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Fluorine in PDB 4h3j: Structure of Bace Bound to 2-Fluoro-5-(5-(2-Imino-3-Methyl-4-Oxo-6- Phenyloctahydro-1H-Pyrrolo[3,4-D]Pyrimidin-7A-Yl)Thiophen-2-Yl) Benzonitrile

Enzymatic activity of Structure of Bace Bound to 2-Fluoro-5-(5-(2-Imino-3-Methyl-4-Oxo-6- Phenyloctahydro-1H-Pyrrolo[3,4-D]Pyrimidin-7A-Yl)Thiophen-2-Yl) Benzonitrile

All present enzymatic activity of Structure of Bace Bound to 2-Fluoro-5-(5-(2-Imino-3-Methyl-4-Oxo-6- Phenyloctahydro-1H-Pyrrolo[3,4-D]Pyrimidin-7A-Yl)Thiophen-2-Yl) Benzonitrile:
3.4.23.46;

Protein crystallography data

The structure of Structure of Bace Bound to 2-Fluoro-5-(5-(2-Imino-3-Methyl-4-Oxo-6- Phenyloctahydro-1H-Pyrrolo[3,4-D]Pyrimidin-7A-Yl)Thiophen-2-Yl) Benzonitrile, PDB code: 4h3j was solved by C.Strickland, M.Mandal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.568, 89.462, 131.091, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Bace Bound to 2-Fluoro-5-(5-(2-Imino-3-Methyl-4-Oxo-6- Phenyloctahydro-1H-Pyrrolo[3,4-D]Pyrimidin-7A-Yl)Thiophen-2-Yl) Benzonitrile (pdb code 4h3j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Bace Bound to 2-Fluoro-5-(5-(2-Imino-3-Methyl-4-Oxo-6- Phenyloctahydro-1H-Pyrrolo[3,4-D]Pyrimidin-7A-Yl)Thiophen-2-Yl) Benzonitrile, PDB code: 4h3j:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4h3j

Go back to Fluorine Binding Sites List in 4h3j
Fluorine binding site 1 out of 2 in the Structure of Bace Bound to 2-Fluoro-5-(5-(2-Imino-3-Methyl-4-Oxo-6- Phenyloctahydro-1H-Pyrrolo[3,4-D]Pyrimidin-7A-Yl)Thiophen-2-Yl) Benzonitrile


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Bace Bound to 2-Fluoro-5-(5-(2-Imino-3-Methyl-4-Oxo-6- Phenyloctahydro-1H-Pyrrolo[3,4-D]Pyrimidin-7A-Yl)Thiophen-2-Yl) Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:21.7
occ:1.00
 F1 A:10W502 0.0 21.7 1.0
C15 A:10W502 1.3 19.1 1.0
C16 A:10W502 2.3 17.5 1.0
C14 A:10W502 2.4 15.2 1.0
C A:GLN73 2.7 14.6 1.0
O A:GLN73 2.8 14.8 1.0
C18 A:10W502 2.9 15.9 1.0
CA A:GLN73 3.0 14.8 1.0
O A:HOH1048 3.1 21.0 1.0
O A:GLY72 3.1 17.2 1.0
O A:HOH1046 3.2 19.4 1.0
N A:GLY74 3.3 13.0 1.0
N A:GLN73 3.6 12.3 1.0
C A:GLY72 3.6 15.4 1.0
C17 A:10W502 3.6 15.1 1.0
C13 A:10W502 3.6 13.7 1.0
N5 A:10W502 3.7 17.4 1.0
O A:HOH1058 3.7 30.0 1.0
CA A:GLY74 4.0 12.3 1.0
C12 A:10W502 4.1 14.5 1.0
O A:HOH1071 4.3 39.5 1.0
CB A:GLN73 4.4 15.5 1.0
O A:SER71 4.6 14.7 1.0
O A:HOH1097 4.7 46.1 1.0
OG1 A:THR293 4.7 12.9 1.0
CA A:GLY72 4.8 14.8 1.0

Fluorine binding site 2 out of 2 in 4h3j

Go back to Fluorine Binding Sites List in 4h3j
Fluorine binding site 2 out of 2 in the Structure of Bace Bound to 2-Fluoro-5-(5-(2-Imino-3-Methyl-4-Oxo-6- Phenyloctahydro-1H-Pyrrolo[3,4-D]Pyrimidin-7A-Yl)Thiophen-2-Yl) Benzonitrile


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Bace Bound to 2-Fluoro-5-(5-(2-Imino-3-Methyl-4-Oxo-6- Phenyloctahydro-1H-Pyrrolo[3,4-D]Pyrimidin-7A-Yl)Thiophen-2-Yl) Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:22.5
occ:1.00
 F1 B:10W503 0.0 22.5 1.0
C15 B:10W503 1.3 18.1 1.0
C16 B:10W503 2.3 17.6 1.0
C14 B:10W503 2.4 15.6 1.0
C B:GLN73 2.9 13.7 1.0
C18 B:10W503 2.9 16.0 1.0
O B:GLN73 2.9 14.8 1.0
O B:HOH996 3.0 24.5 1.0
CA B:GLN73 3.0 14.2 1.0
O B:GLY72 3.1 16.6 1.0
O B:HOH993 3.1 27.5 1.0
N B:GLY74 3.5 11.4 1.0
O B:HOH1043 3.5 38.1 1.0
C B:GLY72 3.5 11.6 1.0
N B:GLN73 3.6 12.2 1.0
C17 B:10W503 3.6 15.3 1.0
C13 B:10W503 3.7 13.7 1.0
N5 B:10W503 3.7 18.7 1.0
C12 B:10W503 4.1 14.0 1.0
CA B:GLY74 4.3 13.6 1.0
CB B:GLN73 4.4 14.9 1.0
O B:SER71 4.7 13.7 1.0
OG1 B:THR293 4.7 13.1 1.0
CA B:GLY72 4.8 10.6 1.0
CZ2 B:TRP176 4.8 17.6 1.0

Reference:

M.Mandal, Z.Zhu, J.N.Cumming, X.Liu, C.Strickland, R.D.Mazzola, J.P.Caldwell, P.Leach, M.Grzelak, L.Hyde, Q.Zhang, G.Terracina, L.Zhang, X.Chen, R.Kuvelkar, M.E.Kennedy, L.Favreau, K.Cox, P.Orth, A.Buevich, J.Voigt, H.Wang, I.Kazakevich, B.A.Mckittrick, W.Greenlee, E.M.Parker, A.W.Stamford. Design and Validation of Bicyclic Iminopyrimidinones As Beta Amyloid Cleaving Enzyme-1 (BACE1) Inhibitors: Conformational Constraint to Favor A Bioactive Conformation. J.Med.Chem. V. 55 9331 2012.
ISSN: ISSN 0022-2623
PubMed: 22989333
DOI: 10.1021/JM301039C
Page generated: Thu Aug 1 02:02:12 2024

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