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Chlorine in PDB 5htz: BACE1 in Complex with (S)-5-(3-Chloro-5-(5-(Prop-1-Yn-1-Yl)Pyridin-3- Yl)Thiophen-2-Yl)-2,5-Dimethyl-1,2,4-Thiadiazinan-3-Iminium 1,1- Dioxide

Enzymatic activity of BACE1 in Complex with (S)-5-(3-Chloro-5-(5-(Prop-1-Yn-1-Yl)Pyridin-3- Yl)Thiophen-2-Yl)-2,5-Dimethyl-1,2,4-Thiadiazinan-3-Iminium 1,1- Dioxide

All present enzymatic activity of BACE1 in Complex with (S)-5-(3-Chloro-5-(5-(Prop-1-Yn-1-Yl)Pyridin-3- Yl)Thiophen-2-Yl)-2,5-Dimethyl-1,2,4-Thiadiazinan-3-Iminium 1,1- Dioxide:
3.4.23.46;

Protein crystallography data

The structure of BACE1 in Complex with (S)-5-(3-Chloro-5-(5-(Prop-1-Yn-1-Yl)Pyridin-3- Yl)Thiophen-2-Yl)-2,5-Dimethyl-1,2,4-Thiadiazinan-3-Iminium 1,1- Dioxide, PDB code: 5htz was solved by P.Orth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.10 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.353, 89.978, 131.636, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the BACE1 in Complex with (S)-5-(3-Chloro-5-(5-(Prop-1-Yn-1-Yl)Pyridin-3- Yl)Thiophen-2-Yl)-2,5-Dimethyl-1,2,4-Thiadiazinan-3-Iminium 1,1- Dioxide (pdb code 5htz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the BACE1 in Complex with (S)-5-(3-Chloro-5-(5-(Prop-1-Yn-1-Yl)Pyridin-3- Yl)Thiophen-2-Yl)-2,5-Dimethyl-1,2,4-Thiadiazinan-3-Iminium 1,1- Dioxide, PDB code: 5htz:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5htz

Go back to Chlorine Binding Sites List in 5htz
Chlorine binding site 1 out of 2 in the BACE1 in Complex with (S)-5-(3-Chloro-5-(5-(Prop-1-Yn-1-Yl)Pyridin-3- Yl)Thiophen-2-Yl)-2,5-Dimethyl-1,2,4-Thiadiazinan-3-Iminium 1,1- Dioxide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of BACE1 in Complex with (S)-5-(3-Chloro-5-(5-(Prop-1-Yn-1-Yl)Pyridin-3- Yl)Thiophen-2-Yl)-2,5-Dimethyl-1,2,4-Thiadiazinan-3-Iminium 1,1- Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:30.3
occ:1.00
 CL23 A:66J501 0.0 30.3 1.0
C22 A:66J501 1.7 26.6 1.0
C21 A:66J501 2.8 25.9 1.0
C7 A:66J501 2.8 22.5 1.0
C8 A:66J501 3.4 20.5 1.0
CD2 A:TYR132 3.4 31.6 1.0
C13 A:66J501 3.4 21.7 1.0
C14 A:66J501 3.6 19.1 1.0
O18 A:66J501 3.7 20.8 1.0
CD1 A:PHE169 3.8 31.1 1.0
O A:GLY135 3.8 38.5 1.0
CE1 A:PHE169 3.8 32.5 1.0
CE2 A:TYR132 3.9 31.7 1.0
C20 A:66J501 4.0 22.8 1.0
CG A:TYR132 4.0 31.9 1.0
S9 A:66J501 4.2 22.0 1.0
S19 A:66J501 4.2 20.6 1.0
CB A:TYR132 4.3 33.3 1.0
N A:GLY135 4.3 36.1 1.0
C A:GLY135 4.3 37.9 1.0
C A:GLN134 4.3 43.0 1.0
CA A:GLY135 4.3 34.2 1.0
O A:GLN134 4.4 45.2 1.0
CB A:GLN134 4.5 40.3 1.0
O A:HOH782 4.5 30.5 1.0
N12 A:66J501 4.8 20.6 1.0
CZ A:TYR132 4.8 37.9 1.0
CD1 A:TYR132 4.9 33.3 1.0
CA A:GLN134 5.0 39.5 1.0
CD1 A:ILE179 5.0 35.3 1.0

Chlorine binding site 2 out of 2 in 5htz

Go back to Chlorine Binding Sites List in 5htz
Chlorine binding site 2 out of 2 in the BACE1 in Complex with (S)-5-(3-Chloro-5-(5-(Prop-1-Yn-1-Yl)Pyridin-3- Yl)Thiophen-2-Yl)-2,5-Dimethyl-1,2,4-Thiadiazinan-3-Iminium 1,1- Dioxide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of BACE1 in Complex with (S)-5-(3-Chloro-5-(5-(Prop-1-Yn-1-Yl)Pyridin-3- Yl)Thiophen-2-Yl)-2,5-Dimethyl-1,2,4-Thiadiazinan-3-Iminium 1,1- Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:27.0
occ:1.00
 CL23 B:66J501 0.0 27.0 1.0
C22 B:66J501 1.7 24.7 1.0
C21 B:66J501 2.8 23.8 1.0
C7 B:66J501 2.8 21.4 1.0
C8 B:66J501 3.3 20.6 1.0
CD2 B:TYR132 3.3 23.1 1.0
C13 B:66J501 3.4 21.0 1.0
O18 B:66J501 3.6 23.6 1.0
C14 B:66J501 3.7 17.9 1.0
O B:GLY135 3.7 26.4 1.0
CD1 B:PHE169 3.8 25.6 1.0
CE2 B:TYR132 3.8 22.1 1.0
CE1 B:PHE169 3.9 26.7 1.0
C20 B:66J501 4.0 22.1 1.0
CG B:TYR132 4.0 24.2 1.0
S9 B:66J501 4.1 22.8 1.0
N B:GLY135 4.2 27.2 1.0
CB B:TYR132 4.2 24.1 1.0
S19 B:66J501 4.2 20.5 1.0
C B:GLY135 4.2 28.0 1.0
CA B:GLY135 4.3 25.6 1.0
C B:GLN134 4.3 33.4 1.0
O B:GLN134 4.4 34.0 1.0
CB B:GLN134 4.4 31.4 1.0
O B:HOH777 4.6 23.7 1.0
N12 B:66J501 4.8 18.4 1.0
CZ B:TYR132 4.8 27.0 1.0
CD1 B:TYR132 4.9 26.1 1.0
CA B:GLN134 4.9 29.9 1.0

Reference:

J.D.Scott, S.W.Li, A.P.Brunskill, X.Chen, K.Cox, J.N.Cumming, M.Forman, E.J.Gilbert, R.A.Hodgson, L.A.Hyde, Q.Jiang, U.Iserloh, I.Kazakevich, R.Kuvelkar, H.Mei, J.Meredith, J.Misiaszek, P.Orth, L.M.Rossiter, M.Slater, J.Stone, C.O.Strickland, J.H.Voigt, G.Wang, H.Wang, Y.Wu, W.J.Greenlee, E.M.Parker, M.E.Kennedy, A.W.Stamford. Discovery of the 3-Imino-1,2,4-Thiadiazinane 1,1-Dioxide Derivative Verubecestat (Mk-8931)-A Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 Inhibitor For the Treatment of Alzheimer'S Disease. J. Med. Chem. V. 59 10435 2016.
ISSN: ISSN 1520-4804
PubMed: 27933948
DOI: 10.1021/ACS.JMEDCHEM.6B00307
Page generated: Sat Jul 12 02:53:51 2025

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