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

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

All present enzymatic activity of Bace-1 Incomplex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methoxy-6-Methylpyrimidin-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 Incomplex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methoxy-6-Methylpyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium, PDB code: 5hdv 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 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.410, 89.320, 131.280, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Bace-1 Incomplex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methoxy-6-Methylpyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium (pdb code 5hdv). 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 Incomplex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methoxy-6-Methylpyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium, PDB code: 5hdv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5hdv

Go back to Fluorine Binding Sites List in 5hdv
Fluorine binding site 1 out of 2 in the Bace-1 Incomplex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methoxy-6-Methylpyrimidin-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 Incomplex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methoxy-6-Methylpyrimidin-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:F501

b:26.6
occ:1.00
 F A:60V501 0.0 26.6 1.0
C15 A:60V501 1.3 26.3 1.0
C16 A:60V501 2.4 27.6 1.0
C13 A:60V501 2.4 23.3 1.0
O1 A:60V501 2.7 31.9 1.0
C14 A:60V501 2.9 20.7 1.0
O A:HOH816 3.0 18.8 1.0
OD1 A:ASN98 3.1 17.6 1.0
CG A:ASN98 3.5 22.3 1.0
N6 A:60V501 3.6 21.7 1.0
N5 A:60V501 3.6 20.9 1.0
CB A:ASN98 3.6 14.0 1.0
CG A:ARG189 3.7 22.8 1.0
CZ2 A:TRP137 3.8 28.1 1.0
C12 A:60V501 4.0 21.3 1.0
C17 A:60V501 4.0 32.0 1.0
CB A:ARG189 4.1 18.3 1.0
CG2 A:VAL130 4.2 42.5 1.0
CG1 A:VAL130 4.2 42.1 1.0
ND2 A:ASN98 4.4 16.6 1.0
N A:ASN98 4.6 12.1 1.0
CE2 A:TRP137 4.6 29.8 1.0
NE1 A:TRP137 4.7 29.5 1.0
N A:ARG189 4.7 16.9 1.0
CH2 A:TRP137 4.7 27.0 1.0
CA A:ASN98 4.8 12.8 1.0
CB A:VAL130 4.8 42.6 1.0
CB A:SER96 4.8 14.4 1.0

Fluorine binding site 2 out of 2 in 5hdv

Go back to Fluorine Binding Sites List in 5hdv
Fluorine binding site 2 out of 2 in the Bace-1 Incomplex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methoxy-6-Methylpyrimidin-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 Incomplex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(5-Fluoro-4- Methoxy-6-Methylpyrimidin-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:19.1
occ:1.00
 F B:60V502 0.0 19.1 1.0
C15 B:60V502 1.3 16.8 1.0
C16 B:60V502 2.4 17.0 1.0
C13 B:60V502 2.4 14.9 1.0
O1 B:60V502 2.7 17.8 1.0
C14 B:60V502 2.9 15.1 1.0
O B:HOH834 3.0 16.4 1.0
OD1 B:ASN98 3.1 12.8 1.0
CG B:ASN98 3.4 19.7 1.0
CZ2 B:TRP137 3.6 17.4 1.0
N6 B:60V502 3.6 15.8 1.0
CB B:ASN98 3.6 12.5 1.0
N5 B:60V502 3.6 14.6 1.0
CG B:ARG189 3.7 19.2 1.0
C12 B:60V502 4.0 16.5 1.0
CG1 B:VAL130 4.1 19.0 1.0
C17 B:60V502 4.1 17.7 1.0
NE1 B:TRP137 4.2 18.4 1.0
CB B:ARG189 4.2 13.8 1.0
CE2 B:TRP137 4.2 18.6 1.0
CG2 B:VAL130 4.3 19.5 1.0
ND2 B:ASN98 4.4 14.7 1.0
N B:ASN98 4.4 11.7 1.0
CB B:SER96 4.6 13.3 1.0
CH2 B:TRP137 4.6 16.4 1.0
CA B:ASN98 4.7 11.8 1.0
CB B:VAL130 4.7 18.4 1.0
N B:ARG189 4.7 14.0 1.0
N B:SER97 5.0 10.0 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 09:46:56 2024

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