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Fluorine in PDB 5he5: Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methyl-6-(Methylamino)Pyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H- Pyrrolo[3,4-D]Pyrimidin-2-Iminium

Enzymatic activity of Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methyl-6-(Methylamino)Pyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H- Pyrrolo[3,4-D]Pyrimidin-2-Iminium

All present enzymatic activity of Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methyl-6-(Methylamino)Pyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H- Pyrrolo[3,4-D]Pyrimidin-2-Iminium:
3.4.23.46;

Protein crystallography data

The structure of Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methyl-6-(Methylamino)Pyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H- Pyrrolo[3,4-D]Pyrimidin-2-Iminium, PDB code: 5he5 was solved by P.Orth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.458, 89.308, 131.437, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 20.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methyl-6-(Methylamino)Pyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H- Pyrrolo[3,4-D]Pyrimidin-2-Iminium (pdb code 5he5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methyl-6-(Methylamino)Pyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H- Pyrrolo[3,4-D]Pyrimidin-2-Iminium, PDB code: 5he5:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5he5

Go back to Fluorine Binding Sites List in 5he5
Fluorine binding site 1 out of 2 in the Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methyl-6-(Methylamino)Pyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H- Pyrrolo[3,4-D]Pyrimidin-2-Iminium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methyl-6-(Methylamino)Pyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H- Pyrrolo[3,4-D]Pyrimidin-2-Iminium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:19.9
occ:1.00
 F26 A:60S502 0.0 19.9 1.0
C14 A:60S502 1.3 16.6 1.0
C10 A:60S502 2.3 19.6 1.0
C17 A:60S502 2.4 13.4 1.0
N20 A:60S502 2.7 24.5 1.0
C28 A:60S502 2.9 13.8 1.0
CG A:ARG189 3.1 20.4 1.0
O A:HOH697 3.1 21.1 1.0
O A:HOH800 3.2 14.6 1.0
NE A:ARG189 3.3 40.3 1.0
O A:ILE187 3.4 12.7 1.0
N8 A:60S502 3.6 16.6 1.0
N12 A:60S502 3.6 12.3 1.0
CZ A:ARG189 3.7 53.1 1.0
CD A:ARG189 3.8 29.8 1.0
CG1 A:VAL130 3.9 22.5 1.0
NH1 A:ARG189 4.0 34.2 1.0
C7 A:60S502 4.0 13.4 1.0
C29 A:60S502 4.1 26.2 1.0
CB A:ARG189 4.3 15.2 1.0
OD1 A:ASN98 4.4 12.9 1.0
NH2 A:ARG189 4.4 39.5 1.0
C A:ILE187 4.6 12.7 1.0
N A:ARG189 4.7 13.0 1.0
CG2 A:VAL130 4.9 21.6 1.0
C A:ALA188 5.0 15.0 1.0

Fluorine binding site 2 out of 2 in 5he5

Go back to Fluorine Binding Sites List in 5he5
Fluorine binding site 2 out of 2 in the Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methyl-6-(Methylamino)Pyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H- Pyrrolo[3,4-D]Pyrimidin-2-Iminium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methyl-6-(Methylamino)Pyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H- Pyrrolo[3,4-D]Pyrimidin-2-Iminium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:16.1
occ:1.00
 F26 B:60S502 0.0 16.1 1.0
C14 B:60S502 1.3 12.5 1.0
C10 B:60S502 2.3 17.5 1.0
C17 B:60S502 2.4 8.9 1.0
N20 B:60S502 2.7 21.7 1.0
C28 B:60S502 2.9 10.8 1.0
CG B:ARG189 3.1 16.1 1.0
O B:HOH738 3.2 18.2 1.0
NE B:ARG189 3.3 29.7 1.0
O B:HOH777 3.3 13.1 1.0
O B:ILE187 3.5 11.4 1.0
N8 B:60S502 3.5 14.0 1.0
N12 B:60S502 3.6 9.2 1.0
CZ B:ARG189 3.6 41.8 1.0
CD B:ARG189 3.7 21.4 1.0
NH2 B:ARG189 3.9 22.0 1.0
CG1 B:VAL130 4.0 14.0 1.0
C7 B:60S502 4.0 10.8 1.0
C29 B:60S502 4.1 23.8 1.0
CB B:ARG189 4.3 11.7 1.0
NH1 B:ARG189 4.3 30.9 1.0
OD1 B:ASN98 4.5 10.6 1.0
C B:ILE187 4.7 10.8 1.0
N B:ARG189 4.7 11.4 1.0
CG2 B:VAL130 4.9 12.9 1.0

Reference:

M.Mandal, Y.Wu, J.Misiaszek, G.Li, A.Buevich, J.P.Caldwell, X.Liu, R.D.Mazzola, P.Orth, C.Strickland, J.Voigt, H.Wang, Z.Zhu, X.Chen, M.Grzelak, L.A.Hyde, R.Kuvelkar, P.T.Leach, G.Terracina, L.Zhang, Q.Zhang, M.S.Michener, B.Smith, K.Cox, D.Grotz, L.Favreau, K.Mitra, I.Kazakevich, B.A.Mckittrick, W.Greenlee, M.E.Kennedy, E.M.Parker, J.N.Cumming, A.W.Stamford. Structure-Based Design of An Iminoheterocyclic Beta-Site Amyloid Precursor Protein Cleaving Enzyme (Bace) Inhibitor That Lowers Central A Beta in Nonhuman Primates. J.Med.Chem. V. 59 3231 2016.
ISSN: ISSN 0022-2623
PubMed: 26937601
DOI: 10.1021/ACS.JMEDCHEM.5B01995
Page generated: Thu Aug 1 09:50:14 2024

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