Iodine in PDB 5t1w: Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality

Enzymatic activity of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality

All present enzymatic activity of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality:
3.4.23.46;

Protein crystallography data

The structure of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality, PDB code: 5t1w was solved by K.D.Parris, F.Vajdos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.65 / 2.96
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.460, 101.460, 170.660, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 25

Other elements in 5t1w:

The structure of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality (pdb code 5t1w). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality, PDB code: 5t1w:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 5t1w

Go back to Iodine Binding Sites List in 5t1w
Iodine binding site 1 out of 3 in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:29.9
occ:1.00
N A:SER105 3.8 7.1 1.0
N A:GLU104 3.8 7.0 1.0
CA A:GLU104 3.9 8.2 1.0
C A:THR103 3.9 8.8 1.0
OG A:SER105 3.9 21.0 1.0
C A:GLU104 4.0 13.2 1.0
O A:THR103 4.0 8.2 1.0
CD2 A:HIS45 4.1 14.5 1.0
CB A:SER105 4.1 9.1 1.0
CE1 A:PHE109 4.1 12.1 1.0
CG2 A:ILE102 4.2 11.5 1.0
CB A:HIS45 4.3 10.6 1.0
CG A:HIS45 4.5 13.4 1.0
CA A:THR103 4.5 5.1 1.0
CA A:SER105 4.6 5.4 1.0
O A:ILE102 4.6 7.1 1.0
O A:GLU104 4.7 14.4 1.0
N A:THR103 4.7 5.9 1.0
C A:ILE102 4.8 9.3 1.0
CD1 A:PHE109 4.8 10.8 1.0
CB A:ALA43 4.9 12.1 1.0

Iodine binding site 2 out of 3 in 5t1w

Go back to Iodine Binding Sites List in 5t1w
Iodine binding site 2 out of 3 in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:69.3
occ:1.00
CZ A:PHE47 4.1 14.4 1.0
CB A:ASN111 4.2 7.7 1.0
CE1 A:PHE47 4.6 15.3 1.0
ND2 A:ASN111 4.7 15.8 1.0
CG A:ASN111 4.9 26.8 1.0
CE2 A:PHE47 4.9 16.8 1.0

Iodine binding site 3 out of 3 in 5t1w

Go back to Iodine Binding Sites List in 5t1w
Iodine binding site 3 out of 3 in the Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:31.8
occ:0.50
CE A:LYS239 3.7 28.9 1.0
N A:LYS239 3.9 6.8 1.0
CB A:LYS239 4.0 6.9 1.0
CG A:LYS239 4.0 3.0 1.0
NZ A:LYS239 4.3 26.8 1.0
CD A:LYS239 4.4 17.8 1.0
CB A:LYS238 4.4 5.7 1.0
CE2 A:TYR222 4.4 12.3 1.0
CA A:LYS239 4.5 6.0 1.0
CD2 A:TYR222 4.7 12.0 1.0
C A:LYS238 4.9 11.9 1.0
CG A:LYS238 4.9 3.0 1.0
CA A:LYS238 5.0 7.3 1.0

Reference:

C.R.Butler, K.Ogilvie, L.Martinez-Alsina, G.Barreiro, E.M.Beck, C.E.Nolan, K.Atchison, E.Benvenuti, L.Buzon, S.Doran, C.Gonzales, C.J.Helal, X.Hou, M.H.Hsu, E.F.Johnson, K.Lapham, L.Lanyon, K.Parris, B.T.O'neill, D.Riddell, A.Robshaw, F.Vajdos, M.A.Brodney. Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality. J. Med. Chem. V. 60 386 2017.
ISSN: ISSN 1520-4804
PubMed: 27997172
DOI: 10.1021/ACS.JMEDCHEM.6B01451
Page generated: Sun Dec 13 19:41:03 2020

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