 N A:GLY11 3.2 34.6 1.0
N A:GLY13 3.7 27.1 1.0
CA A:GLY11 3.9 35.0 1.0
C34 A:8QV406 3.9 28.1 1.0
OG1 A:THR232 3.9 31.9 1.0
N A:GLN12 4.0 30.7 1.0
O A:LYS9 4.1 33.5 1.0
C A:SER10 4.1 36.0 1.0
CA A:GLY13 4.1 24.9 1.0
CA A:SER10 4.2 37.6 1.0
C33 A:8QV406 4.2 27.1 1.0
C A:GLY11 4.3 32.9 1.0
CE1 A:TYR14 4.3 27.3 1.0
C A:GLY13 4.6 23.7 1.0
CG2 A:THR232 4.7 33.5 1.0
OE2 A:GLU339 4.7 34.6 1.0
O A:GLY13 4.7 23.6 1.0
CD1 A:TYR14 4.7 25.3 1.0
C32 A:8QV406 4.7 24.4 1.0
O A:HOH708 4.8 52.0 1.0
CB A:THR232 4.8 31.3 1.0
C A:GLN12 4.8 27.9 1.0
CB A:ALA335 4.9 26.7 1.0
C A:LYS9 4.9 34.5 1.0
N A:SER10 5.0 36.8 1.0

Reference:

J.D.Low, M.D.Bartberger, K.Chen, Y.Cheng, M.R.Fielden, V.Gore, D.Hickman, Q.Liu, E.Allen Sickmier, H.M.Vargas, J.Werner, R.D.White, D.A.Whittington, S.Wood, A.E.Minatti. Development of 2-Aminooxazoline 3-Azaxanthene Beta-Amyloid Cleaving Enzyme (Bace) Inhibitors with Improved Selectivity Against Cathepsin D. Medchemcomm V. 8 1196 2017.
ISSN: ISSN 2040-2503
PubMed: 30108829
DOI: 10.1039/C7MD00106A
Page generated: Sun Aug 11 22:01:15 2024

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