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Chlorine in PDB 4frs: Structure of Bace in Complex with (S)-4-(3-Chloro-5-(5-(Prop-1-Yn-1- Yl)Pyridin-3-Yl)Thiophen-2-Yl)-1,4-Dimethyl-6-Oxotetrahydropyrimidin- 2(1H)-Iminium

Enzymatic activity of Structure of Bace in Complex with (S)-4-(3-Chloro-5-(5-(Prop-1-Yn-1- Yl)Pyridin-3-Yl)Thiophen-2-Yl)-1,4-Dimethyl-6-Oxotetrahydropyrimidin- 2(1H)-Iminium

All present enzymatic activity of Structure of Bace in Complex with (S)-4-(3-Chloro-5-(5-(Prop-1-Yn-1- Yl)Pyridin-3-Yl)Thiophen-2-Yl)-1,4-Dimethyl-6-Oxotetrahydropyrimidin- 2(1H)-Iminium:
3.4.23.46;

Protein crystallography data

The structure of Structure of Bace in Complex with (S)-4-(3-Chloro-5-(5-(Prop-1-Yn-1- Yl)Pyridin-3-Yl)Thiophen-2-Yl)-1,4-Dimethyl-6-Oxotetrahydropyrimidin- 2(1H)-Iminium, PDB code: 4frs was solved by P.Orth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.17 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.473, 89.495, 131.427, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 22.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Bace in Complex with (S)-4-(3-Chloro-5-(5-(Prop-1-Yn-1- Yl)Pyridin-3-Yl)Thiophen-2-Yl)-1,4-Dimethyl-6-Oxotetrahydropyrimidin- 2(1H)-Iminium (pdb code 4frs). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Structure of Bace in Complex with (S)-4-(3-Chloro-5-(5-(Prop-1-Yn-1- Yl)Pyridin-3-Yl)Thiophen-2-Yl)-1,4-Dimethyl-6-Oxotetrahydropyrimidin- 2(1H)-Iminium, PDB code: 4frs:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4frs

Go back to Chlorine Binding Sites List in 4frs
Chlorine binding site 1 out of 2 in the Structure of Bace in Complex with (S)-4-(3-Chloro-5-(5-(Prop-1-Yn-1- Yl)Pyridin-3-Yl)Thiophen-2-Yl)-1,4-Dimethyl-6-Oxotetrahydropyrimidin- 2(1H)-Iminium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Bace in Complex with (S)-4-(3-Chloro-5-(5-(Prop-1-Yn-1- Yl)Pyridin-3-Yl)Thiophen-2-Yl)-1,4-Dimethyl-6-Oxotetrahydropyrimidin- 2(1H)-Iminium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:28.6
occ:1.00
 CL A:0V6501 0.0 28.6 1.0
C3 A:0V6501 1.7 24.5 1.0
C2 A:0V6501 2.7 21.4 1.0
C4 A:0V6501 2.8 19.1 1.0
C11 A:0V6501 3.3 20.5 1.0
C6 A:0V6501 3.4 20.2 1.0
CD2 A:TYR132 3.4 35.5 1.0
O A:GLY135 3.4 48.4 1.0
N A:GLY135 3.5 49.4 1.0
C12 A:0V6501 3.6 20.3 1.0
CD1 A:PHE169 3.6 27.4 1.0
CE1 A:PHE169 3.7 28.6 1.0
CB A:GLN134 3.7 51.0 1.0
CE2 A:TYR132 3.9 35.6 1.0
CG A:TYR132 4.0 35.8 1.0
C5 A:0V6501 4.0 21.4 1.0
CA A:GLY135 4.1 47.5 1.0
C A:GLY135 4.1 47.6 1.0
S1 A:0V6501 4.2 20.2 1.0
CB A:TYR132 4.3 37.9 1.0
C7 A:0V6501 4.3 23.6 1.0
C A:GLN134 4.4 53.9 1.0
O21 A:0V6501 4.5 25.6 1.0
O A:HOH955 4.6 31.7 1.0
CA A:GLN134 4.6 50.1 1.0
CG A:GLN134 4.8 61.1 1.0
N10 A:0V6501 4.8 16.8 1.0
CZ A:TYR132 4.8 42.0 1.0
CD1 A:TYR132 4.9 36.6 1.0
CG A:PHE169 4.9 25.2 1.0
CD1 A:ILE179 4.9 30.4 1.0
CZ A:PHE169 5.0 26.3 1.0

Chlorine binding site 2 out of 2 in 4frs

Go back to Chlorine Binding Sites List in 4frs
Chlorine binding site 2 out of 2 in the Structure of Bace in Complex with (S)-4-(3-Chloro-5-(5-(Prop-1-Yn-1- Yl)Pyridin-3-Yl)Thiophen-2-Yl)-1,4-Dimethyl-6-Oxotetrahydropyrimidin- 2(1H)-Iminium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Bace in Complex with (S)-4-(3-Chloro-5-(5-(Prop-1-Yn-1- Yl)Pyridin-3-Yl)Thiophen-2-Yl)-1,4-Dimethyl-6-Oxotetrahydropyrimidin- 2(1H)-Iminium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:26.0
occ:1.00
 CL B:0V6501 0.0 26.0 1.0
C3 B:0V6501 1.7 23.8 1.0
C2 B:0V6501 2.7 19.7 1.0
C4 B:0V6501 2.8 21.9 1.0
C6 B:0V6501 3.3 21.6 1.0
C11 B:0V6501 3.3 19.3 1.0
CD2 B:TYR132 3.4 27.1 1.0
C12 B:0V6501 3.6 18.6 1.0
O B:GLY135 3.6 27.4 1.0
CD1 B:PHE169 3.7 24.1 1.0
CE1 B:PHE169 3.8 25.5 1.0
CE2 B:TYR132 3.9 27.6 1.0
N B:GLY135 3.9 28.2 1.0
C B:GLN134 4.0 35.5 1.0
C5 B:0V6501 4.0 22.0 1.0
CA B:GLY135 4.0 26.6 1.0
CG B:TYR132 4.0 27.2 1.0
C B:GLY135 4.1 27.9 1.0
O B:GLN134 4.1 36.9 1.0
C7 B:0V6501 4.2 23.5 1.0
CB B:GLN134 4.2 34.5 1.0
S1 B:0V6501 4.2 19.4 1.0
CB B:TYR132 4.2 28.1 1.0
CG B:GLN134 4.3 41.5 1.0
O21 B:0V6501 4.4 23.8 1.0
CA B:GLN134 4.7 32.9 1.0
O B:HOH925 4.7 25.9 1.0
N10 B:0V6501 4.7 18.6 1.0
CZ B:TYR132 4.9 32.3 1.0
CD1 B:TYR132 5.0 28.9 1.0
CG B:PHE169 5.0 21.2 1.0

Reference:

A.W.Stamford, J.D.Scott, S.W.Li, S.Babu, D.Tadesse, R.Hunter, Y.Wu, J.Misiaszek, J.N.Cumming, E.J.Gilbert, C.Huang, B.A.Mckittrick, L.Hong, T.Guo, Z.Zhu, C.Strickland, P.Orth, J.H.Voigt, M.E.Kennedy, X.Chen, R.Kuvelkar, R.Hodgson, L.A.Hyde, K.Cox, L.Favreau, E.M.Parker, W.J.Greenlee. Discovery of An Orally Available, Brain Penetrant BACE1 Inhibitor That Affords Robust Cns A(Beta) Reduction Acs Med Chem Lett V. 3 897 2012.
ISSN: ISSN 1948-5875
PubMed: 23412139
DOI: 10.1021/ML3001165
Page generated: Fri Jul 11 15:21:06 2025

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